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- PDB-6jis: Crystal structure of the histidine racemase CntK in cobalt and ni... -

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Basic information

Entry
Database: PDB / ID: 6jis
TitleCrystal structure of the histidine racemase CntK in cobalt and nickel transporter system of staphylococcus aureus
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / histidine racemase / cobalt and nickel transporter system
Function / homologyhistidine racemase / isomerase activity / : / Histidine racemase / Diaminopimelate epimerase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)33,88415
Polymers32,5991
Non-polymers1,28514
Water3,495194
1
A: Diaminopimelate epimerase
hetero molecules

A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,76730
Polymers65,1972
Non-polymers2,57028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6350 Å2
ΔGint-474 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.850, 60.374, 76.755
Angle α, β, γ (deg.)90.00, 116.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Diaminopimelate epimerase / Histidine racemase CntK


Mass: 32598.684 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.47 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.82→32.24 Å / Num. obs: 25303 / % possible obs: 96.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 1.82→1.86 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1523

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIW

6jiw


Resolution: 1.82→32.24 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.275 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24861 1245 4.9 %RANDOM
Rwork0.19545 ---
obs0.19797 24057 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.533 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å2-0 Å20.84 Å2
2---1.65 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.82→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 26 194 2249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171841
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6362867
X-RAY DIFFRACTIONr_angle_other_deg1.3531.564271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71423.83899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97515330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.704156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
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_it1.7262.2061060
X-RAY DIFFRACTIONr_mcbond_other1.7262.2051059
X-RAY DIFFRACTIONr_mcangle_it2.6973.3011325
X-RAY DIFFRACTIONr_mcangle_other2.6963.3011326
X-RAY DIFFRACTIONr_scbond_it2.2712.4841053
X-RAY DIFFRACTIONr_scbond_other2.272.4841054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.553.6111543
X-RAY DIFFRACTIONr_long_range_B_refined5.73627.8612360
X-RAY DIFFRACTIONr_long_range_B_other5.59327.5382321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.259 1821 -
obs--97.37 %

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