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- PDB-3doa: The crystal structure of the fibrinogen binding protein from Stap... -

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Basic information

Entry
Database: PDB / ID: 3doa
TitleThe crystal structure of the fibrinogen binding protein from Staphylococcus aureus
ComponentsFibrinogen binding protein
KeywordsPROTEIN BINDING / The fibrinogen binding protein / structural genomics / MCSG. / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


RQC complex / ribosomal large subunit binding / rescue of stalled ribosome / tRNA binding / rRNA binding
Similarity search - Function
fibrinogen binding protein from staphylococcus aureus domain like / ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / Ribonuclease HI; Chain A / Rqc2 homolog RqcH, bacterial / : / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 ...fibrinogen binding protein from staphylococcus aureus domain like / ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / Ribonuclease HI; Chain A / Rqc2 homolog RqcH, bacterial / : / NFACT, RNA-binding domain / NFACT protein RNA binding domain / NFACT N-terminal and middle domains / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rqc2 homolog RqcH / Rqc2 homolog RqcH
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsZhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2008
Title: The crystal structure of the fibrinogen binding protein from Staphylococcus aureus
Authors: Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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


Theoretical massNumber of molelcules
Total (without water)33,6111
Polymers33,6111
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.269, 102.269, 166.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

Detailsprotein existed as monomer

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Components

#1: Protein Fibrinogen binding protein


Mass: 33611.199 Da / Num. of mol.: 1 / Fragment: residues 1-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: ubsp. aureus Mu50 / Gene: SAV1208 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99UR0, UniProt: A0A0H3JV08*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG4000, 45% tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors
RadiationMonochromator: Si channel 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.81→87.04 Å / Num. all: 10661 / Num. obs: 10541 / % possible obs: 98.87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.9 % / Rsym value: 0.145 / Net I/σ(I): 21.84
Reflection shellResolution: 2.81→2.88 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.639 / % possible all: 88.09

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→87.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.891 / SU B: 29.329 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.357
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27048 530 4.8 %RANDOM
Rwork0.1872 ---
obs0.1908 10541 98.87 %-
all-10661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.353 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--1.32 Å20 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.81→87.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 0 30 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222233
X-RAY DIFFRACTIONr_bond_other_d0.0040.021542
X-RAY DIFFRACTIONr_angle_refined_deg2.2821.963014
X-RAY DIFFRACTIONr_angle_other_deg1.15133770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4825265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02424.69113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.89715411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.241513
X-RAY DIFFRACTIONr_chiral_restr0.1270.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined0.2640.2580
X-RAY DIFFRACTIONr_nbd_other0.2230.21709
X-RAY DIFFRACTIONr_nbtor_refined0.2020.21084
X-RAY DIFFRACTIONr_nbtor_other0.1030.21283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1121.51696
X-RAY DIFFRACTIONr_mcbond_other0.1631.5534
X-RAY DIFFRACTIONr_mcangle_it1.41522186
X-RAY DIFFRACTIONr_scbond_it2.28631006
X-RAY DIFFRACTIONr_scangle_it3.4524.5828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.808→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 39 -
Rwork0.301 671 -
obs--88.09 %
Refinement TLS params.Method: refined / Origin x: 46.629 Å / Origin y: 24.733 Å / Origin z: 73.341 Å
111213212223313233
T0.0511 Å2-0.0177 Å2-0.0579 Å2--0.0037 Å20.0516 Å2---0.0824 Å2
L0.8793 °20.3131 °2-0.5539 °2-1.9509 °2-1.4214 °2--3.0924 °2
S0.0416 Å °0.0953 Å °-0.0533 Å °-0.1389 Å °0.0466 Å °0.1299 Å °0.3454 Å °-0.0021 Å °-0.0882 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 501 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 146101 - 146
4X-RAY DIFFRACTION1AA152 - 200152 - 200
5X-RAY DIFFRACTION1AA201 - 240201 - 240
6X-RAY DIFFRACTION1AA241 - 279241 - 279

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