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- PDB-4y4v: Structure of Helicobacter pylori Csd6 in the D-Ala-bound state -

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Basic information

Entry
Database: PDB / ID: 4y4v
TitleStructure of Helicobacter pylori Csd6 in the D-Ala-bound state
Components(Conserved hypothetical secreted protein) x 2
KeywordsHYDROLASE / Csd6 / cell shape / L / D-carboxypeptidase / Helicobacter pylori / HP0518 / flagellin / peptidoglycan
Function / homologypeptidoglycan L,D-transpeptidase activity / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / NTF2-like domain superfamily / peptidoglycan biosynthetic process / transferase activity / D-ALANINE / Conserved hypothetical secreted protein
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsKim, H.S. / Im, H.N. / Yoon, H.J. / Suh, S.W.
Funding support Korea, Republic Of, United States, 6items
OrganizationGrant numberCountry
National Research Foundation2013R1A2A1A05067303 Korea, Republic Of
Korea Ministry of Health, Welfare & Family AffairsA092006 Korea, Republic Of
National Research Foundation2011-0028885 Korea, Republic Of
National Research Foundation2012-039930 Korea, Republic Of
National Research Foundation2014R1A1A3A04050250 Korea, Republic Of
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090348 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of l,d-Carboxypeptidase
Authors: Kim, H.S. / Im, H.N. / An, D.R. / Yoon, J.Y. / Jang, J.Y. / Mobashery, S. / Hesek, D. / Lee, M. / Yoo, J. / Cui, M. / Choi, S. / Kim, C. / Lee, N.K. / Kim, S.J. / Kim, J.Y. / Bang, G. / Han, ...Authors: Kim, H.S. / Im, H.N. / An, D.R. / Yoon, J.Y. / Jang, J.Y. / Mobashery, S. / Hesek, D. / Lee, M. / Yoo, J. / Cui, M. / Choi, S. / Kim, C. / Lee, N.K. / Kim, S.J. / Kim, J.Y. / Bang, G. / Han, B.W. / Lee, B.I. / Yoon, H.J. / Suh, S.W.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical secreted protein
B: Conserved hypothetical secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9349
Polymers79,2982
Non-polymers6367
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-16 kcal/mol
Surface area30180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.404, 90.607, 127.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conserved hypothetical secreted protein / Csd6


Mass: 39657.035 Da / Num. of mol.: 1 / Fragment: UNP residues 13-330
Source method: isolated from a genetically manipulated source
Details: The Cys176 residue has been oxidized into the sulfenic acid (CSO) in the Chain A only.
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: C694_02665, HP_0518 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25255
#2: Protein Conserved hypothetical secreted protein / Csd6


Mass: 39641.035 Da / Num. of mol.: 1 / Fragment: UNP residues 13-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: C694_02665, HP_0518 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25255
#3: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 % / Description: rod shape
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5%(v/v) Tacsimate, 22%(w/v) PEG 3350, 100 mM sodium-HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 47575 / % possible obs: 99.9 % / Redundancy: 4.78 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 29.3
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.612 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24197 2400 5.1 %RANDOM
Rwork0.19131 ---
obs0.19381 45096 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.857 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å2-0 Å2
2---1.66 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.04→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5249 0 42 315 5606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025407
X-RAY DIFFRACTIONr_bond_other_d0.0020.025155
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9627252
X-RAY DIFFRACTIONr_angle_other_deg0.9033.00211878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24624.783276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.016151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6151524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021301
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_it2.1893.5232533
X-RAY DIFFRACTIONr_mcbond_other2.1883.5232533
X-RAY DIFFRACTIONr_mcangle_it3.3555.2663154
X-RAY DIFFRACTIONr_mcangle_other3.3545.2663155
X-RAY DIFFRACTIONr_scbond_it2.7083.8872874
X-RAY DIFFRACTIONr_scbond_other2.7073.8872874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4035.674099
X-RAY DIFFRACTIONr_long_range_B_refined6.85128.3746272
X-RAY DIFFRACTIONr_long_range_B_other6.80928.336246
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 171 -
Rwork0.247 3224 -
obs--98.86 %

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