3C5Y

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Crystal structure of putative ribose 5-phosphate isomerase (YP_001165900.1) from Novosphingobium aromaticivorans DSM 12444 at 1.81 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose/galactose isomerase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
231Novosphingobium aromaticivorans DSM 12444Mutation(s): 0 
Gene Names: YP_001165900.1Saro_3514
UniProt
Find proteins for A4XEL3 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199))
Explore A4XEL3 
Go to UniProtKB:  A4XEL3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4XEL3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth G]
AC [auth M]
BA [auth B]
BB [auth G]
AA [auth B],
AB [auth G],
AC [auth M],
BA [auth B],
BB [auth G],
BC [auth M],
CA [auth B],
CB [auth G],
CC [auth N],
DA [auth B],
DB [auth G],
DC [auth N],
EA [auth C],
EB [auth G],
EC [auth N],
FA [auth C],
FB [auth G],
GA [auth D],
GB [auth H],
GC [auth P],
HA [auth D],
HB [auth H],
IA [auth E],
IB [auth H],
JA [auth E],
JB [auth H],
KA [auth E],
KB [auth H],
LA [auth E],
LB [auth H],
MA [auth E],
NB [auth I],
OB [auth I],
PB [auth I],
Q [auth A],
QB [auth I],
R [auth A],
RA [auth F],
RB [auth J],
S [auth A],
SA [auth F],
SB [auth J],
T [auth A],
TA [auth F],
TB [auth J],
U [auth A],
UA [auth F],
UB [auth K],
V [auth A],
VA [auth F],
VB [auth K],
W [auth A],
WA [auth F],
WB [auth K],
X [auth A],
XB [auth L],
Y [auth B],
YB [auth M],
Z [auth B],
ZA [auth G],
ZB [auth M]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
FC [auth P]
MB [auth I]
NA [auth F]
OA [auth F]
PA [auth F]
FC [auth P],
MB [auth I],
NA [auth F],
OA [auth F],
PA [auth F],
QA [auth F],
XA [auth G],
YA [auth G]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.754α = 90
b = 109.462β = 102.92
c = 167.569γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.5: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.6: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.7: 2023-11-15
    Changes: Data collection