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 

Starting Model: experimental
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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