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- PDB-4cp6: The Crystal structure of Pneumococcal vaccine antigen PcpA -

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Basic information

Entry
Database: PDB / ID: 4cp6
TitleThe Crystal structure of Pneumococcal vaccine antigen PcpA
ComponentsCHOLINE BINDING PROTEIN PCPA
KeywordsCHOLINE-BINDING PROTEIN / CHOLINE BINDING PROTEIN / LEUCINE-RICH REPEAT
Function / homology
Function and homology information


: / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe ...: / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Choline binding protein PcpA / Choline binding protein PcpA
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.34 Å
AuthorsVallee, F. / Steier, V. / Oloo, E. / Chawla, D. / Vonrhein, C. / Steinmetz, A. / Mathieu, M. / Rak, A. / Mikol, V. / Oomen, R.
CitationJournal: To be Published
Title: The Crystal Structure of Pneumoccocal Vaccine Antigen Pcpa
Authors: Vallee, F. / Steier, V. / Oloo, E. / Chawla, D. / Vonrhein, C. / Steinmetz, A. / Mathieu, M. / Rak, A. / Mikol, V. / Oomen, R.
History
DepositionJan 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHOLINE BINDING PROTEIN PCPA


Theoretical massNumber of molelcules
Total (without water)49,5001
Polymers49,5001
Non-polymers00
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.060, 61.850, 121.200
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 CHOLINE BINDING PROTEIN PCPA


Mass: 49500.129 Da / Num. of mol.: 1 / Fragment: CHOLINE-BINDING DOMAIN, RESIDUES 27-470 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (bacteria) / References: UniProt: Q97NB5, UniProt: A0A0H2USF9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.31 Å3/Da / Density % sol: 46.79 % / Description: USE PLATINIUM K2PTCL4 AS HEAVY ATOM DERIVATIVE
Crystal growpH: 4.6 / Details: pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.34→19.2 Å / Num. obs: 103647 / % possible obs: 98.5 % / Observed criterion σ(I): 1.7 / Redundancy: 6.2 % / Biso Wilson estimate: 15.04 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.1
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / % possible all: 85.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.34→19.2 Å / Cor.coef. Fo:Fc: 0.9565 / Cor.coef. Fo:Fc free: 0.9499 / SU R Cruickshank DPI: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.049
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.186 5108 5.01 %RANDOM
Rwork0.17 ---
obs-102030 98.48 %-
Displacement parametersBiso mean: 19.57 Å2
Baniso -1Baniso -2Baniso -3
1--5.3918 Å20 Å20 Å2
2--3.2957 Å20 Å2
3---2.096 Å2
Refine analyzeLuzzati coordinate error obs: 0.151 Å
Refinement stepCycle: LAST / Resolution: 1.34→19.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 0 682 3867
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013274HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144426HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1183SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes466HARMONIC5
X-RAY DIFFRACTIONt_it3274HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.66
X-RAY DIFFRACTIONt_other_torsion13.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4520SEMIHARMONIC4
LS refinement shellResolution: 1.34→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2328 354 5.37 %
Rwork0.232 6233 -
all0.232 6587 -
obs--98.48 %

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