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- PDB-1klx: Helicobacter pylori cysteine rich protein B (hcpB) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1klx
TitleHelicobacter pylori cysteine rich protein B (hcpB)
ComponentsCysteine Rich Protein B
KeywordsHYDROLASE / Structural Genomics / helix-turn-helix / right handed super helix / modular structure'
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase HcpB-like / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsLuethy, L. / Gruetter, M.G. / Mittl, P.R.E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The crystal structure of Helicobacter pylori cysteine-rich protein B reveals a novel fold for a penicillin-binding protein.
Authors: Luthy, L. / Grutter, M.G. / Mittl, P.R.
History
DepositionDec 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine Rich Protein B


Theoretical massNumber of molelcules
Total (without water)15,3681
Polymers15,3681
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.360, 51.360, 205.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cysteine Rich Protein B


Mass: 15367.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0336 / Plasmid: pTFT74 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25103
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3
Details: PEG 8000, sodium citrate, pH 3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.4 mg/mlprotein1drop
240 mMsodium acetate1drop
31 mMEDTA1droppH5.5
425 %PEG80001reservoir
50.1 Msodium citrate1reservoirpH3.0

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.9791, 0.9794, 0.8856
SYNCHROTRONESRF ID14-320.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.88561
40.9331
ReflectionResolution: 1.95→30 Å / Num. all: 12606 / Num. obs: 12049 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2.001 Å / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 49.8 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.951 / SU B: 3.738 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.23844 1239 10.28 %RANDOM
Rwork0.18672 ---
obs0.19232 12049 95.58 %-
all-12606 --
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.926 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 0 189 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.0221047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4381.9881396
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7413132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89115206
X-RAY DIFFRACTIONr_chiral_restr0.2250.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02770
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.3533
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.345
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.519
X-RAY DIFFRACTIONr_mcbond_it2.0431.5650
X-RAY DIFFRACTIONr_mcangle_it3.34421020
X-RAY DIFFRACTIONr_scbond_it5.8293397
X-RAY DIFFRACTIONr_scangle_it9.6094.5376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 62
Rwork0.199 730
Refinement
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.2384 / Rfactor Rwork: 0.1867
Solvent computation
*PLUS
Displacement parameters
*PLUS

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