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- PDB-6l4l: Crystal structure of S. aureus CntK in inactive state -

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Basic information

Entry
Database: PDB / ID: 6l4l
TitleCrystal structure of S. aureus CntK in inactive state
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / disulfide / racemase
Function / homologyhistidine racemase / isomerase activity / Histidine racemase / Diaminopimelate epimerase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJu, Y. / Luo, S. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81773636 China
National Science Foundation (China)81803435 China
CitationJournal: To Be Published
Title: Crystal structure of S. aureus CntK in inactive state
Authors: Ju, Y. / Luo, S. / Zhou, H.
History
DepositionOct 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2333
Polymers32,1091
Non-polymers1242
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.748, 60.293, 76.991
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Diaminopimelate epimerase / Histidine racemase CntK


Mass: 32109.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dapF, cntK, DB727_02910, 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05 M HEPES pH7.5, 26% PEG 400 / PH range: 7.3-7.7

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19154 / % possible obs: 98 % / Redundancy: 3.3 % / Rrim(I) all: 0.072 / Net I/σ(I): 20.646
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 1897

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIS

6jis


Resolution: 2→30.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.62 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 878 4.6 %RANDOM
Rwork0.2007 ---
obs0.2022 18276 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.54 Å2 / Biso mean: 36.799 Å2 / Biso min: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å21.02 Å2
2---0.86 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 8 60 2068
Biso mean--33.64 48.68 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132060
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171806
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.6332794
X-RAY DIFFRACTIONr_angle_other_deg1.3581.564195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.62124.68194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.718153
X-RAY DIFFRACTIONr_chiral_restr0.0550.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
LS refinement shellResolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 45 -
Rwork0.257 1289 -
all-1334 -
obs--93.22 %

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