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- PDB-6c4l: Yersinopine dehydrogenase (YpODH) - Apo -

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Basic information

Entry
Database: PDB / ID: 6c4l
TitleYersinopine dehydrogenase (YpODH) - Apo
ComponentsYersinopine dehydrogenase
KeywordsOXIDOREDUCTASE / Opine Dehydrogenase / Metallophore Siderophore / Yersinopine Pseudopaline Staphylopine
Function / homologyOxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / NAD(P)-binding domain superfamily / Yersinopine synthase
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMcFarlane, J.S. / Davis, C.L. / Lamb, A.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1403293 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103418 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase.
Authors: McFarlane, J.S. / Davis, C.L. / Lamb, A.L.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _struct_keywords.text
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Yersinopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)53,1151
Polymers53,1151
Non-polymers00
Water84747
1
C: Yersinopine dehydrogenase

C: Yersinopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)106,2302
Polymers106,2302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1740 Å2
ΔGint-21 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.902, 124.125, 87.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Yersinopine dehydrogenase


Mass: 53115.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: y2835, YP_1249 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CKU7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.5 M sodium formation pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→38.43 Å / Num. obs: 36673 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.039 / Num. unique obs: 2550

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.89 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.73
RfactorNum. reflection% reflection
Rfree0.2453 1995 5.46 %
Rwork0.1996 --
obs0.2021 36544 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 47 3372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093401
X-RAY DIFFRACTIONf_angle_d1.0084639
X-RAY DIFFRACTIONf_dihedral_angle_d11.9742048
X-RAY DIFFRACTIONf_chiral_restr0.054530
X-RAY DIFFRACTIONf_plane_restr0.007596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04520.36851330.34182297X-RAY DIFFRACTION95
2.0452-2.10050.32641400.29382448X-RAY DIFFRACTION100
2.1005-2.16230.32951420.25982440X-RAY DIFFRACTION100
2.1623-2.23210.30791420.23592461X-RAY DIFFRACTION100
2.2321-2.31180.25361410.22322453X-RAY DIFFRACTION100
2.3118-2.40440.31261430.20932453X-RAY DIFFRACTION100
2.4044-2.51380.2671410.19482452X-RAY DIFFRACTION100
2.5138-2.64630.28321410.20582469X-RAY DIFFRACTION100
2.6463-2.8120.26191430.21752468X-RAY DIFFRACTION100
2.812-3.02910.26451430.22052471X-RAY DIFFRACTION100
3.0291-3.33380.21571430.21272473X-RAY DIFFRACTION100
3.3338-3.81580.25781450.1842513X-RAY DIFFRACTION100
3.8158-4.8060.19831460.1562525X-RAY DIFFRACTION100
4.806-38.18740.20451520.1842626X-RAY DIFFRACTION100

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