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- PDB-5c7h: Crystal structure of aldo-keto reductase from Sinorhizobium melil... -

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Basic information

Entry
Database: PDB / ID: 5c7h
TitleCrystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH
ComponentsAldo-keto reductase
KeywordsOXIDOREDUCTASE / aldo-keto reductase / AKR / NADPH / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function
NADP-dependent oxidoreductase domain / 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
Chem-NDP / Oxidoreductase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Seidel, R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH
Authors: Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Seidel, R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5032
Polymers30,7571
Non-polymers7451
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.049, 78.669, 79.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldo-keto reductase


Mass: 30757.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc01429 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92NR7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 68811 / Num. obs: 68759 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Rsym value: 0.02 / Χ2: 0.899 / Net I/av σ(I): 29.917 / Net I/σ(I): 9.2 / Num. measured all: 404374
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.325.40.672.133800.7490.3180.7440.714100
1.32-1.355.70.58834030.8030.2670.6480.723100
1.35-1.375.80.51633880.8520.2340.5680.755100
1.37-1.45.80.42334010.8910.1910.4650.738100
1.4-1.435.80.37734170.920.170.4140.773100
1.43-1.465.90.3233650.9420.1440.3520.799100
1.46-1.55.90.25934170.9560.1160.2840.81100
1.5-1.545.90.22134000.9670.0990.2430.846100
1.54-1.595.90.19334060.9750.0860.2120.884100
1.59-1.645.90.15534260.9810.0690.170.898100
1.64-1.760.13634340.9870.060.1490.938100
1.7-1.7660.1134020.9920.0490.1210.937100
1.76-1.8460.08734320.9950.0390.0960.947100
1.84-1.9460.06834280.9960.030.0751.003100
1.94-2.0660.05634430.9970.0250.0611.067100
2.06-2.2260.04534590.9980.020.051.0899.9
2.22-2.4560.0434750.9980.0180.0441.13499.9
2.45-2.86.10.03234850.9990.0140.0350.97699.9
2.8-3.5360.02535120.9990.0110.0280.9299.8
3.53-505.60.02436860.9990.0110.0260.9599.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
REFMAC5.8.0107refinement
HKL-3000phasing
MLPHAREphasing
SHELXphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XAP

4xap


Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.1376 / WRfactor Rwork: 0.1121 / FOM work R set: 0.9155 / SU B: 1.304 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0389 / SU Rfree: 0.0377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / SU Rfree Cruickshank DPI: 0.0376 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1401 3483 5.1 %RANDOM
Rwork0.1152 ---
obs0.1165 65197 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.4 Å2 / Biso mean: 15.157 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.16 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 48 432 2587
Biso mean--9.75 31.72 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022334
X-RAY DIFFRACTIONr_bond_other_d0.0020.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9893197
X-RAY DIFFRACTIONr_angle_other_deg1.96635084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52422.941102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07615374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4741524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212670
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02525
X-RAY DIFFRACTIONr_mcbond_it1.3321.2331165
X-RAY DIFFRACTIONr_mcbond_other1.3322.0671164
X-RAY DIFFRACTIONr_mcangle_it1.7051.8591464
X-RAY DIFFRACTIONr_rigid_bond_restr1.24932334
X-RAY DIFFRACTIONr_sphericity_free24.4750.00177
X-RAY DIFFRACTIONr_sphericity_bonded11.6640.0012539
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 235 -
Rwork0.211 4814 -
all-5049 -
obs--99.74 %

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