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- PDB-2v1z: Structure of a TEM-1 beta-lactamase insertant allosterically regu... -

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Basic information

Entry
Database: PDB / ID: 2v1z
TitleStructure of a TEM-1 beta-lactamase insertant allosterically regulated by kanamycin and anions.
ComponentsBETA-LACTAMASE TEM
KeywordsHYDROLASE / INSERTION MUTANT / ANTIBIOTIC RESISTANCE / ALLOSTERIC REGULATION
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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEvrard, C. / Barrios, H. / Mathonet, P. / Soumillion, P. / Fastrez, J. / Declercq, J.P.
CitationJournal: Chembiochem / Year: 2011
Title: Engineering an Allosteric Binding Site for Aminoglycosides Into Tem1-Beta-Lactamase.
Authors: Volkov, A.N. / Barrios, H. / Mathonet, P. / Evrard, C. / Ubbink, M. / Declercq, J.P. / Soumillion, P. / Fastrez, J.
History
DepositionMay 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5122
Polymers32,4471
Non-polymers651
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.113, 70.609, 78.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-LACTAMASE TEM / TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / ...TEM-1 / TEM-2 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2 / TEM-16/CAZ-7 / TEM-24/CAZ-6 / IRT-4 / PENICILLINASE ALLOSTERIC BETA-LACTAMASE INSERTANT


Mass: 32447.049 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-38,41-286 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PBAD-MYC-HIS-TETR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP 10 / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 82 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 102 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, VAL 82 TO ILE ENGINEERED RESIDUE IN CHAIN A, GLU 102 TO LYS ENGINEERED RESIDUE IN CHAIN A, ALA 182 TO VAL ENGINEERED RESIDUE IN CHAIN A, GLU 237 TO ARG ENGINEERED RESIDUE IN CHAIN A, GLN 265 TO ARG ENGINEERED RESIDUE IN CHAIN A, ALA 266 TO LYS ENGINEERED RESIDUE IN CHAIN A, THR 267 TO LYS ENGINEERED RESIDUE IN CHAIN A, MET 268 TO THR
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 Å3/Da / Density % sol: 38.9 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.2
Details: RESERVOIR: BIS-TRIS 0.1M PH6.2, PEG6000 25%(W/V), NACL 0.3M, NAN3 0.02%(W/V). HANGING DROP: 1UL PROTEIN AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97976
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2005 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING.
RadiationMonochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT. SI(111) OR SI(311)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 34091 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.9
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.2 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0031refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTL

1btl


Resolution: 1.6→52.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.462 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1710 5 %RANDOM
Rwork0.169 ---
obs0.171 32339 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 1 352 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222137
X-RAY DIFFRACTIONr_bond_other_d0.0030.021501
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9772892
X-RAY DIFFRACTIONr_angle_other_deg1.0653.0023646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5932390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8511522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
X-RAY DIFFRACTIONr_nbd_refined0.220.2481
X-RAY DIFFRACTIONr_nbd_other0.2030.21641
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21061
X-RAY DIFFRACTIONr_nbtor_other0.0880.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4371.51749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59922167
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7493895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9734.5724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 127
Rwork0.19 2199

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