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- PDB-1m40: ULTRA HIGH RESOLUTION CRYSTAL STRUCTURE OF TEM-1 -

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Basic information

Entry
Database: PDB / ID: 1m40
TitleULTRA HIGH RESOLUTION CRYSTAL STRUCTURE OF TEM-1
ComponentsBETA-LACTAMASE TEM
KeywordsHYDROLASE / BETA-LACTAMASE / ACYLATION MECHANISM
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-CB4 / : / PHOSPHATE ION / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsMinasov, G. / Wang, X. / Shoichet, B.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation.
Authors: Minasov, G. / Wang, X. / Shoichet, B.K.
History
DepositionJul 1, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJul 17, 2002ID: 1L7U
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_alt_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.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 1.4Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Remark 999SEQUENCE THE SEQUENCE NUMBERING IS NOT SEQUENTIAL. NUMBERS 239 AND 253 ARE NOT USED IN THE COORDINATES.

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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)29,6839
Polymers28,9121
Non-polymers7718
Water10,196566
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.313, 61.641, 89.252
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


Mass: 28911.904 Da / Num. of mol.: 1 / Mutation: M182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II - TEM-1 / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15BN4O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium-potassium buffer, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlenzyme1drop
22.5 mMcompound 11drop
30.65 Msodium potassium phosphate1droppH8.0
41.4 Msodium potassium phosphate1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.7999
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 7, 2001 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 0.85→15 Å / Num. all: 200302 / Num. obs: 200302 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.7
Reflection shellResolution: 0.85→0.87 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / Num. unique all: 13237 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 1143489
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 13237 / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JWP

1jwp


Resolution: 0.85→10 Å / Num. parameters: 36034 / Num. restraintsaints: 76566 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.112 6015 -RANDOM
Rwork0.091 ---
all-199928 --
obs-199928 97 %-
Displacement parametersBiso mean: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.9345 Å20 Å20 Å2
2--0.9147 Å20 Å2
3---0.7803 Å2
Refine analyzeNum. disordered residues: 448 / Occupancy sum hydrogen: 1684 / Occupancy sum non hydrogen: 2507.95
Refinement stepCycle: LAST / Resolution: 0.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 57 707 6476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.012
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.023
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.071
LS refinement shellResolution: 0.85→0.878 Å
RfactorNum. reflection% reflection
Rfree0.197 534 -
Rwork0.18 --
obs-17797 97.06 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.1117 / Rfactor Rwork: 0.091
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.6

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