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- PDB-9vrg: Carbonyl reductase SxPR mutant-T149AF153A -

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Basic information

Entry
Database: PDB / ID: 9vrg
TitleCarbonyl reductase SxPR mutant-T149AF153A
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: 1.58 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-T149AF153A
Authors: Zhen, M. / Tingting, Y.
History
DepositionJul 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,2764
Polymers52,7902
Non-polymers1,4872
Water1,18966
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)108,5538
Polymers105,5794
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 area17760 Å2
ΔGint-111 kcal/mol
Surface area33930 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)108,5538
Polymers105,5794
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 area17440 Å2
ΔGint-113 kcal/mol
Surface area34570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.050, 80.070, 131.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 259 / Label seq-ID: 2 - 259

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carbonyl Reductase


Mass: 26394.779 Da / Num. of mol.: 2
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.: 66 / 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 Å3/Da / Density % sol: 38.52 %
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, L10.504
11-K, -H, -L20.496
ReflectionResolution: 1.58→43.94 Å / Num. obs: 58073 / % possible obs: 99.7 % / Redundancy: 12.1 % / Rpim(I) all: 0.066 / Net I/σ(I): 10.6
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 2854 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→42.94 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.424 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23709 2816 4.9 %RANDOM
Rwork0.20419 ---
obs0.20573 54957 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.797 Å2
Baniso -1Baniso -2Baniso -3
1--7.64 Å2-0 Å2-0 Å2
2---7.49 Å2-0 Å2
3---15.13 Å2
Refinement stepCycle: 1 / Resolution: 1.58→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 96 66 3782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193783
X-RAY DIFFRACTIONr_bond_other_d0.0010.023648
X-RAY DIFFRACTIONr_angle_refined_deg1.4562.0015158
X-RAY DIFFRACTIONr_angle_other_deg0.80238339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79223.517145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561534
X-RAY DIFFRACTIONr_chiral_restr0.0830.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.55.7332018
X-RAY DIFFRACTIONr_mcbond_other1.4985.7322017
X-RAY DIFFRACTIONr_mcangle_it2.5238.5972517
X-RAY DIFFRACTIONr_mcangle_other2.5238.5992518
X-RAY DIFFRACTIONr_scbond_it1.3345.7911764
X-RAY DIFFRACTIONr_scbond_other1.3335.7931765
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2178.6352639
X-RAY DIFFRACTIONr_long_range_B_refined4.85567.1664161
X-RAY DIFFRACTIONr_long_range_B_other4.8567.2434154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7511 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 220 -
Rwork0.2 3978 -
obs--98.31 %

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