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- PDB-4oqg: Crystal structure of TEM-1 beta-lactamase in complex with boron-b... -

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Basic information

Entry
Database: PDB / ID: 4oqg
TitleCrystal structure of TEM-1 beta-lactamase in complex with boron-based inhibitor EC25
ComponentsAmpicillin resistance protein
Keywordshydrolase/hydrolase inhibitor / Beta-lactamase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2UL / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDellus-Gur, E. / Elias, M. / Fraser, J.S. / Tawfik, D.S.
CitationJournal: J. Mol. Biol. / Year: 2015
Title: Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.
Authors: Dellus-Gur, E. / Elias, M. / Caselli, E. / Prati, F. / Salverda, M.L. / de Visser, J.A. / Fraser, J.S. / Tawfik, D.S.
History
DepositionFeb 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Other
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Ampicillin resistance protein
B: Ampicillin resistance protein
C: Ampicillin resistance protein
D: Ampicillin resistance protein
E: Ampicillin resistance protein
F: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,68112
Polymers173,9046
Non-polymers1,7766
Water1,27971
1
A: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3262
Polymers28,9841
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3923
Polymers28,9841
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3262
Polymers28,9841
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3262
Polymers28,9841
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Ampicillin resistance protein


Theoretical massNumber of molelcules
Total (without water)28,9841
Polymers28,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Ampicillin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3262
Polymers28,9841
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.690, 81.690, 497.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Ampicillin resistance protein / Beta lactamase / Beta-lactamase / Betalactamase TEM-116 / BlaTEM / Extended spectrum beta-lactamase ...Beta lactamase / Beta-lactamase / Betalactamase TEM-116 / BlaTEM / Extended spectrum beta-lactamase / Mutant extended-spectrum beta-lactamase / TEM extended spectrum beta-lactamase


Mass: 28984.076 Da / Num. of mol.: 6 / Fragment: TEM-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaTEM-116 / Production host: Escherichia coli (E. coli) / References: UniProt: Q79DR3, beta-lactamase
#2: Chemical
ChemComp-2UL / 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid


Mass: 342.154 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H19BN2O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 6% PEG 8000, 100 mM MES buffer, 200mM Ca(OAc)2 and 50 M NaF, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.82658
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82658 Å / Relative weight: 1
ReflectionResolution: 2.4→45.81 Å / Num. obs: 65358 / % possible obs: 96.4 % / Observed criterion σ(I): 3 / Redundancy: 5.06 % / Rsym value: 0.071 / Net I/σ(I): 14.64
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 3 / Rsym value: 0.539 / % possible all: 97.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZG4

1zg4


Resolution: 2.4→45.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.976 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3268 5 %RANDOM
Rwork0.203 ---
obs0.206 62086 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12180 0 126 71 12377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212184
X-RAY DIFFRACTIONr_angle_refined_deg0.7971.98616963
X-RAY DIFFRACTIONr_angle_other_deg0.5163.00227924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.62351566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26923.78537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.801152215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6415110
X-RAY DIFFRACTIONr_chiral_restr0.0450.21950
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022662
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9934.9736300
X-RAY DIFFRACTIONr_mcbond_other4.994.9736299
X-RAY DIFFRACTIONr_mcangle_it6.847.4517845
X-RAY DIFFRACTIONr_mcangle_other6.847.4517846
X-RAY DIFFRACTIONr_scbond_it5.7055.6276232
X-RAY DIFFRACTIONr_scbond_other5.7055.6266229
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2818.219111
X-RAY DIFFRACTIONr_long_range_B_refined10.61940.64614601
X-RAY DIFFRACTIONr_long_range_B_other10.61940.64914602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 239 -
Rwork0.306 4542 -
obs--98.23 %

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