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

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Basic information

Entry
Database: PDB / ID: 4ibx
TitleCrystal structure of stabilized TEM-1 beta-lactamase variant v.13
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / TEM-1 beta-lactamase
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: 2.68 Å
AuthorsDellus-Gur, E. / Toth-Petroczy, A. / Elias, M. / Tawfik, D.S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs.
Authors: Dellus-Gur, E. / Toth-Petroczy, A. / Elias, M. / Tawfik, D.S.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
E: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,61611
Polymers143,8545
Non-polymers7626
Water1,72996
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0063
Polymers28,7711
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9662
Polymers28,7711
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9073
Polymers28,7711
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9662
Polymers28,7711
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,7711
Polymers28,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.900, 239.000, 159.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11E-309-

HOH

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Components

#1: Protein
Beta-lactamase TEM / 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: 28770.779 Da / Num. of mol.: 5 / Mutation: A42G, N52A, I84V, R120G, M182T, L201A, T265M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.68→80 Å / Num. all: 44433 / Num. obs: 43737 / % possible obs: 98.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rsym value: 0.125

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZG4

1zg4


Resolution: 2.68→48.68 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 28.873 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 2.923 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26529 2187 5 %RANDOM
Rwork0.23232 ---
obs0.23394 41550 100 %-
all-44433 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10075 0 43 96 10214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02210346
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6991.97914015
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.09651315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41323.891442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.133151821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8171586
X-RAY DIFFRACTIONr_chiral_restr0.0530.21606
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217701
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7161.56534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.355210488
X-RAY DIFFRACTIONr_scbond_it2.30833812
X-RAY DIFFRACTIONr_scangle_it3.7744.53519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 154 -
Rwork0.331 2934 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42970.1406-0.08980.51950.37780.94380.03060.0263-0.01670.05740.0346-0.03850.0339-0.0423-0.06520.05360.0294-0.01510.07980.00680.051714.5284-60.2906-26.3296
20.2646-0.0387-0.05810.5035-0.28270.76160.0169-0.0015-0.0359-0.02430.01370.00410.01090.0397-0.03060.0499-0.0335-0.01670.1072-0.02020.05585.202-59.899314.0314
30.23710.2803-0.29760.9272-0.15740.97860.0253-0.0071-0.0736-0.07640.0449-0.02640.18960.0086-0.07020.1389-0.0216-0.0960.02130.00890.1082.9022-99.8151-46.1489
40.4227-0.43260.32731.46880.13960.64070.03240.07450.1055-0.03150.0075-0.0877-0.09610.0173-0.03990.10970.03870.09730.07690.08680.133422.0886-20.5017-46.9769
50.6005-0.302-0.54311.51290.93861.6361-0.0502-0.0226-0.03510.250.0857-0.06930.3005-0.0413-0.03550.149-0.0083-0.05240.01690.00030.06230.4026-96.6287-6.8718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 290
2X-RAY DIFFRACTION2B26 - 290
3X-RAY DIFFRACTION3C26 - 290
4X-RAY DIFFRACTION4D26 - 290
5X-RAY DIFFRACTION5E26 - 290

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