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- PDB-1w33: BbCRASP-1 from Borrelia Burgdorferi -

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Basic information

Entry
Database: PDB / ID: 1w33
TitleBbCRASP-1 from Borrelia Burgdorferi
ComponentsBBCRASP-1
KeywordsCOMPLEMENT REGULATOR / COMPLEMENT REGULATOR ACQUIRING SURFACE PROTEIN / LYME BORRELIOSIS / FACTOR H BINDING / TICK / MEMBRANE PROTEIN
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 / OTHER / Resolution: 2.7 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 13, 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 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,1414
Polymers42,9572
Non-polymers1842
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.803, 89.803, 145.580
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(0.91122, 0.40814, 0.05571), (0.40496, -0.91234, 0.06031), (0.07544, -0.03239, -0.99662)-36.094, 145.8708, 163.1118
2given(0.91321, 0.40292, 0.0608), (0.39949, -0.91469, 0.06129), (0.08031, -0.03168, -0.99627)-36.1312, 146.0028, 163.0098
3given(0.90887, 0.4134, 0.05521), (0.41, -0.90987, 0.06347), (0.07647, -0.03505, -0.99646)-36.5589, 145.2762, 163.3388
4given(0.91934, 0.39051, 0.04811), (0.38782, -0.91999, 0.05663), (0.06638, -0.0334, -0.99724)-33.3659, 147.1354, 163.2
5given(0.88333, 0.45971, 0.09159), (0.46115, -0.8873, 0.00598), (0.08402, 0.03696, -0.99578)-43.3688, 148.6451, 157.2775

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Components

#1: Protein BBCRASP-1


Mass: 21478.592 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 70-250
Source method: isolated from a genetically manipulated source
Details: FACTOR H BINDING DIMER
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): JM109 / References: UniProt: Q7AUV9, UniProt: O50957*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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: 3

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 63 %
Description: 4 SE SITES FOUND IN HYSS USING PK WAVELENGTH ANOMALOUS PATTERSON
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25% PEG 600 200 MM IMIDAZOLE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934, 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 10, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.9791
ReflectionResolution: 2.7→40.2 Å / Num. obs: 15999 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
HYSSphasing
SHARPphasing
TNT5.6.1refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.7→19.88 Å / Isotropic thermal model: TNT BCORREL.DAT / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO.DAT
Details: REFINED IN BUSTER-TNT 1.0.2 THE FIRST 44 RESIDUES (26-69) ARE DISORDERED IN THIS CRYSTAL
RfactorNum. reflection
all0.226 15962
obs-15962
Solvent computationSolvent model: BABINET SCALING / Bsol: 84 Å2 / ksol: 0.34 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 12 41 3050
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01130502
X-RAY DIFFRACTIONt_angle_deg0.95840743
X-RAY DIFFRACTIONt_dihedral_angle_d20.618990
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0051155
X-RAY DIFFRACTIONt_gen_planes0.0184025
X-RAY DIFFRACTIONt_it1.96305020
X-RAY DIFFRACTIONt_nbd0.076755
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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