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- PDB-2qff: Crystal structure of Staphylococcal Complement Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2qff
TitleCrystal structure of Staphylococcal Complement Inhibitor
ComponentsHypothetical protein
KeywordsHydrolase Inhibitor / Complement / Inhibitor / Inflammation / Bacterial / Molecular 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 / MAD / Resolution: 1.8 Å
AuthorsMilder, F.J. / Rooijakkers, S.H.M. / Bardoel, B.W. / Ruyken, M. / Van Strijp, J.A.G. / Gros, P.
CitationJournal: J.Immunol. / Year: 2007
Title: Staphylococcal complement inhibitor: structure and active sites.
Authors: Rooijakkers, S.H. / Milder, F.J. / Bardoel, B.W. / Ruyken, M. / van Strijp, J.A. / Gros, P.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)9,5331
Polymers9,5331
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.017, 42.775, 63.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein


Mass: 9533.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MRSA252 / Gene: YP_041408/SAR2035 / Plasmid: prSETB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: Q2FFF8, UniProt: Q6GFB4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.65 Å3/Da / Density % sol: 25.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: protein solution: 24 mg/ml SCIN in 50 mM NaCl, 20 mM TRIS, pH 8.0 well solution: 35% (w/v) PEG 1000, 0.1 M PCB-buffer (0.04 M sodium propionate, 0.02 M sodium cacodylate, 0.04 M bis-tris- ...Details: protein solution: 24 mg/ml SCIN in 50 mM NaCl, 20 mM TRIS, pH 8.0 well solution: 35% (w/v) PEG 1000, 0.1 M PCB-buffer (0.04 M sodium propionate, 0.02 M sodium cacodylate, 0.04 M bis-tris-propane) pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793, 0.9795, 0.9763
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.97631
ReflectionResolution: 1.8→40 Å / Num. obs: 6281 / Redundancy: 7.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→35.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.349 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 294 4.7 %RANDOM
Rwork0.20113 ---
obs0.20221 5952 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms607 0 0 42 649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022633
X-RAY DIFFRACTIONr_angle_refined_deg0.7921.999847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.311576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60326.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99615138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.364151
X-RAY DIFFRACTIONr_chiral_restr0.0640.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02460
X-RAY DIFFRACTIONr_nbd_refined0.1750.2302
X-RAY DIFFRACTIONr_nbtor_refined0.2880.2454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.25
X-RAY DIFFRACTIONr_mcbond_it0.3081.5399
X-RAY DIFFRACTIONr_mcangle_it0.4782603
X-RAY DIFFRACTIONr_scbond_it0.9423279
X-RAY DIFFRACTIONr_scangle_it1.5284.5243
LS refinement shellHighest resolution: 1.8 Å / Num. reflection Rwork: 430 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.1395-13.5559-2.51731.362-0.79936.70090.58680.64591.0103-1.3641-0.2369-0.8357-0.86280.2294-0.34980.195-0.16160.07620.05160.0339-0.084417.058726.59762.6182
26.2518-4.67972.815516.6885-18.108122.81780.09120.4367-0.4053-0.2672-0.1255-0.61080.19990.29340.0343-0.1073-0.00350.0251-0.0189-0.1168-0.005523.2466.96687.818
36.0561-3.22685.242212.1928-7.624111.4972-0.1060.0106-0.2945-0.15960.078-0.01970.2738-0.03780.0281-0.1075-0.00880.0174-0.0433-0.0308-0.001815.77555.887713.2328
417.4137-4.53475.809925.7137-9.610111.628-0.15490.8861-0.5024-1.83910.43670.77210.669-0.2151-0.28180.171-0.0863-0.14480.0642-0.0349-0.03378.947717.55332.4555
512.1841-5.64123.681513.7706-4.02848.261-0.224-0.14910.1181-0.4960.51030.4845-0.2918-0.4345-0.2863-0.0372-0.0393-0.0515-0.04440.0104-0.024210.941722.754610.0372
611.2298-8.60827.211114.3875-5.07235.8601-0.2329-0.17340.13650.35980.1306-0.3244-0.1739-0.0360.1022-0.0675-0.02530.0075-0.0467-0.0139-0.028923.907512.748715.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 24
2X-RAY DIFFRACTION2A25 - 36
3X-RAY DIFFRACTION3A37 - 48
4X-RAY DIFFRACTION4A49 - 58
5X-RAY DIFFRACTION5A59 - 70
6X-RAY DIFFRACTION6A71 - 82

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