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- PDB-4r4r: Crystal structure of chimeric beta-lactamase cTEM-19m at 1.2 angs... -

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Basic information

Entry
Database: PDB / ID: 4r4r
TitleCrystal structure of chimeric beta-lactamase cTEM-19m at 1.2 angstrom resolution
ComponentsBeta-lactamase TEM,Beta-lactamase PSE-4
KeywordsHYDROLASE
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
Beta-lactamase PSE-4 / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsPark, J. / Gobeil, S. / Pelletier, J.N. / Berghuis, A.M.
CitationJournal: Sci Rep / Year: 2019
Title: The Structural Dynamics of Engineered beta-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function.
Authors: Gobeil, S.M.C. / Ebert, M.C.C.J.C. / Park, J. / Gagne, D. / Doucet, N. / Berghuis, A.M. / Pleiss, J. / Pelletier, J.N.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / 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_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.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_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.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM,Beta-lactamase PSE-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0438
Polymers28,8281
Non-polymers2157
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.690, 58.790, 109.830
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,Beta-lactamase PSE-4 / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28827.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6, pse4, carB1 / Production host: Escherichia coli (E. coli)
References: UniProt: P62593, UniProt: P16897, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M magnesium chloride, 0.1M TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 11, 2011
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.2→31.13 Å / Num. all: 73668 / Num. obs: 73668 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.3
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5000 / % possible all: 91.6

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Processing

Software
NameVersionClassification
MxDCdata collection
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4QY5

4qy5


Resolution: 1.2→31.13 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.995 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13751 3688 5 %RANDOM
Rwork0.10504 ---
all0.10664 69928 --
obs0.10664 69928 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 7 408 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192321
X-RAY DIFFRACTIONr_bond_other_d0.0040.022238
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9823179
X-RAY DIFFRACTIONr_angle_other_deg0.96235183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85223.738107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91215429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0081525
X-RAY DIFFRACTIONr_chiral_restr0.1410.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02511
X-RAY DIFFRACTIONr_mcbond_it1.1160.8781181
X-RAY DIFFRACTIONr_mcbond_other1.1140.8771180
X-RAY DIFFRACTIONr_mcangle_it1.521.3251513
X-RAY DIFFRACTIONr_mcangle_other1.521.3261514
X-RAY DIFFRACTIONr_scbond_it2.2091.2171140
X-RAY DIFFRACTIONr_scbond_other2.2091.2171140
X-RAY DIFFRACTIONr_scangle_other2.5591.7151659
X-RAY DIFFRACTIONr_long_range_B_refined4.39910.2193245
X-RAY DIFFRACTIONr_long_range_B_other3.2828.6332925
X-RAY DIFFRACTIONr_rigid_bond_restr6.06434559
X-RAY DIFFRACTIONr_sphericity_free31.286573
X-RAY DIFFRACTIONr_sphericity_bonded11.26754858
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 263 -
Rwork0.136 4730 -
obs-4993 90.7 %

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