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- PDB-1xa1: Crystal structure of the sensor domain of BlaR1 from Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 1xa1
TitleCrystal structure of the sensor domain of BlaR1 from Staphylococcus aureus in its apo form
ComponentsRegulatory protein blaR1
KeywordsSIGNALING PROTEIN / beta-lactamase / BlaR1 / sensor domain / staphylococcus aureus / antibiotic resistance
Function / homology
Function and homology information


penicillin binding / plasma membrane
Similarity search - Function
: / Peptidase M56 / BlaR1 peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / PYROPHOSPHATE 2- / Regulatory protein BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWilke, M.S. / Hills, T.L. / Zhang, H.Z. / Chambers, H.F. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structures of the Apo and penicillin-acylated forms of the BlaR1 beta-lactam sensor of Staphylococcus aureus.
Authors: Wilke, M.S. / Hills, T.L. / Zhang, H.Z. / Chambers, H.F. / Strynadka, N.C.
History
DepositionAug 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein blaR1
B: Regulatory protein blaR1
C: Regulatory protein blaR1
D: Regulatory protein blaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,99611
Polymers120,0074
Non-polymers9897
Water18,5731031
1
A: Regulatory protein blaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3684
Polymers30,0021
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein blaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2733
Polymers30,0021
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Regulatory protein blaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1782
Polymers30,0021
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Regulatory protein blaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1782
Polymers30,0021
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.876, 104.893, 90.273
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Regulatory protein blaR1


Mass: 30001.791 Da / Num. of mol.: 4 / Fragment: C-terminal Domain (residues 331-585)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Plasmid: pET41b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P18357
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2.2 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 18-23% PEG 3350, 0.2M NaH2PO4, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 95274 / Num. obs: 95274 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: benzylpenicillin-acylated BlaR1 C-terminal domain, PDB entry 1XA7

1xa7


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.958 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 4770 5 %RANDOM
Rwork0.18618 ---
all0.18824 95247 --
obs0.18824 90477 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.1 Å2
2---0.3 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8135 0 51 1031 9217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228385
X-RAY DIFFRACTIONr_bond_other_d0.0020.027048
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.93911265
X-RAY DIFFRACTIONr_angle_other_deg0.767316638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029139
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021701
X-RAY DIFFRACTIONr_nbd_refined0.2120.21771
X-RAY DIFFRACTIONr_nbd_other0.240.28232
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.24481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.2147
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.54840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39327791
X-RAY DIFFRACTIONr_scbond_it2.04433545
X-RAY DIFFRACTIONr_scangle_it3.3354.53474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 263
Rwork0.253 4841

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