4H19

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

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 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mandelate racemase372Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: Atu4120
UniProt
Find proteins for Q7CU39 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CU39 
Go to UniProtKB:  Q7CU39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CU39
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0YR
Query on 0YR

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AC [auth G]
BB [auth D]
EE [auth P]
FD [auth L]
IA [auth B]
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
Query on GOL

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AB [auth D]
AE [auth P]
BE [auth P]
CE [auth P]
DD [auth L]
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
Query on CA

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AA [auth B]
BC [auth H]
FE [auth J]
GD [auth M]
ND [auth N]
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
Query on CL

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AD [auth L]
BA [auth B]
BD [auth L]
CA [auth B]
CB [auth E]
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
Query on MG

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CD [auth L]
EA [auth B]
FB [auth E]
FC [auth H]
IE [auth J]
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 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.363α = 90
b = 395.688β = 90
c = 177.802γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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