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- PDB-3up8: Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B -

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Basic information

Entry
Database: PDB / ID: 3up8
TitleCrystal structure of a putative 2,5-diketo-D-gluconic acid reductase B
ComponentsPutative 2,5-diketo-D-gluconic acid reductase B
KeywordsOXIDOREDUCTASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / TIM barrel / aldehyde reductase / xylose reductase / Potassium channel / NADPH-dependent
Function / homology
Function and homology information


2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming) / 2,5-didehydrogluconate reductase activity
Similarity search - Function
Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative 2,5-diketo-D-gluconic acid reductase B
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 2,5-diketo-D-gluconic acid reductase B
B: Putative 2,5-diketo-D-gluconic acid reductase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1474
Polymers67,0292
Non-polymers1182
Water2,396133
1
A: Putative 2,5-diketo-D-gluconic acid reductase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5742
Polymers33,5151
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative 2,5-diketo-D-gluconic acid reductase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5742
Polymers33,5151
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.283, 88.768, 123.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative 2,5-diketo-D-gluconic acid reductase B


Mass: 33514.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: dkgB, R00966, SMc00101 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q92RC6, 2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming)
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 45807 / Num. obs: 45807 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.505 / Num. unique all: 4538 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VBJ

1vbj


Resolution: 1.96→44.85 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.917 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 2295 5 %RANDOM
Rwork0.21086 ---
all0.237 45627 --
obs0.21233 43327 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.447 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 8 133 4521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224474
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9496069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.125560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52523.555211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72515745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1351539
X-RAY DIFFRACTIONr_chiral_restr0.0770.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213423
X-RAY DIFFRACTIONr_mcbond_it0.6421.52800
X-RAY DIFFRACTIONr_mcangle_it1.21824485
X-RAY DIFFRACTIONr_scbond_it1.8731674
X-RAY DIFFRACTIONr_scangle_it3.0494.51584
LS refinement shellResolution: 1.962→2.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 167 -
Rwork0.257 3000 -
obs--95.71 %

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