1YBY

Conserved hypothetical protein Cth-95 from Clostridium thermocellum

PDB DOI: https://doi.org/10.2210/pdb1YBY/pdb

Classification: TRANSLATION
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-21 Released: 2005-02-01
Deposition Author(s): Zhao, M., Zhou, W., Chang, J., Habel, J., Kataeva, I., Xu, H., Chen, L., Lee, D., Nguyen, J., Chang, S.-H., Horanyi, P., Florence, Q., Tempel, W., Lin, D., Zhang, H., Ljundahl, L., Liu, Z.-J., Rose, J., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.270
R-Value Work: 0.228
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Conserved hypothetical protein Cth-95 from Clostridium thermocellum

Zhao, M., Zhou, W., Chang, J., Habel, J., Kataeva, I., Xu, H., Chen, L., Lee, D., Nguyen, J., Chang, S.-H., Horanyi, P., Florence, Q., Tempel, W., Lin, D., Zhang, H., Ljundahl, L., Liu, Z.-J., Rose, J., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 48.35 kDa
Atom Count: 2,929
Modelled Residue Count: 354
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation elongation factor P	A, B	215	Acetivibrio thermocellus	Mutation(s): 5
UniProt
Find proteins for A3DDQ3 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DDQ3 Go to UniProtKB: A3DDQ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DDQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.270
R-Value Work: 0.228
R-Value Observed: 0.229
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.915	α = 90
b = 55.476	β = 120.84
c = 88.462	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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1YBY

Conserved hypothetical protein Cth-95 from Clostridium thermocellum

Conserved hypothetical protein Cth-95 from Clostridium thermocellum

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)