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- PDB-4bxi: Crystal structure of ATP binding domain of AgrC from Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 4bxi
TitleCrystal structure of ATP binding domain of AgrC from Staphylococcus aureus
ComponentsACCESSORY GENE REGULATOR PROTEIN C
KeywordsATP-BINDING PROTEIN
Function / homology
Function and homology information


membrane => GO:0016020 / identical protein binding / membrane
Similarity search - Function
Sensor histidine kinase NatK, C-terminal domain / GHKL domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Accessory gene regulator protein C / Accessory gene regulator protein C
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSrivastava, S.K. / Rajasree, K. / Gopal, B.
CitationJournal: J.Bacteriol. / Year: 2014
Title: Influence of the Agrc-Agra Complex in the Response Time of Staphylococcus Aureus Quorum Sensing
Authors: Srivastava, S.K. / Rajasree, K. / Fasim, A. / Arakere, G. / Gopal, B.
History
DepositionJul 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACCESSORY GENE REGULATOR PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4446
Polymers16,9641
Non-polymers4805
Water95553
1
A: ACCESSORY GENE REGULATOR PROTEIN C
hetero molecules

A: ACCESSORY GENE REGULATOR PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,88812
Polymers33,9292
Non-polymers95910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4030 Å2
ΔGint-46.3 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.370, 67.370, 101.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

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Components

#1: Protein ACCESSORY GENE REGULATOR PROTEIN C / AGRC


Mass: 16964.387 Da / Num. of mol.: 1 / Fragment: ATP BINDING DOMAIN, RESIDUES 278-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: COL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: Q5HEG3, UniProt: A0A0H2WWL2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.41 Å3/Da / Density % sol: 63.99 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97895
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.2→34.81 Å / Num. obs: 12556 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 28.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C2A

2c2a


Resolution: 2.2→34.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.939 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 388 TO 394 ARE NOT MODELLED DUE TO POOR ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.22516 600 4.8 %RANDOM
Rwork0.19623 ---
obs0.19757 11909 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.343 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 32 53 1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191149
X-RAY DIFFRACTIONr_bond_other_d0.0010.021171
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9971553
X-RAY DIFFRACTIONr_angle_other_deg0.69932679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59626.80947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58215209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.117154
X-RAY DIFFRACTIONr_chiral_restr0.0590.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 51 -
Rwork0.199 870 -
obs--100 %

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