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- PDB-3t47: Crystal Structure of truncated form of Staphylococcal Complement ... -

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Basic information

Entry
Database: PDB / ID: 3t47
TitleCrystal Structure of truncated form of Staphylococcal Complement Inhibitor D (SCIN-D) at 1.3 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 subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.301 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3572
Polymers18,3572
Non-polymers00
Water2,774154
1
A: SCIN-D


Theoretical massNumber of molelcules
Total (without water)9,1781
Polymers9,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SCIN-D


Theoretical massNumber of molelcules
Total (without water)9,1781
Polymers9,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.152, 94.356, 29.196
Angle α, β, γ (deg.)90.000, 97.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SCIN-D


Mass: 9178.323 Da / Num. of mol.: 2 / Fragment: SCIN-D, residues 37-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV0229 / 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.: 154 / 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: 1.95 Å3/Da / Density % sol: 36.82 %
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: 18.7 % / Av σ(I) over netI: 35.61 / Number: 593190 / Rmerge(I) obs: 0.078 / Χ2: 1.05 / D res high: 1.3 Å / D res low: 50 Å / Num. obs: 31662 / % possible obs: 92.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.85096.310.0591.09920.8
2.222.889.110.0610.97420.5
1.942.2289.310.0741.04820.5
1.761.9491.210.1041.04720.5
1.641.7692.410.1471.07620.4
1.541.6493.210.1791.07420.5
1.461.5493.510.2461.03920
1.41.4694.310.3520.99918.2
1.351.492.910.411.13514.7
1.31.3589.310.461.0410.9
ReflectionResolution: 1.3→50 Å / Num. all: 32500 / Num. obs: 31662 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.7 % / Rmerge(I) obs: 0.078 / Χ2: 1.053 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.3510.90.4630451.04189.3
1.35-1.414.70.4131831.135192.9
1.4-1.4618.20.35232540.999194.3
1.46-1.54200.24632111.039193.5
1.54-1.6420.50.17931721.074193.2
1.64-1.7620.40.14731601.076192.4
1.76-1.9420.50.10431361.047191.2
1.94-2.2220.50.07430661.048189.3
2.22-2.820.50.06130670.974189.1
2.8-5020.80.05933681.099196.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.59 / Model details: Phaser MODE: MR_AUTO

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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: 3T48

3t48


Resolution: 1.301→28.967 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.9059 / SU ML: 0.12 / σ(F): 1.38 / Phase error: 16.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 2000 6.33 %random
Rwork0.1554 ---
all0.1573 31618 --
obs0.1573 31615 91.99 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.162 Å2 / ksol: 0.433 e/Å3
Displacement parametersBiso max: 62.76 Å2 / Biso mean: 19.6224 Å2 / Biso min: 4.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.8557 Å20 Å20.5197 Å2
2---0.2157 Å2-0 Å2
3----0.6399 Å2
Refinement stepCycle: LAST / Resolution: 1.301→28.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 154 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111187
X-RAY DIFFRACTIONf_angle_d1.0821605
X-RAY DIFFRACTIONf_chiral_restr0.069187
X-RAY DIFFRACTIONf_plane_restr0.005205
X-RAY DIFFRACTIONf_dihedral_angle_d13.88457
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 (%)
1.301-1.33320.27361330.22621974210786
1.3332-1.36920.21851430.18472100224392
1.3692-1.40950.19411450.162160230595
1.4095-1.4550.17741470.14592170231793
1.455-1.5070.15151430.12512131227495
1.507-1.56730.15621460.12662148229493
1.5673-1.63870.17631440.12322145228992
1.6387-1.7250.19961440.13852127227193
1.725-1.83310.18551420.14952104224691
1.8331-1.97460.18481390.14672060219990
1.9746-2.17330.18331400.14332079221990
2.1733-2.48760.16581380.14122035217390
2.4876-3.13350.18881420.16062090223290
3.1335-28.97370.19651540.17672292244698

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