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- PDB-1w3z: SeMet derivative of BbCRASP-1 from Borrelia Burgdorferi -

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Basic information

Entry
Database: PDB / ID: 1w3z
TitleSeMet derivative of BbCRASP-1 from Borrelia Burgdorferi
ComponentsBBCRASP-1
KeywordsCOMPLEMENT REGULATOR / COMPLEMENT REGULATOR ACQUIRING SURFACE PROTEIN / LYME BORRELIOSIS / FACTOR H BINDING / TICK / SELENOMETHIONINE
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / Complement regulator-acquiring surface protein 1 (CRASP-1) / Complement regulator-acquiring surface protein 1 (CRASP-1)
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsCordes, F.S. / Roversi, P. / Goodstadt, L. / Ponting, C. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Zipfel, P. ...Cordes, F.S. / Roversi, P. / Goodstadt, L. / Ponting, C. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Zipfel, P. / Wallich, R. / Lea, S.M.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A Novel Fold for the Factor H-Binding Protein Bbcrasp-1 of Borrelia Burgdorferi
Authors: Cordes, F.S. / Roversi, P. / Kraiczy, P. / Simon, M.M. / Brade, V. / Jahraus, O. / Wallis, R. / Skerka, C. / Zipfel, P. / Wallich, R. / Lea, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallisation and Preliminary Crystallographic Analysis of Bbcrasp-1, a Complement Regulator-Acquiring Surface Protein of Borrelia Burgdorferi
Authors: Cordes, F.S. / Kraiczy, P. / Roversi, P. / Kraiczy, P. / Skerka, C. / Kirschfink, M. / Simon, M.M. / Brade, V. / Lowe, E. / Zipfel, P. / Wallich, R. / Lea, S.M.
History
DepositionJul 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BBCRASP-1
B: BBCRASP-1


Theoretical massNumber of molelcules
Total (without water)43,1452
Polymers43,1452
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.558, 91.558, 146.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.90484, 0.41755, 0.08315), (0.42085, -0.90675, -0.02627), (0.06442, 0.05876, -0.99619)-40.57939, 154.53285, 156.76448
2given(0.91112, 0.40173, 0.09206), (0.406, -0.91328, -0.03289), (0.07087, 0.06734, -0.99521)-40.20348, 155.74326, 155.96274
3given(0.90441, 0.41835, 0.08375), (0.42224, -0.90581, -0.03497), (0.06124, 0.06699, -0.99587)-40.67791, 155.12709, 156.2002
4given(0.91442, 0.40017, 0.06075), (0.40222, -0.91518, -0.02576), (0.04529, 0.04799, -0.99782)-38.59413, 155.47997, 157.60861
5given(0.89358, 0.41709, 0.166), (0.41611, -0.90833, 0.04235), (0.16844, 0.03123, -0.98522)-47.04373, 149.63425, 157.82404

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Components

#1: Protein BBCRASP-1


Mass: 21572.383 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 70-250
Source method: isolated from a genetically manipulated source
Details: FACTOR H BINDING DIMER SELENOMETHIONINE DERIVATIVE
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: ZS7 / Description: TICK ISOLATE GERMANY / Variant: TICK ISOLATE / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7AUV9, UniProt: O50957*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 1-25 AND 251 WERE LACKING FROM THE CONSTRUCT

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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: 3 Å3/Da / Density % sol: 59 %
Description: TWO-WAVELENGTH MAD WITH PEAK AND LOW-ENERGY REMOTE LAMBDA 0.984 A
Crystal growpH: 6 / Details: 25% PEG600 200 MM IMIDAZOLE PH 6.0 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→73.3 Å / Num. obs: 10849 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
HYSSphasing
SHARPphasing
TNT5.6refinement
RefinementMethod to determine structure: MAD / Resolution: 3.2→76.7 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO / Details: BUSTER-TNT VERSION 1.0.3
RfactorNum. reflection
Rwork0.239 -
all0.24 10258
obs0.239 10824
Solvent computationSolvent model: BABINET SCALING / Bsol: 87 Å2 / ksol: 0.31 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 0 8 3005
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130402
X-RAY DIFFRACTIONt_angle_deg1.01340643
X-RAY DIFFRACTIONt_dihedral_angle_d20.8218990
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0091135
X-RAY DIFFRACTIONt_gen_planes0.0154005
X-RAY DIFFRACTIONt_it2.07304020
X-RAY DIFFRACTIONt_nbd0.0631085
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact

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