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- PDB-3q7z: CBAP-acylated BlaR1 sensor domain from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3q7z
TitleCBAP-acylated BlaR1 sensor domain from Staphylococcus aureus
ComponentsBeta-lactamase regulatory protein BlaR1
KeywordsHYDROLASE REGULATOR/ANTIBIOTIC / antibiotic-binding / MRSA / antibiotic-binding-antibiotic complex / HYDROLASE REGULATOR-ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / 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
Chem-BOU / Beta-lactamase regulatory protein BlaR1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBorbulevych, O.Y. / Mobashery, S. / Baker, B.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Lysine Nzeta-decarboxylation switch and activation of the beta-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus.
Authors: Borbulevych, O. / Kumarasiri, M. / Wilson, B. / Llarrull, L.I. / Lee, M. / Hesek, D. / Shi, Q. / Peng, J. / Baker, B.M. / Mobashery, S.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase regulatory protein BlaR1
B: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0554
Polymers59,1712
Non-polymers8852
Water4,071226
1
A: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0282
Polymers29,5851
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase regulatory protein BlaR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0282
Polymers29,5851
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.690, 107.197, 56.422
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase regulatory protein BlaR1 / Bla regulator protein blaR1


Mass: 29585.252 Da / Num. of mol.: 2 / Fragment: residues 332-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1, VRA0048 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WU28
#2: Chemical ChemComp-BOU / (2R,4S)-2-[(1R)-1-{[(2'-carboxybiphenyl-2-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / CBAP, open form / benzoyl-6-amino penicilloic acid, open form


Mass: 442.485 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N2O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000 30%, TRIS 0.1M, NH4SSO4 0.2M, pH 8.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2010
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 43364 / Num. obs: 43148 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Χ2: 1.341 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.87-1.93.80.63521541.2231100
1.9-1.943.80.55121561.2951100
1.94-1.973.80.47621391.2571100
1.97-2.013.80.38422001.3251100
2.01-2.063.80.31521291.3271100
2.06-2.113.80.26921731.3821100
2.11-2.163.80.23121691.3711100
2.16-2.223.80.19621561.4171100
2.22-2.283.80.17221411.4511100
2.28-2.363.80.15521811.4281100
2.36-2.443.80.12821821.3791100
2.44-2.543.80.1121411.4231100
2.54-2.653.80.09321591.3341100
2.65-2.793.80.07621711.341100
2.79-2.973.80.06821761.2921100
2.97-3.193.80.05721581.3281100
3.19-3.513.80.04921831.367199.9
3.51-4.023.80.04321691.432199.3
4.02-5.053.70.04321171.177196.9
5.05-203.60.04520941.257194.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2296 / WRfactor Rwork: 0.1813 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.847 / SU B: 7.944 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1536 / SU Rfree: 0.1441 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2167 5 %RANDOM, 5%
Rwork0.1831 ---
all0.1854 43420 --
obs0.1854 43117 99.3 %-
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 max: 55.55 Å2 / Biso mean: 36.225 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-1.83 Å2
2---0.66 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 62 226 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224354
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9515876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40825.225222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33315786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3011510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023346
X-RAY DIFFRACTIONr_mcbond_it0.6841.52508
X-RAY DIFFRACTIONr_mcangle_it1.27524034
X-RAY DIFFRACTIONr_scbond_it2.17331846
X-RAY DIFFRACTIONr_scangle_it3.414.51840
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 151 -
Rwork0.234 2905 -
all-3056 -
obs--96.86 %
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)
12.418-0.05920.70962.16070.07041.89760.03-0.02410.08070.0638-0.0150.0491-0.0214-0.0328-0.01490.020800.01710.0229-0.00470.0164-5.888-0.53323.378
21.383-0.00350.30492.1636-0.58383.059-0.01630.0767-0.1251-0.0753-0.0905-0.02170.12350.16170.10670.0660.00690.00490.06470.00690.0629-17.542-24.688-1.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A332 - 583
2X-RAY DIFFRACTION2B332 - 583

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