4H19 | pdb_00004h19

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop

• PDB DOI: https://doi.org/10.2210/pdb4H19/pdb

• Classification: LYASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-10 Released: 2012-10-31 
• Deposition Author(s): Vetting, M.W., Bouvier, J.T., Morisco, L.L., Wasserman, S.R., Sojitra, S., 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: 1.80 Å
• R-Value Free: 
  0.175 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop

Vetting, M.W., Bouvier, J.T., Morisco, L.L., Wasserman, S.R., Sojitra, S., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 667.45 kDa 
• Atom Count: 53,008 
• Modeled Residue Count: 5,952 
• Deposited Residue Count: 5,952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase	A, B, C, D, E, F, G, H, I, J [auth K], K [auth L], L [auth M], M [auth N], N [auth P], O [auth J], P [auth O]	372	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu4120
UniProt
Find proteins for Q7CU39 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CU39  Go to UniProtKB:  Q7CU39

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0YR	AC [auth G], BB [auth D], EE [auth P], FD [auth L], IA [auth B], JB [auth E], JC [auth H], MD [auth M], ME [auth J], PC [auth I], QA [auth C], RB [auth F], UE [auth O], VD [auth N], YC [auth K], Z [auth A]	(2R,3R,4R)-N,2,3,4,5-pentakis(oxidanyl)pentanamide C5 H11 N O6 AGVYHANDLPZRFS-BXXZVTAOSA-N
GOL	AB [auth D], AE [auth P], BE [auth P], CE [auth P], DD [auth L], DE [auth P], ED [auth L], FA [auth B], GA [auth B], GB [auth E], GC [auth H], HA [auth B], HB [auth E], HC [auth H], IB [auth E], IC [auth H], JE [auth J], KE [auth J], LD [auth M], LE [auth J], NA [auth C], OA [auth C], OB [auth F], OC [auth I], PA [auth C], PB [auth F], QB [auth F], SD [auth N], SE [auth O], TD [auth N], TE [auth O], UD [auth N], V [auth A], VC [auth K], W [auth A], WC [auth K], X [auth A], XB [auth G], XC [auth K], Y [auth A], YA [auth D], YB [auth G], ZA [auth D], ZB [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	AA [auth B], BC [auth H], FE [auth J], GD [auth M], ND [auth N], NE [auth O], Q [auth A], QC [auth K], RA [auth D], SB [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	AD [auth L], BA [auth B], BD [auth L], CA [auth B], CB [auth E], CC [auth H], DA [auth B], DB [auth E], DC [auth H], EB [auth E], EC [auth H], GE [auth J], HD [auth M], HE [auth J], ID [auth M], JA [auth C], JD [auth M], KA [auth C], KB [auth F], KC [auth I], LA [auth C], LB [auth F], LC [auth I], MB [auth F], MC [auth I], OD [auth N], OE [auth O], PD [auth N], PE [auth O], QD [auth N], QE [auth O], R [auth A], RC [auth K], S [auth A], SA [auth D], SC [auth K], T [auth A], TA [auth D], TB [auth G], TC [auth K], UA [auth D], UB [auth G], VA [auth D], VB [auth G], WA [auth D], WD [auth P], XD [auth P], YD [auth P], ZC [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	CD [auth L], EA [auth B], FB [auth E], FC [auth H], IE [auth J], KD [auth M], MA [auth C], NB [auth F], NC [auth I], RD [auth N], RE [auth O], U [auth A], UC [auth K], WB [auth G], XA [auth D], ZD [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.175 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.363	α = 90
b = 395.688	β = 90
c = 177.802	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description