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- PDB-4bl4: Further structural insights into the binding of complement factor... -

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Basic information

Entry
Database: PDB / ID: 4bl4
TitleFurther structural insights into the binding of complement factor H by complement regulator acquiring surface protein 1, CspA (BbCRASP-1), of Borrelia burgdorferi.
ComponentsCOMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
KeywordsPROTEIN BINDING
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / 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 / MOLECULAR REPLACEMENT / Resolution: 4.06 Å
AuthorsCaesar, J.J.E. / Wallich, R. / Kraiczy, P. / Zipfel, P.F. / Lea, S.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Further Structural Insights Into the Binding of Complement Factor H by Complement Regulator-Acquiring Surface Protein 1 (CspA) of Borrelia Burgdorferi.
Authors: Caesar, J.J.E. / Wallich, R. / Kraiczy, P. / Zipfel, P.F. / Lea, S.M.
History
DepositionMay 1, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJun 5, 2013ID: 4ATR
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
B: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
C: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
D: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)


Theoretical massNumber of molelcules
Total (without water)85,9144
Polymers85,9144
Non-polymers00
Water00
1
A: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
B: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)


Theoretical massNumber of molelcules
Total (without water)42,9572
Polymers42,9572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-36.5 kcal/mol
Surface area19390 Å2
MethodPISA
2
C: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)
D: COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1)


Theoretical massNumber of molelcules
Total (without water)42,9572
Polymers42,9572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-37.3 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.370, 44.160, 186.540
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.753, 0.645, -0.131), (0.645, 0.685, -0.339), (-0.129, -0.34, -0.931)-140.986, 26.037, -138.032
2given(0.997, -0.005, 0.075), (0.007, -0.986, -0.164), (0.075, 0.164, -0.984)63.594, 16.496, -89.959
3given(-0.761, 0.621, -0.187), (-0.618, -0.608, 0.499), (0.196, 0.495, 0.846)-86.628, 13.215, 40.557

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Components

#1: Protein
COMPLEMENT REGULATOR-ACQUIRING SURFACE PROTEIN 1 (CRASP-1) / CSPA


Mass: 21478.592 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 70-250
Source method: isolated from a genetically manipulated source
Details: COMPLEMENT FACTOR H BINDING DIMER
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: ZS7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50957, UniProt: A0A0H3BZN5*PLUS

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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: 2.75 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growDetails: 18% (W/V) PEG 8000, 5MM ZINC ACETATE, 100MM SODIUM CACODYLATE, PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 2009 / Details: PT COATED MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 4.06→93.26 Å / Num. obs: 7629 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 78.37 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.7
Reflection shellResolution: 4.06→4.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W33

1w33


Resolution: 4.06→93.26 Å / Cor.coef. Fo:Fc: 0.8504 / Cor.coef. Fo:Fc free: 0.8606 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.966
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 747 9.8 %RANDOM
Rwork0.2621 ---
obs0.2629 7626 95.88 %-
Displacement parametersBiso mean: 85.28 Å2
Baniso -1Baniso -2Baniso -3
1-17.6264 Å20 Å2-3.2224 Å2
2---38.6132 Å20 Å2
3---20.9869 Å2
Refine analyzeLuzzati coordinate error obs: 1.254 Å
Refinement stepCycle: LAST / Resolution: 4.06→93.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 0 0 6004
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096084HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.18144HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2360SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes800HARMONIC5
X-RAY DIFFRACTIONt_it6084HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion20.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion812SEMIHARMONIC5
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_contact6865SEMIHARMONIC4
LS refinement shellResolution: 4.06→4.54 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2701 207 9.58 %
Rwork0.2675 1953 -
all0.2677 2160 -
obs--95.88 %

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