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- PDB-3toi: Tailoring Enzyme Stability and Exploiting Stability-Trait Linkage... -

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Basic information

Entry
Database: PDB / ID: 3toi
TitleTailoring Enzyme Stability and Exploiting Stability-Trait Linkage by Iterative Truncation and Optimization
ComponentsAmpicillin resistance protein
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 TEM / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTam, H.K. / Einsle, O.
CitationJournal: Biochemistry / Year: 2012
Title: Exploring the Molecular Linkage of Protein Stability Traits for Enzyme Optimization by Iterative Truncation and Evolution.
Authors: Speck, J. / Hecky, J. / Tam, H.K. / Arndt, K.M. / Einsle, O. / Muller, K.M.
History
DepositionSep 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ampicillin resistance protein
B: Ampicillin resistance protein


Theoretical massNumber of molelcules
Total (without water)55,3992
Polymers55,3992
Non-polymers00
Water4,504250
1
A: Ampicillin resistance protein


Theoretical massNumber of molelcules
Total (without water)27,6991
Polymers27,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ampicillin resistance protein


Theoretical massNumber of molelcules
Total (without water)27,6991
Polymers27,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.003, 47.525, 258.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A40 - 287
2114B40 - 287

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.20602, 0.970309, 0.126713), (0.968042, -0.221016, 0.118517), (0.143004, 0.098247, -0.984834)15.15401, -27.561, 67.40736

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Components

#1: Protein Ampicillin resistance protein / Beta-lactamase / Betalactamase TEM-116 / Extended spectrum beta-lactamase / Mutant extended- ...Beta-lactamase / Betalactamase TEM-116 / Extended spectrum beta-lactamase / Mutant extended-spectrum beta-lactamase / TEM extended spectrum beta-lactamase


Mass: 27699.457 Da / Num. of mol.: 2 / Fragment: UNP residues 39-283
Mutation: I56V, R120G, M182T, T195S, I208M, A224V, R241H, T265M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaTEM-116 / Plasmid: pJH_BlaSS / Production host: Escherichia coli (E. coli) / Strain (production host): RV308
References: UniProt: Q79DR3, UniProt: P62593*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M imidazole maleate, 44% PEG600, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 30, 2010
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→46.744 Å / Num. all: 41888 / Num. obs: 41888 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.6.0113refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CMZ

3cmz


Resolution: 1.9→46.74 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.266 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23713 2115 5 %RANDOM
Rwork0.19931 ---
obs0.20124 39772 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 250 3998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193810
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9785159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1625491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9323.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16715668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7061532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212842
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1868 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.360.5
MEDIUM THERMAL1.512
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 157 -
Rwork0.281 2578 -
obs--99.09 %
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)
10.8092-0.10070.45130.43870.00991.1261-0.0151-0.0277-0.00270.0097-0.00250.0077-0.0191-0.04060.01750.032-0.01160.01080.0137-0.00650.0047-10.9217-10.040817.7698
20.4093-0.0419-0.00791.1549-0.46591.0957-0.0014-0.00410.011-0.0019-0.0243-0.0811-0.00260.06120.02570.0226-0.0051-0.00870.0281-0.00610.0134.43-34.143647.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 289
2X-RAY DIFFRACTION2B42 - 288

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