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- PDB-6h3f: Staphylopine dehydrogenase in complex with staphylopine and NADP+ -

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Basic information

Entry
Database: PDB / ID: 6h3f
TitleStaphylopine dehydrogenase in complex with staphylopine and NADP+
ComponentsStaphylopine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / staphylopine biosynthesis
Function / homologystaphylopine dehydrogenase / : / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / Chem-8UX / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Staphylopine dehydrogenase CntM / Staphylopine synthase
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsHajjar, C. / Arnoux, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0007-02 France
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis.
Authors: Hajjar, C. / Fanelli, R. / Laffont, C. / Brutesco, C. / Cullia, G. / Tribout, M. / Nurizzo, D. / Borezee-Durant, E. / Voulhoux, R. / Pignol, D. / Lavergne, J. / Cavelier, F. / Arnoux, P.
History
DepositionJul 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Staphylopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5575
Polymers51,1991
Non-polymers1,3584
Water2,000111
1
A: Staphylopine dehydrogenase
hetero molecules

A: Staphylopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,11310
Polymers102,3972
Non-polymers2,7168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7450 Å2
ΔGint-26 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.180, 49.140, 58.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Staphylopine dehydrogenase


Mass: 51198.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: SA2256 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3JNH9, UniProt: A0A0H3JT80*PLUS

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Non-polymers , 5 types, 115 molecules

#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
#3: Chemical ChemComp-8UX / (2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid / staphylopine


Mass: 328.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N4O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium acetate, 20-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→93.59 Å / Num. obs: 118664 / % possible obs: 99.4 % / Redundancy: 4.2 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GMZ

6gmz


Resolution: 2.21→93.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.24 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28848 1438 5.2 %RANDOM
Rwork0.21761 ---
obs0.22113 26431 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.585 Å2
Baniso -1Baniso -2Baniso -3
1--4.99 Å20 Å20 Å2
2---0.27 Å20 Å2
3---5.26 Å2
Refinement stepCycle: 1 / Resolution: 2.21→93.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 90 111 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193704
X-RAY DIFFRACTIONr_bond_other_d0.0030.023390
X-RAY DIFFRACTIONr_angle_refined_deg1.8292.0085017
X-RAY DIFFRACTIONr_angle_other_deg1.02437911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60624.911169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44815661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9471515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213953
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02725
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3075.4861713
X-RAY DIFFRACTIONr_mcbond_other4.2955.4841712
X-RAY DIFFRACTIONr_mcangle_it6.4248.2232141
X-RAY DIFFRACTIONr_mcangle_other6.4188.2232141
X-RAY DIFFRACTIONr_scbond_it5.1496.2011991
X-RAY DIFFRACTIONr_scbond_other5.1486.21991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1159.0282876
X-RAY DIFFRACTIONr_long_range_B_refined10.77165.4594145
X-RAY DIFFRACTIONr_long_range_B_other10.78165.4564137
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.211→2.268 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 102 -
Rwork0.406 1931 -
obs--99.61 %

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