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

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Basic information

Entry
Database: PDB / ID: 6jkp
TitleCrystal structure of sulfoacetaldehyde reductase from Bifidobacterium kashiwanohense in complex with NAD+
ComponentsMethanol dehydrogenase
KeywordsOXIDOREDUCTASE / sulfoacetaldehyde reductase NADH
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / nucleotide binding / metal ion binding
Similarity search - Function
Iron-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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Methanol dehydrogenase
Similarity search - Component
Biological speciesBifidobacterium kashiwanohense PV20-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 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)166,2699
Polymers163,5504
Non-polymers2,7195
Water181
1
A: Methanol dehydrogenase
hetero molecules

B: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1024
Polymers81,7752
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4450 Å2
ΔGint-23 kcal/mol
Surface area27160 Å2
MethodPISA
2
C: Methanol dehydrogenase
hetero molecules

D: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1675
Polymers81,7752
Non-polymers1,3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4510 Å2
ΔGint-63 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.881, 112.317, 93.573
Angle α, β, γ (deg.)90.000, 107.530, 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 289.15 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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 27084 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.124 / Rrim(I) all: 0.23 / Χ2: 0.937 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.052.80.812990.5550.5911.0020.65493.3
3.05-3.1130.80113260.4930.5580.9820.61397.5
3.11-3.173.40.71313450.6730.4560.8490.68799.8
3.17-3.233.50.67913660.7030.4290.8060.72699.6
3.23-3.33.50.60213920.7030.3770.7120.79399.8
3.3-3.383.60.49113720.7960.3040.5790.81399.8
3.38-3.463.60.41413560.8680.2580.4890.92499.8
3.46-3.563.60.36713610.8680.2270.4320.92999.8
3.56-3.663.60.29813800.9280.1830.351.06799.6
3.66-3.783.60.26813480.9220.1640.3151.00199.2
3.78-3.913.60.22713800.9540.1390.2671.05999.3
3.91-4.073.50.1913580.960.1190.2250.99799.3
4.07-4.263.50.17113710.9690.1060.2020.98498.6
4.26-4.483.50.13113370.9850.0820.1551.04598.7
4.48-4.763.40.13613460.9790.0860.1621.08998.3
4.76-5.133.30.13613770.9790.0870.1620.99398.2
5.13-5.643.20.12812900.9730.0840.1541.09994.4
5.64-6.463.10.11912850.9760.0790.1431.06592.1
6.46-8.133.50.10414020.9790.0660.1231.04399.8
8.13-5030.08613930.9840.0610.1061.06997.6

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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: 3.008→43.194 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.79
RfactorNum. reflection% reflection
Rfree0.2573 1983 7.34 %
Rwork0.1999 --
obs0.2043 27020 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.57 Å2 / Biso mean: 60.2774 Å2 / Biso min: 13.43 Å2
Refinement stepCycle: final / Resolution: 3.008→43.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10878 0 177 1 11056
Biso mean--78.63 44.7 -
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 (%)
3.008-3.08320.36221100.27421429153978
3.0832-3.16650.34961480.26331786193499
3.1665-3.25970.32851400.248818351975100
3.2597-3.36490.30581290.242818471976100
3.3649-3.48510.34191640.245918141978100
3.4851-3.62450.33811370.216218301967100
3.6245-3.78940.25261410.20121842198399
3.7894-3.98910.23451540.18651800195499
3.9891-4.23880.21461390.17661836197599
4.2388-4.56570.23451440.1681821196599
4.5657-5.02460.23971430.17871811195498
5.0246-5.75020.24571420.20821746188895
5.7502-7.23910.25261390.21081780191996
7.2391-43.19880.20691530.1661860201398

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