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- PDB-4h6h: Crystal Structure of Staphylococcal Complement Inhibitor SCIN-B(4-85) -

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Basic information

Entry
Database: PDB / ID: 4h6h
TitleCrystal Structure of Staphylococcal Complement Inhibitor SCIN-B(4-85)
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 / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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: 2.5024 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
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)39,9224
Polymers39,9224
Non-polymers00
Water1,13563
1
A: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9801
Polymers9,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9801
Polymers9,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9801
Polymers9,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)9,9801
Polymers9,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.525, 84.525, 72.916
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Fibrinogen-binding protein


Mass: 9980.417 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18mg/ml protein sample stored in 10mM Tris (pH 7.4), 50mM NaCl; Crystallization condition: 0.1M Tris (pH 8.5), 8% PEG 8k. Crystals appeared in 1-3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.972 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2010 / Details: mirror
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 20110 / Num. obs: 17906 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.592.60.4132.12036145.8
2.59-2.690.395158
2.69-2.820.361178.9
2.82-2.960.363195.9
2.96-3.150.347199.5
3.15-3.390.262199.7

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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: PDB ENTRY 3T49

3t49


Resolution: 2.5024→42.262 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7806 / SU ML: 0.33 / σ(F): 1.97 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1752 9.79 %Random
Rwork0.2215 ---
obs0.2236 17887 88.95 %-
all-17887 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.16 Å2 / Biso mean: 56.2493 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.5024→42.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 63 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112643
X-RAY DIFFRACTIONf_angle_d1.0943542
X-RAY DIFFRACTIONf_chiral_restr0.075395
X-RAY DIFFRACTIONf_plane_restr0.006446
X-RAY DIFFRACTIONf_dihedral_angle_d17.6831028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5024-2.570.3161630.292663569845
2.57-2.64560.3182860.285380589157
2.6456-2.7310.3675990.29721006110571
2.731-2.82860.35611380.29621205134388
2.8286-2.94180.33781500.28571363151398
2.9418-3.07570.35421600.284513751535100
3.0757-3.23780.29631520.273513921544100
3.2378-3.44060.26971620.240513721534100
3.4406-3.70610.22581520.234413961548100
3.7061-4.07880.23541560.201913971553100
4.0788-4.66830.23711520.18913981550100
4.6683-5.87910.20441410.198814081549100
5.8791-42.26850.15391410.16581383152499

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