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- PDB-1h8y: Crystal structure of the class D beta-lactamase OXA-13 in complex... -

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Basic information

Entry
Database: PDB / ID: 1h8y
TitleCrystal structure of the class D beta-lactamase OXA-13 in complex with meropenem
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / CLASS D / OXA-13 / MEROPENEM / ACYL- ENZYME
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / 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-MER / Beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structures of the Class D B-Lactamase Oxa-13 in the Native Form and in Complex with Meropenem
Authors: Pernot, L. / Frenois, F. / Rybkine, T. / L'Hermite, G. / Petrella, S. / Delettre, J. / Jarlier, V. / Collatz, E. / Sougakoff, W.
#1: Journal: Microbiology / Year: 1998
Title: Carbapenemns as Inhibitors of Oxa-13, a Novel, Integron-Encoded B-Lactmase in Pseudomonas Aeruginosa
Authors: Mugnier, P. / Podglajen, I. / Goldstein, F.W. / Collatz, E.
History
DepositionFeb 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0568
Polymers54,9012
Non-polymers1,1556
Water5,837324
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-65.9 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.340, 112.300, 124.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.52696, -0.849699, -0.017997), (-0.849705, -0.527169, 0.009671), (-0.017705, 0.010196, -0.999791)
Vector: 112.702, 199.64819, 125.6125)

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Components

#1: Protein BETA-LACTAMASE / BETA-LACTAMASE OXA-13


Mass: 27450.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THERE IS AN ESTER LINK BETWEEN SER A 67 OG AND MER A 300 C7 AND BETWEEN SER B 67 OG AND MER B 300 C7
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAE391 / Gene: BLA OXA-13 / Plasmid: PAZ304 / Gene (production host): BLA OXA-13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 / References: UniProt: Q51400, beta-lactamase
#2: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ...THE FIRST NINETEEN RESIDUES (MET1-ALA19) DESCRIBED IN THE SEQUENCE DEPOSITED IN THE DATABASE TREMBL ARE NOT PRESENT IN THE MATURE PROTEIN

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.5
Details: 15-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-15 mg/mlprotein1drop
215-17 %(w/v)PEG40001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 43003 / % possible obs: 97.7 % / Observed criterion σ(I): 2.5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.5 / % possible all: 87.8
Reflection
*PLUS
Num. measured all: 265500
Reflection shell
*PLUS
% possible obs: 96.2 % / Redundancy: 4 % / Mean I/σ(I) obs: 2.82

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMV. 6.0data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE STARTING MODEL USED WAS THE ONE OF OXA-13

Resolution: 2→30 Å / SU B: 3.94 / SU ML: 0.11 / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17
Details: THE SIDE-CHAINS OF RESIDUES SER A 50, GLU A 199 AND SER B 50 HAVE ALTERNATE CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2172 5 %RANDOM
Rwork0.204 ---
obs-40758 97.7 %-
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 72 324 4266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0240.02
X-RAY DIFFRACTIONp_angle_d0.0250.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.0542
X-RAY DIFFRACTIONp_mcangle_it3.9813
X-RAY DIFFRACTIONp_scbond_it3.7382
X-RAY DIFFRACTIONp_scangle_it5.3563
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.1830.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2660.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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