7E2Q | pdb_00007e2q

Crystal structure of Mycoplasma pneumoniae Enolase

PDB DOI: https://doi.org/10.2210/pdb7E2Q/pdb

Classification: LYASE
Organism(s): Mycoplasmoides pneumoniae
Expression System: Escherichia coli O104:H4 str. 2009EL-2050
Mutation(s): No

Deposited: 2021-02-07 Released: 2022-02-02
Deposition Author(s): Chen, R., Zhang, S., Gan, R., Wang, W., Ran, T., Xiong, Q., Shao, G., Feng, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.223 (Depositor), 0.222 (DCC)
R-Value Work:
0.189 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Evidence for the Rapid and Divergent Evolution of Mycoplasmas: Structural and Phylogenetic Analysis of Enolases.

Chen, R., Zhao, L., Gan, R., Feng, Z., Cui, C., Xie, X., Hao, F., Zhang, Z., Wang, L., Ran, T., Wang, W., Zhang, S., Li, Y., Zhang, W., Pang, M., Xiong, Q., Shao, G.

(2022) Front Mol Biosci 8: 811106-811106

DOI: https://doi.org/10.3389/fmolb.2021.811106

Macromolecule Content

Total Structure Weight: 201.8 kDa
Atom Count: 14,599
Modeled Residue Count: 1,801
Deposited Residue Count: 1,856
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B, C, D	464	Mycoplasmoides pneumoniae	Mutation(s): 0 Gene Names: eno, NCTC10119_00092 EC: 4.2.1.11
UniProt
Find proteins for P75189 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75189 Go to UniProtKB: P75189
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P75189
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.223 (Depositor), 0.222 (DCC)
R-Value Work: 0.189 (Depositor), 0.189 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.074	α = 90
b = 106.548	β = 103.146
c = 128.589	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800160
National Natural Science Foundation of China (NSFC)	China	31800161

Revision History (Full details and data files)

Version 1.0: 2022-02-02
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.