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- PDB-4xk2: Crystal structure of aldo-keto reductase from Polaromonas sp. JS666 -

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Basic information

Entry
Database: PDB / ID: 4xk2
TitleCrystal structure of aldo-keto reductase from Polaromonas sp. JS666
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / aldo-keto reductase / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Sroka, P. / Hillerich, B.S. / Bonanno, J. / Seidel, R. / 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)U54-GM094662 United States
CitationJournal: to be published
Title: Crystal structure of aldo-keto reductase from Polaromonas sp. JS666
Authors: Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Sroka, P. / Minor, W.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo/keto reductase
B: Aldo/keto reductase
C: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,47711
Polymers112,2313
Non-polymers2468
Water17,258958
1
A: Aldo/keto reductase
C: Aldo/keto reductase
hetero molecules

A: Aldo/keto reductase
C: Aldo/keto reductase
hetero molecules

A: Aldo/keto reductase
C: Aldo/keto reductase
hetero molecules

A: Aldo/keto reductase
C: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,03332
Polymers299,2828
Non-polymers75124
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area32380 Å2
ΔGint-406 kcal/mol
Surface area83900 Å2
MethodPISA
2
B: Aldo/keto reductase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)299,75024
Polymers299,2828
Non-polymers46816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area28270 Å2
ΔGint-288 kcal/mol
Surface area84460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.110, 105.110, 479.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

21A-591-

HOH

31A-842-

HOH

41A-850-

HOH

51A-887-

HOH

61A-888-

HOH

71B-566-

HOH

81B-567-

HOH

91B-568-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 0 - 343 / Label seq-ID: 1 - 344

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3
Detailsbiological unit is the same as asym.

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Components

#1: Protein Aldo/keto reductase


Mass: 37410.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Before crystallization protein with His-tag (MHHHHHHSSGVDLGTENLYFQS) was subjected to the limited proteolysis with chymotrypsin.
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Gene: Bpro_4249 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) Ril / References: UniProt: Q124A1
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 958 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 ul of 12 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 Suite 3 condition #81 (0.2M NaCl, 0.1M Na ...Details: 0.2 ul of 12 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 Suite 3 condition #81 (0.2M NaCl, 0.1M Na citrate, 40%v/v 1,2-propanodiol pH=5.5) 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 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 106320 / Num. obs: 106320 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Rsym value: 0.082 / Χ2: 0.864 / Net I/av σ(I): 20.094 / Net I/σ(I): 5.8 / Num. measured all: 630404
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.80.831.952560.7020.3730.910.844100
1.93-1.975.90.67152260.8020.3020.7370.757100
1.97-2.015.90.58352430.8450.2620.640.758100
2.01-2.055.90.48352380.8970.2170.5310.774100
2.05-2.095.90.42852530.9140.1920.470.883100
2.09-2.145.90.33452400.9490.1490.3670.792100
2.14-2.195.90.27552850.9620.1230.3010.789100
2.19-2.255.90.26552300.9680.1180.2910.899100
2.25-2.325.90.23552790.970.1050.2580.809100
2.32-2.3960.18953060.980.0840.2070.806100
2.39-2.4860.15852630.9860.070.1730.806100
2.48-2.5860.13852730.9890.0610.1510.82100
2.58-2.760.12853120.990.0560.140.874100
2.7-2.846.10.10952940.9920.0480.1190.88599.9
2.84-3.026.10.08953190.9940.0390.0981.009100
3.02-3.2560.07153300.9960.0310.0781.052100
3.25-3.5860.05553700.9970.0240.061.04100
3.58-4.095.90.04554090.9980.020.051.012100
4.09-5.165.90.03854580.9980.0170.0420.889100
5.16-505.70.03457360.9980.0150.0370.75799.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JTD

4jtd


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1737 / WRfactor Rwork: 0.1497 / FOM work R set: 0.8623 / SU B: 5.021 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1079 / SU Rfree: 0.1019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / SU Rfree Cruickshank DPI: 0.1019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 5293 5 %RANDOM
Rwork0.1605 100839 --
obs0.1617 100839 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.82 Å2 / Biso mean: 45.569 Å2 / Biso min: 21.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 8 964 8131
Biso mean--47.18 52.72 -
Num. residues----942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197406
X-RAY DIFFRACTIONr_bond_other_d0.0020.027046
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.95810093
X-RAY DIFFRACTIONr_angle_other_deg2.269316094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0035954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18823.386319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.719151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.861557
X-RAY DIFFRACTIONr_chiral_restr0.0710.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218504
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021725
X-RAY DIFFRACTIONr_mcbond_it1.3291.9163786
X-RAY DIFFRACTIONr_mcbond_other1.3291.9163785
X-RAY DIFFRACTIONr_mcangle_it2.142.8414720
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185430.08
12B185430.08
21A191750.07
22C191750.07
31B186170.05
32C186170.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 391 -
Rwork0.238 7350 -
all-7741 -
obs--99.97 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82120.36450.14341.20840.72051.43560.01370.02770.08190.0087-0.0044-0.0098-0.048-0.1275-0.00930.27860.00150.00210.2535-0.01110.28020.130.434102.228
20.9132-0.6181-0.50571.56610.14610.7796-0.0957-0.06210.0680.20910.0987-0.05220.01530.0575-0.0030.30120.0083-0.01340.2695-0.02480.24677.89927.162115.139
30.2552-0.1663-0.08330.60290.08780.2744-0.01210.01540.00780.05280.0217-0.04490.0222-0.0218-0.00970.2821-0.0015-0.00580.272-0.00440.264712.69913.198101.085
40.1889-0.06820.16021.17590.22120.2916-0.01780.02580.05-0.02320.0197-0.147-0.028-0.0093-0.00190.2785-0.00020.00860.2675-0.00370.295412.20531.42393.531
51.9263-3.1750.2225.2975-0.61871.48460.089-0.01470.1808-0.0615-0.0483-0.3136-0.15870.2415-0.04060.219-0.05030.02310.248-0.01810.366121.54144.43392.419
60.0702-0.0979-0.2752.21230.05131.1350.04020.00920.0064-0.0351-0.0509-0.116-0.1357-0.04810.01070.29890.00820.00430.2476-0.00780.28527.16343.19497.472
73.5077-1.62476.00310.7827-2.841111.89910.1015-0.01260.059-0.0419-0.07640.00180.0820.0519-0.02520.3001-0.0124-0.01640.2411-0.01020.28255.5843.414109.12
80.0927-0.1576-0.02571.00921.0841.61160.0440.04650.0834-0.17030.0032-0.1104-0.1408-0.0523-0.04710.3213-0.0160.03570.25420.0210.270410.66338.1279.717
91.1708-0.0141-0.58272.2923-0.42781.5229-0.02150.0662-0.0021-0.00020.11360.0465-0.12-0.2476-0.09210.42310.09660.05030.40970.03790.0215-17.32725.05218.922
100.12590.1064-0.30680.1994-0.081.04540.03690.02280.0331-0.04870.06630.0176-0.2310.0655-0.10320.49270.06530.05210.40140.02870.0584-9.49627.17931.7
110.3227-0.11650.08250.4052-0.09540.6875-0.0092-0.0482-0.0093-0.01120.1122-0-0.12540.008-0.1030.43780.00470.03780.3948-0.01110.05322.79918.49718.398
120.1965-0.50880.11021.6536-0.27720.53410.00370.0362-0.00520.02830.0623-0.0277-0.1891-0.0619-0.0660.49490.04570.05240.35470.01640.0577-7.45429.5339.627
137.11571.1096-1.6041.1701-0.63413.00790.06120.1580.39570.29380.1834-0.0429-0.4502-0.0277-0.24450.50650.14290.08820.19760.03030.0716-15.37549.99210.118
140.5495-0.785-0.38681.6169-0.66783.6597-0.05030.0281-0.04590.25330.16210.126-0.5154-0.2068-0.11180.54950.12620.07690.38150.03730.024-17.16736.76717.781
151.1719-0.07430.29773.9781-0.79791.0318-0.13970.07850.11910.02190.40770.2392-0.2931-0.514-0.2680.56210.25220.12490.46010.17280.1076-21.36141.2079.886
161.2620.2117-0.75523.20770.96691.39380.05290.11050.0926-0.11680.02010.0247-0.2135-0.1628-0.0730.53760.04230.04550.34140.03270.0116-8.24433.664-8.572
171.3481-0.6044-0.01981.2-0.35031.02680.05250.10360.042-0.06810.0121-0.0195-0.15360.1113-0.06460.32170.00520.02430.27770.05740.2435-10.90728.68464.249
180.6469-0.4554-0.24260.6466-0.40111.21780.08440.1182-0.0032-0.1668-0.0345-0.0137-0.0282-0.1466-0.04990.39290.01550.01060.32650.04940.1595-17.25523.07651.446
190.10690.00290.06320.61490.04850.09040.02950.0035-0.0094-0.11950.02090.04570.0030.0114-0.05040.31120.0046-0.00540.30920.01460.2261-16.9438.19164.747
202.0934-2.1347-0.56512.84680.5010.94170.02070.03250.0798-0.1180.04010.011-0.0604-0.0042-0.06080.2625-0.00350.00250.26670.02070.2453-18.07219.79374.567
210.8015-0.40130.25610.9056-0.30981.12380.01670.04570.0543-0.08830.00210.0689-0.0244-0.1238-0.01880.2950.0045-0.00590.30030.04060.2717-25.24928.45971.953
221.91952.4834-0.66745.48540.21832.83640.19550.10290.07860.00850.00920.1255-0.2519-0.5362-0.20460.24490.11540.0130.24740.1120.3152-33.83237.52673.646
231.0385-0.812-0.8811.646-0.24921.62570.23020.13130.0443-0.1596-0.1145-0.0002-0.2332-0.1282-0.11580.36370.05910.01070.26910.07030.2453-21.33836.28865.386
242.5929-0.4865-1.44213.1443-0.39073.06130.3413-0.08620.4259-0.0772-0.01640.0982-0.51970.0299-0.32490.33810.03390.04210.16610.04290.2625-21.71541.85273.018
251.8893-0.75390.69740.7172-0.56981.73680.0098-0.04230.14120.07280.05830.0659-0.0713-0.0568-0.06810.26770.02070.00880.26680.01590.2803-23.36926.20391.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 21
2X-RAY DIFFRACTION2A37 - 88
3X-RAY DIFFRACTION3A89 - 174
4X-RAY DIFFRACTION4A175 - 226
5X-RAY DIFFRACTION5A241 - 259
6X-RAY DIFFRACTION6A260 - 290
7X-RAY DIFFRACTION7A291 - 305
8X-RAY DIFFRACTION8A306 - 343
9X-RAY DIFFRACTION9B0 - 21
10X-RAY DIFFRACTION10B37 - 88
11X-RAY DIFFRACTION11B89 - 172
12X-RAY DIFFRACTION12B173 - 223
13X-RAY DIFFRACTION13B245 - 269
14X-RAY DIFFRACTION14B270 - 297
15X-RAY DIFFRACTION15B298 - 321
16X-RAY DIFFRACTION16B322 - 343
17X-RAY DIFFRACTION17C0 - 21
18X-RAY DIFFRACTION18C37 - 88
19X-RAY DIFFRACTION19C89 - 172
20X-RAY DIFFRACTION20C173 - 196
21X-RAY DIFFRACTION21C197 - 226
22X-RAY DIFFRACTION22C241 - 265
23X-RAY DIFFRACTION23C266 - 297
24X-RAY DIFFRACTION24C298 - 320
25X-RAY DIFFRACTION25C321 - 343

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