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- PDB-9vs0: Carbonyl reductase SxPR mutant-Q158AM198G -

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Basic information

Entry
Database: PDB / ID: 9vs0
TitleCarbonyl reductase SxPR mutant-Q158AM198G
ComponentsCarbonyl Reductase
KeywordsOXIDOREDUCTASE / Carbonyl Reductase / Oxidoreductases
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesStreptomyces xanthophaeus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsZhen, M. / Tingting, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Carbonyl reductase SxPR mutant-Q158AM198G
Authors: Zhen, M. / Tingting, Y.
History
DepositionJul 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonyl Reductase
B: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2264
Polymers52,7392
Non-polymers1,4872
Water1,29772
1
A: Carbonyl Reductase
hetero molecules

A: Carbonyl Reductase
hetero molecules

A: Carbonyl Reductase
hetero molecules

A: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4528
Polymers105,4794
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17580 Å2
ΔGint-101 kcal/mol
Surface area34190 Å2
MethodPISA
2
B: Carbonyl Reductase
hetero molecules

B: Carbonyl Reductase
hetero molecules

B: Carbonyl Reductase
hetero molecules

B: Carbonyl Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4528
Polymers105,4794
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17680 Å2
ΔGint-107 kcal/mol
Surface area34830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.160, 80.290, 132.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Carbonyl Reductase


Mass: 26369.705 Da / Num. of mol.: 2 / Mutation: Q158A,M198G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xanthophaeus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate 0.1 M TRIS hydrochloride pH 8.5 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.489
11-K, -H, -L20.511
ReflectionResolution: 1.49→44.06 Å / Num. obs: 69646 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 13.2
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 3351 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→34.31 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3472 4.98 %RANDOM
Rwork0.2315 ---
obs0.2325 69646 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 48 72 3788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073813
X-RAY DIFFRACTIONf_angle_d1.0855206
X-RAY DIFFRACTIONf_dihedral_angle_d19.9381462
X-RAY DIFFRACTIONf_chiral_restr0.083620
X-RAY DIFFRACTIONf_plane_restr0.008678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.20141340.17712334X-RAY DIFFRACTION90
1.51-1.530.21121270.18962672X-RAY DIFFRACTION100
1.53-1.550.19441330.17592600X-RAY DIFFRACTION100
1.55-1.580.21611440.18372651X-RAY DIFFRACTION100
1.58-1.60.22171260.19342620X-RAY DIFFRACTION100
1.6-1.630.21291430.19912641X-RAY DIFFRACTION100
1.63-1.660.21251440.20392595X-RAY DIFFRACTION100
1.66-1.690.1981922720X-RAY DIFFRACTION100
1.69-1.730.21951192644X-RAY DIFFRACTION100
1.73-1.760.29121640.22622612X-RAY DIFFRACTION100
1.76-1.80.2661460.22842594X-RAY DIFFRACTION100
1.8-1.850.27721550.24362633X-RAY DIFFRACTION100
1.85-1.90.26311450.23692653X-RAY DIFFRACTION100
1.9-1.960.24751630.23782662X-RAY DIFFRACTION100
1.96-2.020.29061430.23562630X-RAY DIFFRACTION100
2.02-2.090.26411080.24432666X-RAY DIFFRACTION100
2.09-2.170.26121270.24522700X-RAY DIFFRACTION100
2.18-2.270.26271540.23572646X-RAY DIFFRACTION100
2.27-2.390.28351550.24372634X-RAY DIFFRACTION100
2.39-2.540.22881402672X-RAY DIFFRACTION100
2.54-2.740.24311292686X-RAY DIFFRACTION100
2.74-3.020.28981370.27212704X-RAY DIFFRACTION100
3.02-3.450.27221700.2412668X-RAY DIFFRACTION100
3.45-4.350.22961460.22462741X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.1524 Å / Origin y: -6.0262 Å / Origin z: 32.4581 Å
111213212223313233
T0.214 Å20.016 Å2-0.0501 Å2-0.2588 Å2-0.0315 Å2--0.098 Å2
L0.2796 °2-0.0538 °2-0.0377 °2-0.3242 °2-0.0246 °2--0.1578 °2
S-0.0297 Å °-0.2384 Å °0.0383 Å °0.2311 Å °0.0429 Å °-0.088 Å °-0.0398 Å °0.0885 Å °-0.0058 Å °
Refinement TLS groupSelection details: all

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