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- PDB-1ouv: Helicobacter cysteine rich protein C (HcpC) -

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Basic information

Entry
Database: PDB / ID: 1ouv
TitleHelicobacter cysteine rich protein C (HcpC)
Componentsconserved hypothetical secreted protein
KeywordsHYDROLASE / TPR REPEAT / HCP REPEAT / CYSTEINE RICH PROTEIN / LOOP-HELIX-TURN-HELIX / REPEAT PROTEIN
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase HcpB-like / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Beta-lactamase HcpB-like / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Putative beta-lactamase HcpC
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMittl, P.R. / Luethy, L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of Helicobacter Cysteine-rich Protein C at 2.0A Resolution: Similar Peptide-binding Sites in TPR and SEL1-like Repeat Proteins
Authors: Luethy, L. / Grutter, M.G. / Mittl, P.R.
History
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical secreted protein


Theoretical massNumber of molelcules
Total (without water)29,9721
Polymers29,9721
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.982, 46.198, 76.390
Angle α, β, γ (deg.)90.00, 120.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein conserved hypothetical secreted protein / Helicobacter cysteine rich protein C / HcpC


Mass: 29971.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP1098 / Plasmid: pTFT74 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25728
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 30% PEG 4000, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
20.1 Msodium citrate1reservoir
30.2 Mammonium acetate1reservoirpH6.4
430 %(w/v)PEG40001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
293.81
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODEENRAF-NONIUS FR59111.5418
SYNCHROTRONSLS X06SA20.9184
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
MARRESEARCH2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.91841
ReflectionResolution: 2→30 Å / Num. obs: 21245 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.43 % / Rmerge(I) obs: 0.068 / Rsym value: 0.074 / Net I/σ(I): 14.37
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.14 / Rsym value: 0.347 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Rmerge(I) obs: 0.347

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KLX

1klx


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 --RANDOM
Rwork0.2016 ---
all0.225 21056 --
obs-20476 97.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.478 Å20 Å2-3.133 Å2
2---3.047 Å20 Å2
3---0.569 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 175 2201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005254
X-RAY DIFFRACTIONc_angle_deg0.97103
X-RAY DIFFRACTIONc_mcbond_it2.531.5
X-RAY DIFFRACTIONc_scbond_it4.1272
X-RAY DIFFRACTIONc_mcangle_it3.322
X-RAY DIFFRACTIONc_scangle_it6.0352.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å

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