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- PDB-6jiw: Crystal structure of S. aureus CntK with C72S mutation -

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Basic information

Entry
Database: PDB / ID: 6jiw
TitleCrystal structure of S. aureus CntK with C72S mutation
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / histidine racemase / cobalt and nickel transporter system
Function / homologyhistidine racemase / isomerase activity / cytoplasm / Histidine racemase / Diaminopimelate epimerase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsLuo, S. / Ju, Y. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
National Science Foundation (China)81803435 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of CntK, the cofactor-independent histidine racemase in staphylopine-mediated metal acquisition of Staphylococcus aureus.
Authors: Luo, S. / Ju, Y. / Zhou, J. / Gu, Q. / Xu, J. / Zhou, H.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2103
Polymers33,0521
Non-polymers1582
Water4,017223
1
A: Diaminopimelate epimerase
hetero molecules

A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4196
Polymers66,1032
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1840 Å2
ΔGint-44 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.090, 60.067, 76.920
Angle α, β, γ (deg.)90.00, 116.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Diaminopimelate epimerase / Histidine racemase CntK


Mass: 33051.566 Da / Num. of mol.: 1 / Mutation: C72S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cntK, dapF, D5R87_08325, D5R88_09755, M1K003_1013 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A389TBD7, UniProt: A0A0H3JU78*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 43.83 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.20 Lithium sulfate, 0.10 M Bis-Tris pH 6.5, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 39036 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.2
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 3894

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→43.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.412 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1902 4.9 %RANDOM
Rwork0.17403 ---
obs0.17526 37077 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.758 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20.08 Å2
2---0.51 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.58→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 9 223 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132140
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171863
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.6412907
X-RAY DIFFRACTIONr_angle_other_deg1.451.5594337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4635267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27424.466103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1815319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.902154
X-RAY DIFFRACTIONr_chiral_restr0.0560.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02430
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_it1.0361.751062
X-RAY DIFFRACTIONr_mcbond_other1.0251.7481061
X-RAY DIFFRACTIONr_mcangle_it1.7012.6211328
X-RAY DIFFRACTIONr_mcangle_other1.7032.6221329
X-RAY DIFFRACTIONr_scbond_it1.711.9851078
X-RAY DIFFRACTIONr_scbond_other1.7121.9851075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.582.8981573
X-RAY DIFFRACTIONr_long_range_B_refined4.24622.1582367
X-RAY DIFFRACTIONr_long_range_B_other4.24522.1562367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 118 -
Rwork0.207 2730 -
obs--99.44 %

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