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- PDB-6jko: Crystal structure of sulfoacetaldehyde reductase from Bifidobacte... -

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Basic information

Entry
Database: PDB / ID: 6jko
TitleCrystal structure of sulfoacetaldehyde reductase from Bifidobacterium kashiwanohense
ComponentsMethanol dehydrogenase
KeywordsOXIDOREDUCTASE / middle chain sulfoacetaldehyde reductase / NADH
Function / homologyIron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / oxidoreductase activity / metal ion binding / Methanol dehydrogenase
Function and homology information
Biological speciesBifidobacterium kashiwanohense PV20-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhou, Y. / Xu, T. / Lin, L. / Zhang, Y. / Yuchi, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31570060 China
National Science Foundation (China)31870049 China
Ministry of Science and Technology (China) China
CitationJournal: Biosci.Rep. / Year: 2019
Title: Identification and characterization of a new sulfoacetaldehyde reductase from the human gut bacteriumBifidobacterium kashiwanohense.
Authors: Zhou, Y. / Wei, Y. / Nanjaraj Urs, A.N. / Lin, L. / Xu, T. / Hu, Y. / Ang, E.L. / Zhao, H. / Yuchi, Z. / Zhang, Y.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methanol dehydrogenase
B: Methanol dehydrogenase
C: Methanol dehydrogenase
D: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,8118
Polymers163,5504
Non-polymers2624
Water19,9431107
1
A: Methanol dehydrogenase
hetero molecules

C: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9064
Polymers81,7752
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2360 Å2
ΔGint-87 kcal/mol
Surface area27860 Å2
MethodPISA
2
B: Methanol dehydrogenase
hetero molecules

D: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9064
Polymers81,7752
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2360 Å2
ΔGint-85 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.468, 112.502, 93.406
Angle α, β, γ (deg.)90.000, 107.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methanol dehydrogenase


Mass: 40887.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium kashiwanohense PV20-2 (bacteria)
Gene: AH68_00250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7I0A5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS, pH 5.5 25% W/V PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 108665 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.052 / Rrim(I) all: 0.097 / Χ2: 0.461 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.50.60453870.6690.3780.7150.599100
1.93-1.973.50.49754090.7680.3120.5890.54399.9
1.97-2.013.40.40854500.8270.2580.4840.49699.9
2.01-2.053.40.3454050.8840.2160.4040.458100
2.05-2.093.40.30453770.8840.1950.3620.45399.9
2.09-2.143.20.25254750.9220.1690.3050.447100
2.14-2.193.20.21853950.9290.1440.2620.44699.9
2.19-2.253.40.19254290.950.1240.2290.458100
2.25-2.323.50.17154090.9650.1070.2020.444100
2.32-2.393.50.15954220.9680.0990.1880.452100
2.39-2.483.50.13454210.9760.0840.1590.443100
2.48-2.583.50.12254180.9810.0760.1440.45100
2.58-2.73.40.10654250.9840.0680.1260.45399.8
2.7-2.843.20.0954320.9850.060.1090.449100
2.84-3.023.50.07554460.9920.0470.0890.46100
3.02-3.253.60.06454400.9930.040.0760.457100
3.25-3.583.50.05354630.9960.0330.0620.45899.9
3.58-4.093.20.04254340.9960.0280.0510.45999.9
4.09-5.163.50.03854950.9970.0240.0450.432100
5.16-503.30.03555330.9980.0220.0420.35399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHD

1vhd


Resolution: 1.9→32.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.33
RfactorNum. reflection% reflection
Rfree0.1927 2015 1.86 %
Rwork0.1566 --
obs0.1573 108623 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.37 Å2 / Biso mean: 24.7972 Å2 / Biso min: 8 Å2
Refinement stepCycle: final / Resolution: 1.9→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11237 0 4 1107 12348
Biso mean--25.38 31.33 -
Num. residues----1504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9004-1.9480.29691380.24377161729994
1.948-2.00060.25631460.199775757721100
2.0006-2.05950.19971480.173776197767100
2.0595-2.12590.24861300.167876397769100
2.1259-2.20190.20961620.161376387800100
2.2019-2.290.18451330.157476327765100
2.29-2.39420.18881480.157876107758100
2.3942-2.52040.211450.160876687813100
2.5204-2.67830.20331470.166376107757100
2.6783-2.88490.22011400.167776587798100
2.8849-3.1750.18171430.160276487791100
3.175-3.63390.21371460.153176797825100
3.6339-4.57630.15491440.127776817825100
4.5763-32.30450.14551450.144277907935100

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