6AI7

Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct

PDB DOI: https://doi.org/10.2210/pdb6AI7/pdb

Classification: FLAVOPROTEIN
Organism(s): Amycolatopsis orientalis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-08-21 Released: 2019-08-28
Deposition Author(s): Li, T.L., Lin, K.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.246
R-Value Work: 0.205
R-Value Observed: 0.207

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct

Li, T.L., Lin, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 38.61 kDa
Atom Count: 2,653
Modelled Residue Count: 329
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxymandelate oxidase	A	360	Amycolatopsis orientalis	Mutation(s): 1 Gene Names: hmo EC: 1.1.3.46
UniProt
Find proteins for O52792 (Amycolatopsis orientalis) Explore O52792 Go to UniProtKB: O52792
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O52792
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9Q6 Query on 9Q6 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-deoxy-1-[(4aS)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol C₁₇ H₂₃ N₄ O₁₀ P XVRDTKNEVFQDDQ-LKQDWFRTSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.246
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.576	α = 90
b = 138.576	β = 90
c = 107.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.