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- PDB-1jvj: CRYSTAL STRUCTURE OF N132A MUTANT OF TEM-1 BETA-LACTAMASE IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1jvj
TitleCRYSTAL STRUCTURE OF N132A MUTANT OF TEM-1 BETA-LACTAMASE IN COMPLEX WITH A N-FORMIMIDOYL-THIENAMYCINE
ComponentsBETA-LACTAMASE TEM
KeywordsHYDROLASE / protein stability / TEM-1 / beta-lactamase / beta-lactam / antibiotic resistance / imipenem
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-IM2 / : / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsWang, X. / Minasov, G. / Shoichet, B.K.
CitationJournal: Proteins / Year: 2002
Title: Noncovalent interaction energies in covalent complexes: TEM-1 beta-lactamase and beta-lactams.
Authors: Wang, X. / Minasov, G. / Shoichet, B.K.
History
DepositionAug 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,3967
Polymers28,8991
Non-polymers4976
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.303, 61.685, 89.139
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


Mass: 28898.971 Da / Num. of mol.: 1 / Fragment: TEM-1 / Mutation: N132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 1.61 Å3/Da / Density % sol: 22.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium-potassium Phospate buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.65 Msodium potassium phosphate1droppH8.0
31.4 Msodium potassium phosphate1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 6, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→15 Å / Num. all: 23324 / Num. obs: 23324 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.49
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2342 / % possible all: 98
Reflection
*PLUS
Num. measured all: 125788 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BT5

1bt5


Resolution: 1.73→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Crystallographic conjugate gradient minimization refinement using maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2152 10 %RANDOM
Rwork0.162 ---
all-23324 --
obs-22431 91.9 %-
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2---3.418 Å20 Å2
3---1.848 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.11 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.73→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 25 418 2467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.73-1.790.2276186100.21991972197290.26
1.79-1.860.23362000.1909198291
1.86-1.950.24911960.2084193089
1.95-2.050.18942270.1547201593
2.05-2.180.21122340.1628206695
2.18-2.350.19362230.1565205794
2.35-2.580.19692350.152206994
2.58-2.950.19492160.1571206893
2.95-3.710.18162060.1413207092
3.71-150.16362290.1535205088
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
% reflection Rfree: 10 %

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