2BB3 | pdb_00002bb3

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

PDB DOI: https://doi.org/10.2210/pdb2BB3/pdb

Classification: TRANSFERASE
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-10-17 Released: 2005-11-29
Deposition Author(s): Kim, Y., Joachimiak, A., Xu, X., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.274 (Depositor), 0.285 (DCC)
R-Value Work:
0.211 (Depositor), 0.228 (DCC)
R-Value Observed:
0.211 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

Kim, Y., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 51.27 kDa
Atom Count: 3,503
Modeled Residue Count: 386
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cobalamin biosynthesis precorrin-6Y methylase (cbiE)	A, B	221	Archaeoglobus fulgidus DSM 4304	Mutation(s): 5 EC: 2.1.1
UniProt
Find proteins for O29536 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29536 Go to UniProtKB: O29536
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 2.27 Å
R-Value Free: 0.274 (Depositor), 0.285 (DCC)
R-Value Work: 0.211 (Depositor), 0.228 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.191	α = 90
b = 88.418	β = 90
c = 115.932	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-11-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-11-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.