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- PDB-4wcn: Crystal Structure of Tripeptide bound Cell Shape Determinant Csd4... -

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Basic information

Entry
Database: PDB / ID: 4wcn
TitleCrystal Structure of Tripeptide bound Cell Shape Determinant Csd4 protein from Helicobacter pylori
ComponentsConserved hypothetical secreted protein
KeywordsHYDROLASE / mixed alpha beta sandwich / carboxypeptidase / M14
Function / homology
Function and homology information


D,L-carboxypeptidase, peptidase domain / Metallo-carboxypeptidase, C-terminal domain / Carboxypeptidase M99, beta-barrel domain / Carboxypeptidase controlling helical cell shape catalytic / C-terminal domain of metallo-carboxypeptidase / beta-barrel domain of carboxypeptidase M99
Similarity search - Domain/homology
Chem-3KS / IODIDE ION / Conserved hypothetical secreted protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsChan, A.C. / Murphy, M.E.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Helical Shape of Helicobacter pylori Requires an Atypical Glutamine as a Zinc Ligand in the Carboxypeptidase Csd4.
Authors: Chan, A.C. / Blair, K.M. / Liu, Y. / Frirdich, E. / Gaynor, E.C. / Tanner, M.E. / Salama, N.R. / Murphy, M.E.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 18, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92546
Polymers50,1791
Non-polymers5,74745
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.230, 66.830, 145.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Conserved hypothetical secreted protein


Mass: 50178.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: HPG27_353 / Plasmid: pET15b(mod) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5ZAD9

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Non-polymers , 5 types, 372 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-3KS / N-acetyl-L-alanyl-N-[(1S,5R)-5-amino-1,5-dicarboxypentyl]-D-glutamine


Mass: 432.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28N4O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16-20% PEG 3350, 0-0.1 mM Tris pH 8 and 0.3-0.4 M NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→49.15 Å / Num. obs: 100396 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 22.12 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.059 / Χ2: 0.97 / Net I/σ(I): 15.35 / Num. measured all: 371684
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.80.6860.5111.8518335748772070.63896.3
1.8-1.840.8020.4032.7322217725772050.48899.3
1.84-1.90.8790.3483.7327260713671360.405100
1.9-1.960.9240.2674.8226072677867780.311100
1.96-2.020.9490.2116.0625833670467040.245100
2.02-2.090.9740.1558.0224828643164310.181100
2.09-2.170.9810.139.5523824615361530.151100
2.17-2.260.9880.10311.9523280600860080.12100
2.26-2.360.9910.08614.0322274573657360.1100
2.36-2.470.9930.07815.621297549754970.091100
2.47-2.610.9950.06318.6620189520052000.074100
2.61-2.770.9960.05521.3319222495149490.063100
2.77-2.960.9970.04624.717911463546340.054100
2.96-3.20.9980.03829.6416562429542910.04499.9
3.2-3.50.9980.03434.1715219396139610.04100
3.5-3.910.9980.0337.1313700359335900.03599.9
3.91-4.520.9990.02739.5612026316731610.03299.8
4.52-5.530.9990.02738.349964265426430.03299.6
5.53-7.830.9990.02537.427619205820230.0398.3
7.830.9980.02540.964052113010890.0396.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementResolution: 1.75→49.146 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 5027 5.01 %
Rwork0.1771 95368 -
obs0.1787 100395 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.29 Å2 / Biso mean: 30.3848 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.75→49.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 102 327 3775
Biso mean--44.48 37.19 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113497
X-RAY DIFFRACTIONf_angle_d1.3344729
X-RAY DIFFRACTIONf_chiral_restr0.059511
X-RAY DIFFRACTIONf_plane_restr0.007618
X-RAY DIFFRACTIONf_dihedral_angle_d13.4141327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.30121620.28513057321995
1.7699-1.79070.30071630.27583104326797
1.7907-1.81260.27551610.24723125328698
1.8126-1.83550.28051710.236931803351100
1.8355-1.85970.28411670.230432163383100
1.8597-1.88510.22641640.224731443308100
1.8851-1.91210.21711720.211632133385100
1.9121-1.94060.23721700.202531953365100
1.9406-1.97090.20051690.193532163385100
1.9709-2.00330.24151630.190331413304100
2.0033-2.03780.24111680.189832303398100
2.0378-2.07490.20071690.180231753344100
2.0749-2.11480.20981670.174232103377100
2.1148-2.15790.18571720.171631833355100
2.1579-2.20480.20461700.169331923362100
2.2048-2.25610.20531680.165331643332100
2.2561-2.31260.20161700.169132553425100
2.3126-2.37510.21451720.163631813353100
2.3751-2.4450.21191630.169131443307100
2.445-2.52390.22141680.17132323400100
2.5239-2.61410.1741650.171831653330100
2.6141-2.71870.23721660.179231833349100
2.7187-2.84250.22561690.179132053374100
2.8425-2.99230.18631670.17532093376100
2.9923-3.17970.15671690.173931843353100
3.1797-3.42520.19641670.172331933360100
3.4252-3.76980.19551620.165631903352100
3.7698-4.3150.19061680.147631773345100
4.315-5.43530.19041730.152831833356100
5.4353-49.16550.24361720.20163122329498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4086-0.0555-0.06091.2534-0.37082.15730.07660.07690.1063-0.0681-0.0688-00.0392-0.15360.01150.09380.00070.00790.0947-0.00370.13284.241333.5321-2.9158
20.5019-0.04590.89690.8843-0.12693.83750.0028-0.1860.01880.1637-0.02780.03390.2183-0.4040.02450.2109-0.0508-0.01290.2168-0.00430.17294.507325.657834.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:267 )A20 - 267
2X-RAY DIFFRACTION2( CHAIN A AND RESID 268:438 )A268 - 438

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