1Y80

Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica

PDB DOI: https://doi.org/10.2210/pdb1Y80/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Moorella thermoacetica
Mutation(s): No

Deposited: 2004-12-10 Released: 2005-01-25
Deposition Author(s): Liu, Z.-J., Fu, Z.-Q., Tempel, W., Das, A., Habel, J., Zhou, W., Chang, J., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Ljungdahl, L., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.210
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica

Liu, Z.-J., Fu, Z.-Q., Tempel, W., Das, A., Habel, J., Zhou, W., Chang, J., Chen, L., Lee, D., Nguyen, D., Chang, S.-H., Ljungdahl, L., Rose, J.P., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 23.68 kDa
Atom Count: 1,087
Modelled Residue Count: 125
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted cobalamin binding protein	A	210	Moorella thermoacetica	Mutation(s): 0
UniProt
Find proteins for Q2RJ67 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320)) Explore Q2RJ67 Go to UniProtKB: Q2RJ67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RJ67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B1M Query on B1M Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CO-5-METHOXYBENZIMIDAZOLYLCOBAMIDE C₆₁ H₈₆ Co N₁₃ O₁₅ P CJVUSTVYODMZMZ-VSTXFNHGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
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 A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.210
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.689	α = 90
b = 62.738	β = 90
c = 34.543	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-01-25

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2005-01-25
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: 2012-07-25
Changes: Other
Version 1.4: 2017-10-11
Changes: Refinement description
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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1Y80

Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica

Structure of a corrinoid (factor IIIm)-binding protein from Moorella thermoacetica

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)