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- PDB-4xap: Crystal structure of aldo-keto reductase from Sinorhizobium melil... -

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Basic information

Entry
Database: PDB / ID: 4xap
TitleCrystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021
ComponentsAldo-keto reductase
KeywordsOXIDOREDUCTASE / PSI-Biology / New York Structural Genomics Research Consortium / aldo-keto reductase / NADP-binding / NYSGRC
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
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsGasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / 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
Authors: Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 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 1.6Sep 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

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase


Theoretical massNumber of molelcules
Total (without water)30,8441
Polymers30,8441
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.533, 78.068, 79.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Aldo-keto reductase


Mass: 30844.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: R02112, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 15 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 PEG/Ion HT condition #70 (0.2M Ammonium Citrate ...Details: 0.2 ul of 15 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 PEG/Ion HT condition #70 (0.2M Ammonium Citrate Tribasic anhydrous, 20% w/v PEG 3350 pH=7) 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14216 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Rsym value: 0.072 / Χ2: 0.883 / Net I/av σ(I): 20.282 / Net I/σ(I): 17.6 / Num. measured all: 65764
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
2.2-2.244.50.6922.16940.8050.3270.7680.71798.7
2.24-2.284.60.5956800.8530.2850.6620.78398.3
2.28-2.324.60.4797140.880.2270.5320.72298.6
2.32-2.374.60.3876760.9010.1840.430.74197.5
2.37-2.424.60.3796820.8870.1810.4210.7798
2.42-2.484.70.3547090.9260.170.3940.78898.6
2.48-2.544.70.3096890.9360.1470.3430.76398.9
2.54-2.614.60.2577020.9610.1230.2860.8198.3
2.61-2.694.70.2086880.9690.10.2320.83797.9
2.69-2.774.70.1757130.9810.0850.1950.80597.8
2.77-2.874.70.1486910.9830.0710.1640.88698.6
2.87-2.994.70.1287090.9850.0620.1430.9598.2
2.99-3.124.70.0947030.9940.0460.1050.89599.2
3.12-3.294.70.0757190.9950.0370.0840.9299.9
3.29-3.494.70.0597210.9970.0290.0660.979100
3.49-3.764.70.0487300.9980.0240.0541.071100
3.76-4.144.60.047260.9980.020.0451.048100
4.14-4.744.60.0337370.9980.0170.0381.04100
4.74-5.974.50.0317580.9990.0150.0340.799100
5.97-504.30.0377750.9980.0190.0421.30895.2

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PMJ
Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2053 / WRfactor Rwork: 0.146 / FOM work R set: 0.8229 / SU B: 13.137 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2534 / SU Rfree: 0.2067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 770 5.4 %RANDOM
Rwork0.1599 13410 --
obs0.1634 13410 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.16 Å2 / Biso mean: 42.116 Å2 / Biso min: 22.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å20 Å2
2--1.12 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 0 103 2222
Biso mean---44.37 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192159
X-RAY DIFFRACTIONr_bond_other_d0.0010.022069
X-RAY DIFFRACTIONr_angle_refined_deg1.721.972934
X-RAY DIFFRACTIONr_angle_other_deg0.85534744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37723.40494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54615348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4441520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_mcbond_it1.5072.3581123
X-RAY DIFFRACTIONr_mcbond_other1.5032.3571122
X-RAY DIFFRACTIONr_mcangle_it2.1953.5311402
LS refinement shellResolution: 2.207→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 45 -
Rwork0.246 925 -
all-970 -
obs--92.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
124.325630.17210.099337.55312.57614.2391-1.35041.4046-1.6033-1.95091.9637-2.0498-0.69960.6316-0.61330.8383-0.37270.09960.57-0.30640.3249-3.1814.91213.562
21.7728-1.92191.67194.3106-2.58833.64930.1048-0.0091-0.11660.0852-0.02240.0505-0.05870.095-0.08230.12750.0084-0.00760.1872-0.01510.1157-7.405-2.4429.308
30.3066-0.3632-0.54721.05860.6942.04060.0537-0.11910.02690.0995-0.09180.03520.01050.00760.03820.2144-0.0266-0.00110.2139-0.03080.0941-7.273-2.8916.894
43.6612-1.2819-1.25482.58370.90254.1290.1458-0.41320.11080.31320.0441-0.17560.2090.2253-0.18980.2076-0.06290.01170.19230.01450.0702-11.949-10.05216.661
52.29991.6009-0.27253.94481.78582.0160.0194-0.0166-0.03090.13940.04880.19810.0814-0.0841-0.06820.15150.0051-0.00440.17510.04970.1028-16.078-12.9364.667
60.87140.0123-0.38581.46481.07552.39290.00550.0054-0.1974-0.028-0.07340.3015-0.0042-0.09180.0680.1524-0.0112-0.0040.18440.00540.1515-15.566-13.6414.157
71.82280.3217-0.06791.0338-0.20990.1626-0.00640.0314-0.0131-0.14460.01880.04810.0460.0284-0.01230.15810.0135-0.00860.2074-0.00350.0772-10.853-6.872-5.884
82.66950.04371.40451.0613-0.18031.18970.0661-0.0131-0.0099-0.021-0.0557-0.1735-0.02040.1058-0.01040.1465-0.00530.00590.2010.01250.1214.7252.5833.859
92.82941.1034-4.55227.978-6.32510.0825-0.0159-0.26940.02840.2513-0.1207-0.2466-0.09620.45110.13660.1892-0.0289-0.02160.2121-0.0370.13461.6625.9215.881
101.12870.60191.79617.52253.01475.4425-0.07780.18360.1268-0.42290.0669-0.2375-0.50580.42780.01090.1182-0.05890.06090.23460.06380.220512.56710.139-1.906
115.36461.5229-5.21773.25920.40846.4182-0.2564-0.3432-0.5167-0.2153-0.1206-0.42440.26280.3840.3770.21410.06810.07110.3470.05440.18665.586-7.616-9.768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 32
3X-RAY DIFFRACTION3A33 - 55
4X-RAY DIFFRACTION4A56 - 74
5X-RAY DIFFRACTION5A75 - 97
6X-RAY DIFFRACTION6A98 - 122
7X-RAY DIFFRACTION7A123 - 183
8X-RAY DIFFRACTION8A184 - 240
9X-RAY DIFFRACTION9A241 - 255
10X-RAY DIFFRACTION10A256 - 271
11X-RAY DIFFRACTION11A272 - 281

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