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- PDB-4oqh: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13... -

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Basic information

Entry
Database: PDB / ID: 4oqh
TitleCrystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S mutation in complex with boron-based inhibitor EC25
ComponentsExtended spectrum beta-lactamase TEM-63
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 / metal ion binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Jan 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_type.id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Extended spectrum beta-lactamase TEM-63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1454
Polymers28,7011
Non-polymers4443
Water6,612367
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Extended spectrum beta-lactamase TEM-63
hetero molecules

A: Extended spectrum beta-lactamase TEM-63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2908
Polymers57,4012
Non-polymers8896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1170 Å2
ΔGint-9 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.540, 47.030, 34.620
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-174-

ASN

21A-302-

CA

31A-644-

HOH

41A-717-

HOH

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Components

#1: Protein Extended spectrum beta-lactamase TEM-63


Mass: 28700.662 Da / Num. of mol.: 1 / Fragment: TEM-1
Mutation: R164S, A42G, N52A, I84V, R120G, M182T, L201A, T265M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaTEM-63 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AGJ5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-2UL / 3-[(2R)-2-{[(2R)-2-amino-2-phenylacetyl]amino}-2-(dihydroxyboranyl)ethyl]benzoic acid


Mass: 342.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19BN2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→45.01 Å / Num. all: 88380 / Num. obs: 25519 / Observed criterion σ(F): 2 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.342 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23277 1276 5 %RANDOM
Rwork0.18696 ---
obs0.18923 24240 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.89 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 30 367 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9943053
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3225295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36224.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.651517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
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_it1.7391.2021126
X-RAY DIFFRACTIONr_mcbond_other1.8841.241125
X-RAY DIFFRACTIONr_mcangle_it2.6731.7961412
X-RAY DIFFRACTIONr_mcangle_other2.8711.8551413
X-RAY DIFFRACTIONr_scbond_it2.3491.4521116
X-RAY DIFFRACTIONr_scbond_other2.3881.4891114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6142.171631
X-RAY DIFFRACTIONr_long_range_B_refined7.60312.5672984
X-RAY DIFFRACTIONr_long_range_B_other7.17811.1282750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 89 -
Rwork0.21 1696 -
obs--86.9 %

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