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- PDB-9vw7: NAD(P)-dependent oxidoreductase from Kutzneria albida -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9vw7
TitleNAD(P)-dependent oxidoreductase from Kutzneria albida
ComponentsDehydrogenase
KeywordsOXIDOREDUCTASE / imine reductase
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Dehydrogenase
Similarity search - Component
Biological speciesKutzneria albida DSM 43870 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsHuang, L. / Fu, H.G. / Yao, Z.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Engineering an Imine Reductase for Enantioselective Synthesis of Atropisomeric Amides.
Authors: Yao, Z. / Meng, R. / Zhou, Z. / Yu, L. / Wu, Z. / Tang, L. / Qiao, T. / Li, K. / Huang, L. / Song, D. / Fu, H.
History
DepositionJul 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5608
Polymers63,4842
Non-polymers2,0766
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-116 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.395, 117.395, 99.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dehydrogenase


Mass: 31741.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kutzneria albida DSM 43870 (bacteria) / Gene: KALB_1124 / Production host: Escherichia coli (E. coli) / References: UniProt: W5W0Y1

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H34O9
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Ammonium Sulfate, 0.1 M HEPES:NaOH pH 7.0, and 0.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.499→45.84 Å / Num. obs: 24403 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.3
Reflection shellResolution: 2.499→2.59 Å / Num. unique obs: 2234 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-3000data reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.499→41.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.077 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.387 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2275 1270 5.205 %
Rwork0.1603 23131 -
all0.164 --
obs-24401 98.854 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0 Å2-0 Å2
2---0.005 Å2-0 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 2.499→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 132 302 4520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124284
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164078
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6335850
X-RAY DIFFRACTIONr_angle_other_deg0.5081.5719315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.065540
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.79354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97410606
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.31210152
X-RAY DIFFRACTIONr_chiral_restr0.0650.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
X-RAY DIFFRACTIONr_nbd_refined0.2370.2990
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.23766
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22152
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.212
X-RAY DIFFRACTIONr_nbd_other0.1720.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.225
X-RAY DIFFRACTIONr_mcbond_it3.8743.7882290
X-RAY DIFFRACTIONr_mcbond_other3.8733.7882289
X-RAY DIFFRACTIONr_mcangle_it5.5046.7982859
X-RAY DIFFRACTIONr_mcangle_other5.5046.7982860
X-RAY DIFFRACTIONr_scbond_it5.144.3231994
X-RAY DIFFRACTIONr_scbond_other5.0684.3091984
X-RAY DIFFRACTIONr_scangle_it7.7517.7182991
X-RAY DIFFRACTIONr_scangle_other7.6327.6912980
X-RAY DIFFRACTIONr_lrange_it8.99237.5814904
X-RAY DIFFRACTIONr_lrange_other9.01536.9064844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.499-2.5640.338950.22615310.23217850.9340.96991.09240.193
2.564-2.6340.291920.22315990.22717290.9370.96997.80220.187
2.634-2.710.272770.20215990.20516940.9570.97498.93740.169
2.71-2.7930.288980.18815560.19416560.950.97799.87920.153
2.793-2.8840.253790.17715110.18115900.9540.9791000.147
2.884-2.9850.224790.16414600.16815390.9620.9821000.139
2.985-3.0970.189940.15514150.15815090.9780.9841000.131
3.097-3.2220.202810.16113600.16314420.9710.98399.93060.139
3.222-3.3650.255730.16313260.16813990.9590.9841000.144
3.365-3.5280.185720.14212490.14413210.9780.9891000.129
3.528-3.7170.186570.14712190.14912760.9760.9891000.139
3.717-3.9410.228550.15411550.15712100.9710.9861000.143
3.941-4.210.185590.14110770.14411360.9780.9871000.133
4.21-4.5430.263440.13410270.13810730.9590.98899.81360.128
4.543-4.9710.188460.1219370.1249830.9850.9911000.116
4.971-5.5480.275580.1678470.1739060.960.98599.88960.155
5.548-6.3870.276340.1987740.2018080.9460.981000.176
6.387-7.7770.127310.156670.1496990.990.98899.85690.143
7.777-10.8110.161250.1145300.1165610.9850.99198.93050.118
10.811-41.540.353210.2482920.2543590.9310.95187.18660.247

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