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- PDB-1alq: CIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 -

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Basic information

Entry
Database: PDB / ID: 1alq
TitleCIRCULARLY PERMUTED BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1
ComponentsCP254 BETA-LACTAMASE
KeywordsHYDROLASE / CIRCULAR PERMUTED / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Beta-lactamase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.8 Å
AuthorsPieper, U. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 1997
Title: Circularly permuted beta-lactamase from Staphylococcus aureus PC1.
Authors: Pieper, U. / Hayakawa, K. / Li, Z. / Herzberg, O.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 A Resolution
Authors: Herzberg, O.
#2: Journal: Science / Year: 1987
Title: Bacterial Resistance to Beta-Lactam Antibiotics: Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 A Resolution
Authors: Herzberg, O. / Moult, J.
History
DepositionJun 2, 1997Processing site: BNL
Revision 1.0Sep 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CP254 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8023
Polymers29,6461
Non-polymers1562
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.900, 94.200, 138.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21A-386-

HOH

31A-388-

HOH

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Components

#1: Protein CP254 BETA-LACTAMASE


Mass: 29646.125 Da / Num. of mol.: 1
Mutation: CIRCULARLY PERMUTED WITH AN EIGHT RESIDUE LINKER INSERTED TO JOIN THE ORIGINAL N- AND C-TERMINI, AND A NEW N-TERMINUS AT RESIDUE 254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P00807, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.96 Å3/Da / Density % sol: 57 %
Description: RESIDUES 31 - 34, 252 - 256, 288 - 290 AND THE SOLVENT WERE EXCLUDED FROM THE STARTING MODEL.
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 70% SATURATED AMMONIUM SULFATE SOLUTION, 0.3M KCL, 100MM NAHCO3 AT PH8.0, 0.5% V/V PEG600
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
230 %satammonium sulfate1drop
35 mMpotassium phosphate1drop
435 %satammonium sulfate1drop
50.15 M1dropKCl
650 mM1dropNaHCO3
70.25 %(v/v)PEG60001drop
870 %satammonium sulfate1reservoir
90.3 M1reservoirKCl
10100 mM1reservoirNaHCO3
110.5 %(v/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 29813 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 1.8 / % possible all: 66
Reflection
*PLUS
Num. measured all: 147535

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Processing

Software
NameVersionClassification
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
XENGENV. 3.0data reduction
XENGENV. 3.0data scaling
SHELXL-97phasing
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 3BLM

3blm


Resolution: 1.8→30 Å / Num. parameters: 9029 / Num. restraintsaints: 8373 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.9 ANGSTROMS. AT R-VALUES OF R=0.189 AND RFREE=0.241 FOR I>I/SIGMA(I) THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2981 10 %EVERY 10TH REFLECTION
all0.196 29777 --
obs0.191 -88.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2122 / Occupancy sum non hydrogen: 2203.5
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 9 212 2254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.034
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.118
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.034

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