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- PDB-1e4d: Structure of OXA10 beta-lactamase at pH 8.3 -

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Basic information

Entry
Database: PDB / ID: 1e4d
TitleStructure of OXA10 beta-lactamase at pH 8.3
ComponentsBETA-LACTAMASE OXA-10
KeywordsBETA-LACTAMASE / ANTIOBITIC RESISTANCE
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / plasma membrane
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
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P.
CitationJournal: Structure / Year: 2000
Title: Insights Into Class D Beta-Lactamases are Revealed by the Crystal Structure of the Oxa10 Enzyme from Pseudomonas Aeruginosa
Authors: Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P.
History
DepositionJul 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: BETA-LACTAMASE OXA-10
B: BETA-LACTAMASE OXA-10
C: BETA-LACTAMASE OXA-10
D: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,17926
Polymers110,2694
Non-polymers1,90922
Water16,988943
1
A: BETA-LACTAMASE OXA-10
C: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02712
Polymers55,1352
Non-polymers89310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-LACTAMASE OXA-10
D: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,15114
Polymers55,1352
Non-polymers1,01712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.279, 82.436, 101.165
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.97698, 0.0204, -0.21237), (-0.01941, -0.99979, -0.00675), (-0.21247, -0.00247, 0.97717)5.33697, 27.58863, -50.08973
2given(-0.82502, 0.53193, -0.19077), (0.53224, 0.61796, -0.57866), (-0.18992, -0.57894, -0.79294)6.79546, 31.40208, 93.78351
3given(-0.84852, -0.40153, 0.34465), (-0.5287, -0.61604, 0.58393), (-0.02215, -0.67769, -0.73501)-20.23644, -4.44905, 40.16423

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Components

#1: Protein
BETA-LACTAMASE OXA-10


Mass: 27567.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Cellular location (production host): EXCRETED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 2.53 Å3/Da / Density % sol: 0.561 %
Crystal growpH: 8.3
Details: AMMONIUMS SULFATE 2.0 M, TRIS HCL 100 MM, PH 8.2-8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMsodium potassium phosphate1drop
32.2 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→29.54 Å / Num. obs: 86153 / % possible obs: 84.4 % / Redundancy: 3 % / Biso Wilson estimate: 22.19 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.331 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 258171 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 91.1 % / Rmerge(I) obs: 0.331

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3U

1e3u


Resolution: 1.8→29.54 Å / SU B: 1.95692 / SU ML: 0.06092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.86904 / ESU R Free: 0.15506
Details: INDIVIDUAL ANISOTROPIC BFACTORS WERE REFINED. THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.24271 4320 5 %RANDOM SAME SET AS MAD STRUCTURE 1E3U
Rwork0.19831 ---
obs-81683 84.3 %-
Displacement parametersBiso mean: 22.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 104 943 8795
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0050.02
X-RAY DIFFRACTIONp_angle_d0.0180.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.912
X-RAY DIFFRACTIONp_mcangle_it1.3635
X-RAY DIFFRACTIONp_scbond_it2.6610
X-RAY DIFFRACTIONp_scangle_it3.55315
X-RAY DIFFRACTIONp_plane_restr0.00740.03
X-RAY DIFFRACTIONp_chiral_restr0.0720.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2270.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1250.3
X-RAY DIFFRACTIONp_planar_tor5.77
X-RAY DIFFRACTIONp_staggered_tor12.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1983 / Rfactor Rfree: 0.24271 / Rfactor Rwork: 0.19831
Solvent computation
*PLUS
Displacement parameters
*PLUS

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