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- PDB-6c4m: Yersinopine dehydrogenase (YpODH) - NADP+ bound -

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Basic information

Entry
Database: PDB / ID: 6c4m
TitleYersinopine dehydrogenase (YpODH) - NADP+ bound
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Yersinopine synthase
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

Downloads & links

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Assembly

Deposited unit
C: Yersinopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8582
Polymers53,1151
Non-polymers7431
Water2,540141
1
C: Yersinopine dehydrogenase
hetero molecules

C: Yersinopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7174
Polymers106,2302
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4060 Å2
ΔGint-25 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.389, 125.669, 88.012
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 / Uncharacterized protein


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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.7 M sodium formate pH 6.0, 1.8% ethyl acetate aided by microseeding

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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: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.94→38.73 Å / Num. obs: 40471 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.2
Reflection shellResolution: 1.94→1.98 Å / Rmerge(I) obs: 0.688 / Num. unique obs: 2598

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→38.73 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.58
RfactorNum. reflection% reflection
Rfree0.2292 1996 4.95 %
Rwork0.1895 --
obs0.1915 40337 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 48 141 3485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013422
X-RAY DIFFRACTIONf_angle_d1.0764676
X-RAY DIFFRACTIONf_dihedral_angle_d12.5322039
X-RAY DIFFRACTIONf_chiral_restr0.056534
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.938-1.98640.35471350.3652591X-RAY DIFFRACTION95
1.9864-2.04010.35281390.31552705X-RAY DIFFRACTION99
2.0401-2.10020.29051420.28742739X-RAY DIFFRACTION99
2.1002-2.16790.31741400.25212702X-RAY DIFFRACTION99
2.1679-2.24540.23551440.22832728X-RAY DIFFRACTION99
2.2454-2.33530.26531410.20882724X-RAY DIFFRACTION99
2.3353-2.44160.25041420.19582708X-RAY DIFFRACTION99
2.4416-2.57030.23441420.19162723X-RAY DIFFRACTION99
2.5703-2.73130.25321440.18582759X-RAY DIFFRACTION100
2.7313-2.94210.26751430.19862748X-RAY DIFFRACTION100
2.9421-3.2380.23051430.18142741X-RAY DIFFRACTION99
3.238-3.70630.20591450.16662788X-RAY DIFFRACTION100
3.7063-4.66820.18571460.14572800X-RAY DIFFRACTION99
4.6682-38.74270.20411500.17852885X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.2324 Å / Origin y: 26.5329 Å / Origin z: 35.0729 Å
111213212223313233
T0.279 Å2-0.0147 Å20.0031 Å2-0.2562 Å20.0019 Å2--0.2639 Å2
L0.6026 °2-0.2178 °20.1207 °2-0.231 °2-0.0277 °2--0.1817 °2
S-0.0445 Å °0.1336 Å °-0.0431 Å °-0.0342 Å °0.0048 Å °0.0054 Å °0.0304 Å °0.0207 Å °-0 Å °
Refinement TLS groupSelection details: all

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