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- PDB-7w5n: The crystal structure of the reduced form of Gluconobacter oxydan... -

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Basic information

Entry
Database: PDB / ID: 7w5n
TitleThe crystal structure of the reduced form of Gluconobacter oxydans WSH-004 SNDH
ComponentsL-sorbosone dehydrogenase, NAD(P) dependent
KeywordsOXIDOREDUCTASE / L-sorbosone dehydrogenase / NAD(P)+
Function / homologyAldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Chem-NDP
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.988 Å
AuthorsLi, D. / Hou, X.D. / Rao, Y.J. / Yin, D.J. / Zhou, J.W. / Chen, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830068 China
CitationJournal: Adv Sci / Year: 2023
Title: Structural Insight into the Catalytic Mechanisms of an L-Sorbosone Dehydrogenase.
Authors: Li, D. / Deng, Z. / Hou, X. / Qin, Z. / Wang, X. / Yin, D. / Chen, Y. / Rao, Y. / Chen, J. / Zhou, J.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-sorbosone dehydrogenase, NAD(P) dependent
B: L-sorbosone dehydrogenase, NAD(P) dependent
C: L-sorbosone dehydrogenase, NAD(P) dependent
D: L-sorbosone dehydrogenase, NAD(P) dependent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,7988
Polymers217,8164
Non-polymers2,9824
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27550 Å2
ΔGint-112 kcal/mol
Surface area56120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.242, 118.817, 109.020
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-sorbosone dehydrogenase, NAD(P) dependent


Mass: 54454.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: WSH-004 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / Details: succinic acid, hepes, pegme 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.988→23.516 Å / Num. obs: 41320 / % possible obs: 99.18 % / Redundancy: 8.86 % / Biso Wilson estimate: 22.89 Å2 / Rsym value: 0.313 / Net I/av σ(I): 15.294 / Net I/σ(I): 9.88
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.989-3.096413200.4461
3.096-3.22374370.4221
3.22-3.366332760.3921
3.366-3.543291580.3651
3.543-3.764250390.3431
3.764-4.053208760.3161
4.053-4.458167460.2941
4.458-5.098125690.2781
5.098-6.40184230.2781
6.401-23.542470.2511

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SAINTV8.38Adata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U4J

3u4j


Resolution: 2.988→23.516 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 16.877 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21932 3990 9.7 %RANDOM
Rwork0.17075 ---
obs0.17546 37268 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å2-0.47 Å2
2--0.93 Å20 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.988→23.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14860 0 192 60 15112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01315368
X-RAY DIFFRACTIONr_bond_other_d0.0010.01514609
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.63820848
X-RAY DIFFRACTIONr_angle_other_deg1.241.5833610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10951960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47321.613744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.456152496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.39315108
X-RAY DIFFRACTIONr_chiral_restr0.0580.22041
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023512
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_it1.1241.8047852
X-RAY DIFFRACTIONr_mcbond_other1.1241.8047851
X-RAY DIFFRACTIONr_mcangle_it1.9252.7029808
X-RAY DIFFRACTIONr_mcangle_other1.9252.7039809
X-RAY DIFFRACTIONr_scbond_it1.362.0447516
X-RAY DIFFRACTIONr_scbond_other1.362.0437514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2463.0211041
X-RAY DIFFRACTIONr_long_range_B_refined3.79221.36516416
X-RAY DIFFRACTIONr_long_range_B_other3.79221.3716416
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.988→3.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 264 -
Rwork0.233 2618 -
obs--95.72 %

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