4H1Z | pdb_00004h1z

Crystal structure of putative isomerase from Sinorhizobium meliloti, open loop conformation (target EFI-502104)

PDB DOI: https://doi.org/10.2210/pdb4H1Z/pdb

Classification: ISOMERASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-11 Released: 2012-09-26
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Enolase Q92Zs5 (Target EFI-502104) from Sinorhizobium meliloti

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 362.37 kDa
Atom Count: 24,833
Modeled Residue Count: 3,034
Deposited Residue Count: 3,296
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase Q92Zs5	A, B, C, D, E A, B, C, D, E, F, G, H	412	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: RA0374, SMa0708 EC: 6
UniProt
Find proteins for Q92ZS5 (Rhizobium meliloti (strain 1021)) Explore Q92ZS5 Go to UniProtKB: Q92ZS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92ZS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	AA [auth G] CA [auth H] J [auth A] M [auth B] R [auth C] AA [auth G], CA [auth H], J [auth A], M [auth B], R [auth C], V [auth E], X [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth E] Focus chain X [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain Y [auth G] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth G] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain Y [auth G]	L [auth B], O [auth C], Q [auth C], T [auth D], Y [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain Y [auth G] Interactions & Density Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain Y [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] SDF format, chain BA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain BA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain BA [auth H]	BA [auth H] I [auth A] K [auth B] P [auth C] S [auth D] BA [auth H], I [auth A], K [auth B], P [auth C], S [auth D], U [auth E], W [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.723	α = 90
b = 121.702	β = 99.79
c = 137.691	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description