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- PDB-3t48: Crystal Structure of truncated form of Staphylococcal Complement ... -

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Basic information

Entry
Database: PDB / ID: 3t48
TitleCrystal Structure of truncated form of Staphylococcal Complement Inhibitor D (SCIN-D) at 1.5 Angstrom
ComponentsSCIN-D
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCIN-D
B: SCIN-D


Theoretical massNumber of molelcules
Total (without water)18,4502
Polymers18,4502
Non-polymers00
Water2,432135
1
A: SCIN-D


Theoretical massNumber of molelcules
Total (without water)9,2251
Polymers9,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SCIN-D


Theoretical massNumber of molelcules
Total (without water)9,2251
Polymers9,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.095, 94.277, 29.097
Angle α, β, γ (deg.)90.000, 97.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SCIN-D


Mass: 9225.219 Da / Num. of mol.: 2 / Fragment: SCIN-D, residues 37-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV_0229 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99WZ4, UniProt: A0A0H3JPM4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10mg/ml protein, 0.1M bis-Tris, 30% PEG 8000, 20 mM sodium thiocyanate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2010 / Details: mirror
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Av σ(I) over netI: 18.46 / Number: 128945 / Rmerge(I) obs: 0.067 / Χ2: 1.06 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 21840 / % possible obs: 97.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.235099.710.0521.0456.6
2.563.2399.610.0580.9956.7
2.242.5699.610.070.9766.6
2.042.2498.710.0850.9736.4
1.892.0498.410.1081.0856.2
1.781.899810.1531.0816.1
1.691.7897.810.2021.0545.9
1.621.699810.241.1465.4
1.551.6295.310.2671.094.9
1.51.5591.810.3081.2464.2
ReflectionResolution: 1.5→50 Å / Num. all: 22335 / Num. obs: 21840 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.057 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.554.20.30820541.246191.8
1.55-1.624.90.26721351.09195.3
1.62-1.695.40.2421641.146198
1.69-1.785.90.20221741.054197.8
1.78-1.896.10.15321951.081198
1.89-2.046.20.10821971.085198.4
2.04-2.246.40.08522050.973198.7
2.24-2.566.60.0722150.976199.6
2.56-3.236.70.05822400.995199.6
3.23-506.60.05222611.045199.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.14phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.5→27.606 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8986 / SU ML: 0.16 / σ(F): 0.13 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 2000 9.27 %random
Rwork0.1531 ---
all0.1568 21586 --
obs0.1568 21583 96.67 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.042 Å2 / ksol: 0.469 e/Å3
Displacement parametersBiso max: 109.62 Å2 / Biso mean: 25.2823 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.4918 Å20 Å20.4941 Å2
2--0.4938 Å2-0 Å2
3----1.9856 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 135 1277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111175
X-RAY DIFFRACTIONf_angle_d1.1441587
X-RAY DIFFRACTIONf_chiral_restr0.066185
X-RAY DIFFRACTIONf_plane_restr0.004203
X-RAY DIFFRACTIONf_dihedral_angle_d14.813447
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 (%)
1.5001-1.53760.22271320.16531288142086
1.5376-1.57920.23421340.16091321145595
1.5792-1.62560.19111400.14331372151293
1.6256-1.67810.20941390.14261351149097
1.6781-1.7380.18551440.14251409155395
1.738-1.80760.21420.14721400154297
1.8076-1.88990.20511430.14341393153698
1.8899-1.98950.18471420.13631402154497
1.9895-2.11410.18051450.13361409155498
2.1141-2.27720.17241460.1371440158699
2.2772-2.50630.17321460.13811431157799
2.5063-2.86860.21011490.152514571606100
2.8686-3.61290.19211480.162814501598100
3.6129-27.61050.19681500.173714601610100

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