3NMI

Crystal structure of the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

PDB DOI: https://doi.org/10.2210/pdb3NMI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-06-22 Released: 2010-11-24
Deposition Author(s): Radford, R.J., Tezcan, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.235
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites.

Radford, R.J., Lawrenz, M., Nguyen, P.C., McCammon, J.A., Tezcan, F.A.

(2011) Chem Commun (Camb) 47: 313-315

PubMed: 20740227 Search on PubMed
DOI: https://doi.org/10.1039/c0cc02168g
Primary Citation of Related Structures:
3NMI, 3NMJ, 3NMK

PubMed Abstract:
Described is an engineered metal-binding protein, MBPPhen2, which forms porous crystalline frameworks that feature coordinatively unsaturated Zn- and Ni-centers.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Dr, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 74.19 kDa
Atom Count: 5,486
Modelled Residue Count: 636
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C, D, E A, B, C, D, E, F	106	Escherichia coli	Mutation(s): 6 Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain V [auth F] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth F] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth F] mmCIF format, chain M [auth C]	G [auth A] K [auth B] M [auth C] P [auth D] R [auth E] G [auth A], K [auth B], M [auth C], P [auth D], R [auth E], V [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain V [auth F]
PXX Query on PXX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain W [auth F]	H [auth A] L [auth B] N [auth C] Q [auth D] S [auth E] H [auth A], L [auth B], N [auth C], Q [auth D], S [auth E], W [auth F]	N-1,10-phenanthrolin-5-ylacetamide C₁₄ H₁₁ N₃ O AAJXINSCZMZERD-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain W [auth F]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain U [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E]	I [auth A], J [auth A], O [auth C], T [auth E], U [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain T [auth E] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.235
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.29	α = 90
b = 91.787	β = 107.99
c = 130.637	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Radford, R.J.

Tezcan, F.A.

Revision History (Full details and data files)

Version 1.0: 2010-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3NMI

Crystal structure of the phenanthroline-modified cytochrome cb562 variant, MBP-Phen2

Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)