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- PDB-1e3u: MAD structure of OXA10 class D beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 1e3u
TitleMAD structure of OXA10 class D beta-lactamase
Components(BETA-LACTAMASE OXA- ...) x 2
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
GOLD (I) CYANIDE ION / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 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
DepositionJun 23, 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 1.3Jul 12, 2017Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)114,25739
Polymers110,0794
Non-polymers4,17835
Water17,096949
1
A: BETA-LACTAMASE OXA-10
C: BETA-LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,12319
Polymers55,0492
Non-polymers2,07517
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)57,13420
Polymers55,0312
Non-polymers2,10318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.530, 82.940, 101.420
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98373, 0.02654, -0.17767), (-0.02302, -0.9995, -0.02185), (-0.17816, -0.0174, 0.98385)4.27241, 28.01285, -50.32816
2given(-0.80793, 0.56034, -0.1824), (0.55322, 0.61462, -0.56231), (-0.20298, -0.55521, -0.80656)7.38369, 30.41618, 94.75005
3given(0.84892, -0.4337, 0.30206), (-0.52478, -0.6238, 0.5792), (-0.06278, -0.65021, -0.75716)-18.97638, -4.12586, 41.37533

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Components

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BETA-LACTAMASE OXA- ... , 2 types, 4 molecules ABCD

#1: Protein BETA-LACTAMASE OXA-10


Mass: 27524.291 Da / Num. of mol.: 3
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: Protein BETA-LACTAMASE OXA-10


Mass: 27506.318 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 984 molecules

#3: Chemical
ChemComp-AUC / GOLD (I) CYANIDE ION


Mass: 249.001 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2AuN2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 0.561 %
Crystal growpH: 8.2
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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95375, 1.0376
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953751
21.03761
ReflectionResolution: 1.653→43.1 Å / Num. obs: 127968 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.315 Å2 / Rsym value: 0.064 / Net I/σ(I): 8.1
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.322 / % possible all: 93.4
Reflection
*PLUS
Num. measured all: 598857 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.322

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
SOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.66→40 Å / SU B: 1.02065 / SU ML: 0.03474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14003 / ESU R Free: 0.09546 / Details: INDIVIDUAL ANISOTROPIC B FACTORS WERE REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.20966 6428 5 %RANDOM
Rwork0.18057 ---
obs-121338 99.8 %-
Displacement parametersBiso mean: 19.74 Å2
Refinement stepCycle: LAST / Resolution: 1.66→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7643 0 163 949 8755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0040.02
X-RAY DIFFRACTIONp_angle_d0.0160.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0170.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7962
X-RAY DIFFRACTIONp_mcangle_it1.1285
X-RAY DIFFRACTIONp_scbond_it2.34910
X-RAY DIFFRACTIONp_scangle_it15
X-RAY DIFFRACTIONp_plane_restr0.00650.03
X-RAY DIFFRACTIONp_chiral_restr0.0670.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2230.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1250.3
X-RAY DIFFRACTIONp_planar_tor5.67
X-RAY DIFFRACTIONp_staggered_tor11.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1806 / Rfactor Rfree: 0.20966 / Rfactor Rwork: 0.18057
Solvent computation
*PLUS
Displacement parameters
*PLUS

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