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- PDB-4h6i: Crystal Structure of Staphylococcal Complement Inhibitor SCIN-B -

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Basic information

Entry
Database: PDB / ID: 4h6i
TitleCrystal Structure of Staphylococcal Complement Inhibitor SCIN-B
ComponentsFibrinogen-binding protein
KeywordsIMMUNE SYSTEM / Complement System / Innate Immunity / Staphylococcus aureus Structural Biology
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Staphylococcal complement inhibitor SCIN / Staphylococcal complement inhibitor SCIN / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Heat shock protein 70kD, C-terminal domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Staphylococcal complement inhibitor / Staphylococcal complement inhibitor
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.091 Å
AuthorsGarcia, B.L. / Geisbrecht, B.V.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A Structurally Dynamic N-terminal Helix Is a Key Functional Determinant in Staphylococcal Complement Inhibitor (SCIN) Proteins.
Authors: Garcia, B.L. / Summers, B.J. / Ramyar, K.X. / Tzekou, A. / Lin, Z. / Ricklin, D. / Lambris, J.D. / Laity, J.H. / Geisbrecht, B.V.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrinogen-binding protein
B: Fibrinogen-binding protein
C: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)30,3713
Polymers30,3713
Non-polymers00
Water00
1
A: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1241
Polymers10,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1241
Polymers10,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1241
Polymers10,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.539, 115.251, 79.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Fibrinogen-binding protein


Mass: 10123.601 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1159, SAV_1159 / Plasmid: pt7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU9, UniProt: A0A0H3JZ23*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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16mg/ml protein sample stored in 10mM Tris (pH 7.4), 50mM NaCl; Crystallization conditions: 0.2M AmSO4, 30% PEG 8k. Crystals appear in 5-7d, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2010 / Details: mirror
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 18.57 / Number: 25131 / Rmerge(I) obs: 0.071 / Χ2: 1.02 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 5479 / % possible obs: 93.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.675097.810.0281.024.4
5.36.6710010.0661.0014.6
4.635.399.710.0741.0124.8
4.214.6310010.0731.0334.9
3.914.2199.710.0890.9774.9
3.683.9199.710.1211.0874.8
3.493.6898.110.1730.9784.5
3.343.4994.410.2231.034.3
3.213.3480.810.1941.0534.1
3.13.2161.410.2721.0244.3
ReflectionResolution: 3.093→50 Å / Num. all: 5479 / Num. obs: 5479 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.091-3.214.30.272161.4
3.21-3.344.10.194180.8
3.34-3.494.30.223194.4
3.49-3.684.50.173198.1
3.68-3.914.80.121199.7
3.91-4.214.90.089199.7
4.21-4.634.90.0731100
4.63-5.34.80.074199.7
5.3-6.674.60.0661100
6.67-504.40.028197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STARTING MODEL 3T49

3t49


Resolution: 3.091→32.741 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 542 9.92 %
Rwork0.2811 --
obs0.2825 5461 92.89 %
all-5149 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.7075 Å2
Refinement stepCycle: LAST / Resolution: 3.091→32.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 0 0 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111908
X-RAY DIFFRACTIONf_angle_d1.4492553
X-RAY DIFFRACTIONf_dihedral_angle_d16.581747
X-RAY DIFFRACTIONf_chiral_restr0.101282
X-RAY DIFFRACTIONf_plane_restr0.008324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.091-3.40170.33641050.3009957X-RAY DIFFRACTION74
3.4017-3.89330.41091370.30121292X-RAY DIFFRACTION98
3.8933-4.90250.26951460.25591299X-RAY DIFFRACTION99
4.9025-32.74270.25661540.2851371X-RAY DIFFRACTION99

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