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- PDB-9ivo: Crystal structure of KRED mutant-Y199A/N149L -

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Basic information

Entry
Database: PDB / ID: 9ivo
TitleCrystal structure of KRED mutant-Y199A/N149L
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / KRED / mutants
Function / homologyoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsXu, H. / Zhang, Z. / Zhang, Y. / Xu, Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Chemoenzymatic synthesis of key squalamine intermediate by engineered ketoreductase mutants from Novosphingobium aromaticivorans
Authors: Zhang, Z. / Xu, H. / Kong, P. / Cao, J. / Shan, L. / Zhang, Y. / Xu, Y. / Zhang, L.
History
DepositionJul 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,95913
Polymers106,9474
Non-polymers3,0129
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18730 Å2
ΔGint-121 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.738, 118.817, 121.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 26736.742 Da / Num. of mol.: 4 / Mutation: Y199A,N149L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Gene: Saro_3543 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XEP2
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→121.28 Å / Num. obs: 87610 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Χ2: 0.96 / Net I/σ(I): 15.9 / Num. measured all: 950198
Reflection shellResolution: 1.78→1.81 Å / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.945 / Num. measured all: 49955 / Num. unique obs: 4417 / CC1/2: 0.917 / Rpim(I) all: 0.292 / Rrim(I) all: 0.989 / Χ2: 0.84 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→84.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.67 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19654 4322 4.9 %RANDOM
Rwork0.16362 ---
obs0.16523 83186 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.303 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å2-0 Å2-0 Å2
2---0.2 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: 1 / Resolution: 1.78→84.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7429 0 196 372 7997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177332
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.62910548
X-RAY DIFFRACTIONr_angle_other_deg1.4481.57316929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31451033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54722.357314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.536151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4841540
X-RAY DIFFRACTIONr_chiral_restr0.0730.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021534
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_it2.3122.7914126
X-RAY DIFFRACTIONr_mcbond_other2.3112.794125
X-RAY DIFFRACTIONr_mcangle_it3.0014.1765152
X-RAY DIFFRACTIONr_mcangle_other3.0014.1765153
X-RAY DIFFRACTIONr_scbond_it3.7373.2543639
X-RAY DIFFRACTIONr_scbond_other3.7363.2543640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3894.7195394
X-RAY DIFFRACTIONr_long_range_B_refined7.14534.5738378
X-RAY DIFFRACTIONr_long_range_B_other7.13434.4588327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76360.07
12B76360.07
21A77370.06
22C77370.06
31A77530.06
32D77530.06
41B76230.06
42C76230.06
51B76140.06
52D76140.06
61C77510.06
62D77510.06
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 319 -
Rwork0.252 6073 -
obs--99.98 %

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