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- PDB-3ay3: Crystal structure of glucuronic acid dehydrogeanse from Chromohal... -

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Basic information

Entry
Database: PDB / ID: 3ay3
TitleCrystal structure of glucuronic acid dehydrogeanse from Chromohalobacter salexigens
ComponentsNAD-dependent epimerase/dehydratase
KeywordsOXIDOREDUCTASE / glucuronic acid dehydrogeanse
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NAD-dependent epimerase/dehydratase
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAhn, J.-W. / Kim, S. / Kim, K.-J.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of glucuronic acid dehydrogenase [correction of dehydrogeanse] from Chromohalobacter salexigens
Authors: Ahn, J.-W. / Lee, S.Y. / Kim, S. / Kim, S.M. / Lee, S.B. / Kim, K.-J.
History
DepositionApr 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase
B: NAD-dependent epimerase/dehydratase
C: NAD-dependent epimerase/dehydratase
D: NAD-dependent epimerase/dehydratase


Theoretical massNumber of molelcules
Total (without water)117,6934
Polymers117,6934
Non-polymers00
Water7,314406
1
A: NAD-dependent epimerase/dehydratase
B: NAD-dependent epimerase/dehydratase


Theoretical massNumber of molelcules
Total (without water)58,8462
Polymers58,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-18 kcal/mol
Surface area21700 Å2
MethodPISA
2
C: NAD-dependent epimerase/dehydratase
D: NAD-dependent epimerase/dehydratase


Theoretical massNumber of molelcules
Total (without water)58,8462
Polymers58,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-19 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.762, 122.762, 150.476
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
NAD-dependent epimerase/dehydratase / glucuronate dehydrogenase


Mass: 29423.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / Gene: Csal_2474 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q1QUN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Ca(C2H3O2)2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 6C111.23985
SYNCHROTRONPAL/PLS 6C120.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 20, 2009
ADSC QUANTUM 2102CCDApr 11, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.239851
20.97951
ReflectionResolution: 2.1→50 Å / Num. all: 80495 / Num. obs: 79652 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.14 Å / % possible all: 88.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.805 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 3687 5 %RANDOM
Rwork0.2148 ---
obs0.2184 69412 97.8 %-
all-73099 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.12 Å2 / Biso mean: 35.6637 Å2 / Biso min: 13.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.82 Å20 Å2
2---1.63 Å20 Å2
3---2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 0 406 8646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228440
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.94811480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30251060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63623.838396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.358151332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8281560
X-RAY DIFFRACTIONr_chiral_restr0.1260.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216556
X-RAY DIFFRACTIONr_mcbond_it0.8571.55284
X-RAY DIFFRACTIONr_mcangle_it1.45428468
X-RAY DIFFRACTIONr_scbond_it2.4933156
X-RAY DIFFRACTIONr_scangle_it3.5864.53012
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 264 -
Rwork0.269 4721 -
all-4985 -
obs--89.58 %

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