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- PDB-6c4t: Staphylopine dehydrogenase (SaODH) - NADP+ bound -

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Basic information

Entry
Database: PDB / ID: 6c4t
TitleStaphylopine dehydrogenase (SaODH) - NADP+ bound
ComponentsStaphylopine dehydrogenase
KeywordsOXIDOREDUCTASE / Opine Dehydrogenase Metallophore Siderophore Yersinopine Pseudopaline Staphylopine
Function / homologystaphylopine dehydrogenase / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / Chem-NA7 / Staphylopine synthase / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 1.4Oct 4, 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

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Assembly

Deposited unit
A: Staphylopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9373
Polymers52,2221
Non-polymers7152
Water18010
1
A: Staphylopine dehydrogenase
hetero molecules

A: Staphylopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8746
Polymers104,4432
Non-polymers1,4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5610 Å2
ΔGint-27 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.096, 49.258, 59.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Staphylopine dehydrogenase


Mass: 52221.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: AB466_12420, AB526_12775, AFP37_00945, APW47_05390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q4GXD5, UniProt: A0A0H3JT80*PLUS
#2: Chemical ChemComp-NA7 / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 623.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O16P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8.0, 100 mM lithium sulfate, 23% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97937 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.49→38.58 Å / Num. obs: 19677 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 2.49→2.59 Å / Rmerge(I) obs: 0.889 / Num. unique obs: 2121

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C4L

6c4l


Resolution: 2.49→38.58 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.57
RfactorNum. reflection% reflection
Rfree0.2659 1959 10 %
Rwork0.2194 --
obs0.224 19584 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.49→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 45 10 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153598
X-RAY DIFFRACTIONf_angle_d1.294869
X-RAY DIFFRACTIONf_dihedral_angle_d17.0192179
X-RAY DIFFRACTIONf_chiral_restr0.061541
X-RAY DIFFRACTIONf_plane_restr0.009615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4933-2.55560.39131270.3091153X-RAY DIFFRACTION92
2.5556-2.62470.32871370.28131228X-RAY DIFFRACTION100
2.6247-2.70190.31921380.2521236X-RAY DIFFRACTION100
2.7019-2.78910.3081380.26041244X-RAY DIFFRACTION99
2.7891-2.88870.29241370.25041235X-RAY DIFFRACTION100
2.8887-3.00440.30731380.2661245X-RAY DIFFRACTION100
3.0044-3.1410.36831400.28071253X-RAY DIFFRACTION100
3.141-3.30660.30121410.26931264X-RAY DIFFRACTION100
3.3066-3.51360.31531400.24221263X-RAY DIFFRACTION100
3.5136-3.78470.28041400.22291259X-RAY DIFFRACTION100
3.7847-4.16510.21861400.20081271X-RAY DIFFRACTION100
4.1651-4.76690.23611430.1711272X-RAY DIFFRACTION100
4.7669-6.00210.20871450.19451314X-RAY DIFFRACTION100
6.0021-38.57990.23151550.18781388X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 66.2626 Å / Origin y: 7.3834 Å / Origin z: 14.8692 Å
111213212223313233
T0.5712 Å2-0.0345 Å20.0778 Å2-0.5259 Å2-0.0196 Å2--0.496 Å2
L2.643 °2-0.2158 °20.4851 °2-0.2632 °2-0.0307 °2--0.2533 °2
S0.0293 Å °-0.4787 Å °0.1295 Å °0.0687 Å °0.0124 Å °-0.0006 Å °-0.0066 Å °-0.0413 Å °-0 Å °
Refinement TLS groupSelection details: all

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