8W21 | pdb_00008w21

Crystal Structure of Enolase from Chlamydia trachomatis (P43212 Form)

PDB DOI: https://doi.org/10.2210/pdb8W21/pdb

Classification: HYDROLASE
Organism(s): Chlamydia trachomatis D/UW-3/CX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-02-19 Released: 2024-03-13
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Enolase from Chlamydia trachomatis (P43212 Form)

Liu, L., Lovell, S., Battaile, K.P., Cooper, A., Cutter, A.P.

To be published.

Macromolecule Content

Total Structure Weight: 374.59 kDa
Atom Count: 26,105
Modeled Residue Count: 3,366
Deposited Residue Count: 3,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B, C, D, E A, B, C, D, E, F, G, H	432	Chlamydia trachomatis D/UW-3/CX	Mutation(s): 2 Gene Names: eno, CT_587 EC: 4.2.1.11
UniProt
Find proteins for O84591 (Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx)) Explore O84591 Go to UniProtKB: O84591
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O84591
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain X [auth D] MOL2 format, chain X [auth D] mmCIF format, chain X [auth D]	X [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain X [auth D] Interactions & Density Focus chain X [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain JA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain JA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] JA [auth H] P [auth C] T [auth D] CA [auth F], FA [auth G], JA [auth H], P [auth C], T [auth D], Y [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain P [auth C] Focus chain T [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain P [auth C] Focus chain T [auth D] Focus chain Y [auth E]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain LA [auth H] SDF format, chain L [auth B] SDF format, chain KA [auth H] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth G] SDF format, chain GA [auth G] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain LA [auth H] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain LA [auth H] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth F] EA [auth F] GA [auth G] HA [auth G] AA [auth E], DA [auth F], EA [auth F], GA [auth G], HA [auth G], I [auth A], J [auth A], KA [auth H], L [auth B], LA [auth H], Q [auth C], R [auth C], U [auth D], V [auth D], Z [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth H] Focus chain L [auth B] Focus chain LA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth H] Focus chain L [auth B] Focus chain LA [auth H] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain MA [auth H] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain IA [auth G] SDF format, chain BA [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain MA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain BA [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain MA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain BA [auth E]	BA [auth E] IA [auth G] K [auth A] M [auth B] MA [auth H] BA [auth E], IA [auth G], K [auth A], M [auth B], MA [auth H], S [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain IA [auth G] Focus chain K [auth A] Focus chain M [auth B] Focus chain MA [auth H] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain IA [auth G] Focus chain K [auth A] Focus chain M [auth B] Focus chain MA [auth H] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/m38w21

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.602	α = 90
b = 140.602	β = 90
c = 409.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394