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

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Basic information

Entry
Database: PDB / ID: 9ivn
TitleCrystal structure of KRED mutant-Y199A/N149L
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / KRED / mutants
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. / Li, S. / 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

Downloads & links

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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
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,99136
Polymers213,8948
Non-polymers7,09728
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42010 Å2
ΔGint-272 kcal/mol
Surface area58810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.486, 122.450, 141.429
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818
1919
2020
2121
2222
2323
2424
2525
2626
2727
2828

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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Protein , 1 types, 8 molecules ABCFGHDE

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 26736.742 Da / Num. of mol.: 8 / 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

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Non-polymers , 7 types, 305 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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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 PILATUS3 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: 2→122.45 Å / Num. obs: 149684 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 1.04 / Net I/σ(I): 14.4 / Num. measured all: 781172
Reflection shellResolution: 2→2.03 Å / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Num. measured all: 28450 / Num. unique obs: 7388 / CC1/2: 0.831 / Rpim(I) all: 0.361 / Rrim(I) all: 0.755 / Χ2: 1 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→92.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.862 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23224 7535 5 %RANDOM
Rwork0.20565 ---
obs0.20695 142046 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-2.65 Å2
2---3.32 Å2-0 Å2
3---3.32 Å2
Refinement stepCycle: 1 / Resolution: 2→92.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14888 0 461 277 15626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01315600
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714747
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.62921158
X-RAY DIFFRACTIONr_angle_other_deg1.3081.57234048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50852062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55222.281627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.857152426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6531581
X-RAY DIFFRACTIONr_chiral_restr0.0660.22116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023073
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_it3.9574.7328260
X-RAY DIFFRACTIONr_mcbond_other3.9574.7328259
X-RAY DIFFRACTIONr_mcangle_it5.127.0910312
X-RAY DIFFRACTIONr_mcangle_other5.127.0910313
X-RAY DIFFRACTIONr_scbond_it4.5145.1027340
X-RAY DIFFRACTIONr_scbond_other4.5055.0947329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2937.47710827
X-RAY DIFFRACTIONr_long_range_B_refined7.74156.40916430
X-RAY DIFFRACTIONr_long_range_B_other7.7456.40416407
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)
11A76890.06
12B76890.06
21A76610.06
22C76610.06
31A77330.05
32F77330.05
41A77010.05
42G77010.05
51A77200.06
52H77200.06
61A77170.05
62D77170.05
71A77060.05
72E77060.05
81B76060.06
82C76060.06
91B76350.06
92F76350.06
101B76620.06
102G76620.06
111B76720.06
112H76720.06
121B76330.06
122D76330.06
131B76520.05
132E76520.05
141C77000.05
142F77000.05
151C76570.06
152G76570.06
161C77010.05
162H77010.05
171C77310.05
172D77310.05
181C77170.05
182E77170.05
191F77090.06
192G77090.06
201F77480.05
202H77480.05
211F77350.04
212D77350.04
221F77520.05
222E77520.05
231G76880.06
232H76880.06
241G76930.05
242D76930.05
251G77180.05
252E77180.05
261H77140.05
262D77140.05
271H77280.05
272E77280.05
281D77080.04
282E77080.04
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 608 -
Rwork0.339 10442 -
obs--99.41 %

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