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- PDB-3t49: Crystal structure of truncated form of Staphylococcal Complement ... -

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Basic information

Entry
Database: PDB / ID: 3t49
TitleCrystal structure of truncated form of Staphylococcal Complement Inhibitor B (SCIN-B) at 1.5 Angstrom
ComponentsFibrinogen-binding protein
KeywordsIMMUNE SYSTEM / Secreted / Virulence
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: 1.45 Å
AuthorsGarcia, B.L. / Geisbrecht, B.V. / Summers, B.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Diversity in the C3b Convertase Contact Residues and Tertiary Structures of the Staphylococcal Complement Inhibitor (SCIN) Protein Family.
Authors: Garcia, B.L. / Summers, B.J. / Lin, Z. / Ramyar, K.X. / Ricklin, D. / Kamath, D.V. / Fu, Z.Q. / Lambris, J.D. / Geisbrecht, B.V.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,61012
Polymers32,8584
Non-polymers7538
Water7,674426
1
A: Fibrinogen-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4994
Polymers8,2141
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibrinogen-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4073
Polymers8,2141
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fibrinogen-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3993
Polymers8,2141
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fibrinogen-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3072
Polymers8,2141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.668, 66.937, 60.407
Angle α, β, γ (deg.)90.000, 95.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fibrinogen-binding protein / SCIN-B


Mass: 8214.452 Da / Num. of mol.: 4 / Fragment: SCIN-B, residues 49-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV1159 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU9, UniProt: A0A0H3JZ23*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 12mg/ml protein, 0.1M sodium citrate, 1M ammonium sulfate, pH 3.5, 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: Mar 23, 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: 7 % / Av σ(I) over netI: 30.29 / Number: 436966 / Rmerge(I) obs: 0.058 / Χ2: 1.01 / D res high: 1.45 Å / D res low: 50 Å / Num. obs: 62067 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.125099.710.0271.0147.5
2.483.1210010.0540.987.6
2.172.4810010.0610.9437.6
1.972.1710010.0750.9877.5
1.831.9799.910.1171.0417.5
1.721.8399.810.1661.0417.5
1.631.7299.610.2170.9717.4
1.561.6399.310.2741.0396.9
1.51.5696.910.3481.0856
1.451.590.310.381.0764.8
ReflectionResolution: 1.45→50 Å / Num. all: 64317 / Num. obs: 62067 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Χ2: 1.013 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.54.80.3856691.076190.3
1.5-1.5660.34860711.085196.9
1.56-1.636.90.27462451.039199.3
1.63-1.727.40.21762410.971199.6
1.72-1.837.50.16662331.041199.8
1.83-1.977.50.11763001.041199.9
1.97-2.177.50.07562820.9871100
2.17-2.487.60.06163030.9431100
2.48-3.127.60.05463200.981100
3.12-507.50.02764031.014199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFF

2qff


Resolution: 1.45→23.927 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.9098 / SU ML: 0.13 / σ(F): 0 / Phase error: 15.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1661 1932 3.24 %random
Rwork0.1406 ---
all0.1415 61920 --
obs0.1415 59720 94.76 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.778 Å2 / ksol: 0.437 e/Å3
Displacement parametersBiso max: 76.27 Å2 / Biso mean: 19.5499 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.1526 Å2-0 Å2-0.4746 Å2
2--0.668 Å2-0 Å2
3----0.8205 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 44 426 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142402
X-RAY DIFFRACTIONf_angle_d1.5313239
X-RAY DIFFRACTIONf_chiral_restr0.08361
X-RAY DIFFRACTIONf_plane_restr0.007405
X-RAY DIFFRACTIONf_dihedral_angle_d12.305978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48430.23881080.17973189329773
1.4843-1.52440.23961230.15523703382686
1.5244-1.56930.18221310.14093915404691
1.5693-1.61990.1951390.12654083422294
1.6199-1.67780.19011360.11974156429295
1.6778-1.7450.15021400.11444175431596
1.745-1.82430.13211370.11034193433097
1.8243-1.92050.15951450.11824258440398
1.9205-2.04080.1561420.12014292443499
2.0408-2.19820.15281460.11934321446799
2.1982-2.41930.13591440.119543364480100
2.4193-2.76890.14211460.13574367451399
2.7689-3.48680.15271460.150743724518100
3.4868-23.93030.20091490.17944284577100

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