3UGV | pdb_00003ugv

Crystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG

PDB DOI: https://doi.org/10.2210/pdb3UGV/pdb

Classification: LYASE
Organism(s): alpha proteobacterium BAL199
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-03 Released: 2011-11-23
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., 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: 2.30 Å
R-Value Free:
0.208 (Depositor), 0.200 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG

Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., 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)

To be published.

Macromolecule Content

Total Structure Weight: 344.12 kDa
Atom Count: 23,260
Modeled Residue Count: 2,905
Deposited Residue Count: 3,120
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	390	alpha proteobacterium BAL199	Mutation(s): 0 Gene Names: BAL199_22462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain L [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain L [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain L [auth A]	L [auth A], Y [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Y [auth F] Interactions & Density Focus chain L [auth A] Focus chain Y [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A]	K [auth A], O [auth B], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth H] CA [auth H] I [auth A] J [auth A] AA [auth G], BA [auth H], CA [auth H], I [auth A], J [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth D], S [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.208 (Depositor), 0.200 (DCC)
R-Value Work: 0.161 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.711	α = 90
b = 152.984	β = 90
c = 173.535	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description