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- PDB-5fq9: Crystal structure of the OXA10 with 1C -

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Basic information

Entry
Database: PDB / ID: 5fq9
TitleCrystal structure of the OXA10 with 1C
ComponentsBETA-LACTAMASE OXA-10
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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
ACETATE ION / Chem-C6S / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrem, J. / McDonough, M.A. / Cain, R. / Clifton, I. / Fishwick, C.W.G. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J.
History
DepositionDec 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Jan 10, 2024Group: 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,63111
Polymers55,5112
Non-polymers1,1209
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-37.4 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.898, 103.109, 125.529
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: (0.8054, 0.591, 0.0452), (0.5907, -0.8066, 0.0216), (0.0492, 0.0093, -0.9987)
Vector: -2.545, 6.5599, 15.9364)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE OXA-10


Mass: 27755.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 1C BOUND TO THE ACTIVE SITE / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase

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Non-polymers , 6 types, 500 molecules

#2: Chemical ChemComp-C6S / (3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid


Mass: 317.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20BNO5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 3.17 Å3/Da / Density % sol: 61.15 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.2M NACL, 0.1M NA ACETATE PH 5.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2015 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→15.44 Å / Num. obs: 253261 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K6R

1k6r


Resolution: 1.5→15.424 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 5021 4.9 %
Rwork0.1569 --
obs0.158 102233 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.325 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 76 491 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144102
X-RAY DIFFRACTIONf_angle_d1.3445579
X-RAY DIFFRACTIONf_dihedral_angle_d21.3751527
X-RAY DIFFRACTIONf_chiral_restr0.094611
X-RAY DIFFRACTIONf_plane_restr0.01715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.3481580.31063226X-RAY DIFFRACTION100
1.517-1.53480.29921610.30343197X-RAY DIFFRACTION100
1.5348-1.55350.29811690.28273177X-RAY DIFFRACTION100
1.5535-1.57320.25671620.27533224X-RAY DIFFRACTION100
1.5732-1.59390.26311580.25333185X-RAY DIFFRACTION100
1.5939-1.61570.24831450.25033236X-RAY DIFFRACTION100
1.6157-1.63870.2411890.23483203X-RAY DIFFRACTION100
1.6387-1.66320.24351720.21833197X-RAY DIFFRACTION100
1.6632-1.68910.20491740.20833201X-RAY DIFFRACTION100
1.6891-1.71680.22771630.19523179X-RAY DIFFRACTION100
1.7168-1.74630.21931740.19133258X-RAY DIFFRACTION100
1.7463-1.77810.20711740.18443159X-RAY DIFFRACTION100
1.7781-1.81220.19121620.17673254X-RAY DIFFRACTION100
1.8122-1.84910.20391650.16713200X-RAY DIFFRACTION100
1.8491-1.88930.17971780.15973210X-RAY DIFFRACTION100
1.8893-1.93310.19491520.16143237X-RAY DIFFRACTION100
1.9331-1.98140.17011620.14553229X-RAY DIFFRACTION100
1.9814-2.03490.18841830.14533228X-RAY DIFFRACTION100
2.0349-2.09460.17741610.14313200X-RAY DIFFRACTION100
2.0946-2.1620.14731750.13633235X-RAY DIFFRACTION100
2.162-2.23910.15371860.13313232X-RAY DIFFRACTION100
2.2391-2.32840.16861550.13733289X-RAY DIFFRACTION100
2.3284-2.4340.18061610.13643232X-RAY DIFFRACTION100
2.434-2.56180.16741590.13753252X-RAY DIFFRACTION100
2.5618-2.72150.17231820.143263X-RAY DIFFRACTION100
2.7215-2.93030.17681720.14443265X-RAY DIFFRACTION100
2.9303-3.22270.20021500.15053303X-RAY DIFFRACTION100
3.2227-3.68350.16751540.14413335X-RAY DIFFRACTION100
3.6835-4.62010.13181640.12393340X-RAY DIFFRACTION100
4.6201-15.42430.16672010.1473466X-RAY DIFFRACTION100

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