4GGH | pdb_00004ggh

Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, hepes, and ethylene glycol bound (ordered loops, space group c2221)

• PDB DOI: https://doi.org/10.2210/pdb4GGH/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio harveyi 1DA3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-06 Released: 2012-09-05 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.203 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, hepes, and ethylene glycol bound (ordered loops, space group c2221)

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 195.23 kDa 
• Atom Count: 14,691 
• Modeled Residue Count: 1,588 
• Deposited Residue Count: 1,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C, D	422	Vibrio harveyi 1DA3	Mutation(s): 0  Gene Names: VME_00770
UniProt
Find proteins for D0X4R4 (Vibrio harveyi (strain 1DA3)) Explore D0X4R4  Go to UniProtKB:  D0X4R4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	EA [auth D], G [auth A], N [auth B], U [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	DA [auth D], T [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	FA [auth D], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C], Y [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth C], BA [auth C], L [auth A], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	CA [auth D], E [auth A], F [auth A], M [auth B], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.203 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.948	α = 90
b = 209.55	β = 90
c = 208.468	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description