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- PDB-2gom: Crystal structure of Efb-C from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 2gom
TitleCrystal structure of Efb-C from Staphylococcus aureus
ComponentsFibrinogen-binding protein
KeywordsCELL ADHESION/TOXIN / three-helix closed bundle with left-hand twist / CELL ADHESION-TOXIN COMPLEX
Function / homology
Function and homology information


complement binding / : / extracellular space
Similarity search - Function
Extracellular fibrinogen binding protein, C-terminal / Efb, C-terminal domain superfamily / Extracellular fibrinogen binding protein C terminal / Sbi, C3 binding domain IV / Sbi, C3 binding domain IV / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fibrinogen-binding protein / Fibrinogen-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsHammel, M. / Geisbrecht, B.V.
CitationJournal: Nat.Immunol. / Year: 2007
Title: A structural basis for complement inhibition by Staphylococcus aureus.
Authors: Hammel, M. / Sfyroera, G. / Ricklin, D. / Magotti, P. / Lambris, J.D. / Geisbrecht, B.V.
History
DepositionApr 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibrinogen-binding protein
B: Fibrinogen-binding protein


Theoretical massNumber of molelcules
Total (without water)14,4092
Polymers14,4092
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.598, 59.598, 45.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Fibrinogen-binding protein


Mass: 7204.528 Da / Num. of mol.: 2 / Fragment: C- TERMINAL DOMAIN (Residues 105-165)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: efb / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P68798, UniProt: P68799*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3M Sodium Acetate pH 7.4 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97949, 0.97934, 0.97178
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2005 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979341
30.971781
ReflectionResolution: 1.2→50 Å / Num. obs: 44291 / % possible obs: 86.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5029 / Rsym value: 0.492 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→59.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.182 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21804 2231 5 %RANDOM
Rwork0.21058 ---
all0.211 44291 --
obs0.21095 42060 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.993 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 2 Å
Refinement stepCycle: LAST / Resolution: 1.25→59.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 155 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022995
X-RAY DIFFRACTIONr_angle_refined_deg0.9281.9591328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9015119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74424.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.56815217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.205157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02707
X-RAY DIFFRACTIONr_nbd_refined0.2060.2504
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3650.217
X-RAY DIFFRACTIONr_mcbond_it0.7481.5624
X-RAY DIFFRACTIONr_mcangle_it1.2022972
X-RAY DIFFRACTIONr_scbond_it2.0493403
X-RAY DIFFRACTIONr_scangle_it3.1344.5356
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 153 -
Rwork0.351 3104 -
obs-3257 100 %
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)
10.65740.2412-0.12681.4629-0.0250.17770.00150.03270.00630.0414-0.03220.01120.0196-0.00250.0307-0.0204-0.00270.0078-0.01140.0093-0.003614.803549.415526.9141
20.88130.4644-0.80770.4435-0.32792.2380.03950.08290.0846-0.05840.10910.00690.2776-0.1515-0.14850.0309-0.0148-0.024-0.0232-0.0021-0.0276-2.796530.231723.4994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA105 - 1651 - 61
2X-RAY DIFFRACTION2BB106 - 1652 - 61

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