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- PDB-4rnz: Structure of Helicobacter pylori Csd3 from the hexagonal crystal -

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Basic information

Entry
Database: PDB / ID: 4rnz
TitleStructure of Helicobacter pylori Csd3 from the hexagonal crystal
ComponentsConserved hypothetical secreted protein
KeywordsHYDROLASE / M23B metallopeptidase / metallopeptidase / peptidoglycan
Function / homology
Function and homology information


metalloendopeptidase activity / membrane / metal ion binding
Similarity search - Function
Csd3, N-terminal / Csd3 N-terminal / Nuclear Transport Factor 2; Chain: A, - #350 / Csd3-like, second N-terminal domain / Csd3 second domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 ...Csd3, N-terminal / Csd3 N-terminal / Nuclear Transport Factor 2; Chain: A, - #350 / Csd3-like, second N-terminal domain / Csd3 second domain / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Conserved hypothetical secreted protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsAn, D.R. / Kim, H.S. / Kim, J. / Im, H.N. / Yoon, H.J. / Yoon, J.Y. / Jang, J.Y. / Hesek, D. / Lee, M. / Mobashery, S. ...An, D.R. / Kim, H.S. / Kim, J. / Im, H.N. / Yoon, H.J. / Yoon, J.Y. / Jang, J.Y. / Hesek, D. / Lee, M. / Mobashery, S. / Kim, S.-J. / Lee, B.I. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase.
Authors: An, D.R. / Kim, H.S. / Kim, J. / Im, H.N. / Yoon, H.J. / Yoon, J.Y. / Jang, J.Y. / Hesek, D. / Lee, M. / Mobashery, S. / Kim, S.J. / Lee, B.I. / Suh, S.W.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,37810
Polymers42,6341
Non-polymers7449
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.469, 91.469, 186.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Conserved hypothetical secreted protein / Csd3 cell-shape determinant


Mass: 42634.008 Da / Num. of mol.: 1 / Fragment: UNP residues 42-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: C694_02600, HP_0506 / Production host: Escherichia coli (E. coli) / References: UniProt: O25247

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 200 mM di-ammonium hydrogen phosphate, pH 7.9, 20% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Nov 16, 2012 / Details: hybrid-type of image plates and a CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 31293 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 41.917
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 3.519 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.905 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23858 1672 5.1 %RANDOM
Rwork0.20746 ---
obs0.20903 31293 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å2-0 Å2
2--0.96 Å2-0 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 36 148 3103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193017
X-RAY DIFFRACTIONr_bond_other_d0.0010.022917
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9624058
X-RAY DIFFRACTIONr_angle_other_deg0.73636705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16223.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98415542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02737
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_it2.3983.7751433
X-RAY DIFFRACTIONr_mcbond_other2.3923.7731432
X-RAY DIFFRACTIONr_mcangle_it3.5225.6391786
X-RAY DIFFRACTIONr_mcangle_other3.5215.6411787
X-RAY DIFFRACTIONr_scbond_it2.9384.241584
X-RAY DIFFRACTIONr_scbond_other2.9384.241584
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.696.1782273
X-RAY DIFFRACTIONr_long_range_B_refined6.68330.7473440
X-RAY DIFFRACTIONr_long_range_B_other6.68330.7463440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 113 -
Rwork0.274 2262 -
obs--99.54 %

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