1VR0 | pdb_00001vr0

Crystal structure of putative 2-phosphosulfolactate phosphatase (15026306) from Clostridium acetobutylicum at 2.6 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VR0/pdb

Classification: HYDROLASE
Organism(s): Clostridium acetobutylicum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-01-26 Released: 2005-02-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.190 (Depositor), 0.197 (DCC)
R-Value Observed:
0.192 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site.

DiDonato, M., Krishna, S.S., Schwarzenbacher, R., McMullan, D., Agarwalla, S., Brittain, S.M., Miller, M.D., Abdubek, P., Ambing, E., Axelrod, H.L., Canaves, J.M., Chiu, H.J., Deacon, A.M., Duan, L., Elsliger, M.A., Godzik, A., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Quijano, K., Reyes, R., Rife, C.L., Spraggon, G., Stevens, R.C., van den Bedem, H., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2006) Proteins 65: 771-776

PubMed: 16927339 Search on PubMed
DOI: https://doi.org/10.1002/prot.20978
Primary Citation Related Structures:
1VR0

Organizational Affiliation

The Joint Center for Structural Genomics.

Macromolecule Content

Total Structure Weight: 84.61 kDa
Atom Count: 5,603
Modeled Residue Count: 708
Deposited Residue Count: 741
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 2-phosphosulfolactate phosphatase	A, B, C	247	Clostridium acetobutylicum	Mutation(s): 7 Gene Names: comB EC: 3.1.3.71
UniProt
Find proteins for Q97E82 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97E82 Go to UniProtKB: Q97E82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97E82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3SL Query on 3SL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C]	E [auth A], G [auth B], H [auth C]	(2R)-3-SULFOLACTIC ACID C₃ H₆ O₆ S CQQGIWJSICOUON-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.190 (Depositor), 0.197 (DCC)
R-Value Observed: 0.192 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.686	α = 90
b = 69.193	β = 90
c = 453.518	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
autoSHARP	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-02-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-02-15
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-09
Changes: Data collection, Refinement description, 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.