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- PDB-3zhh: X-ray structure of the full-length beta-lactamase from M.tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3zhh
TitleX-ray structure of the full-length beta-lactamase from M.tuberculosis
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
Function / homology
Function and homology information


penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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 / Beta-lactamase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFeiler, C. / Fisher, A.C. / Marrichi, M.J. / Wright, L. / Schmidpeter, P.A.M. / Blankenfeldt, W. / Pavelka, M. / DeLisa, M.P.
CitationJournal: Plos One / Year: 2013
Title: Directed Evolution of Mycobacterium Tuberculosis Beta-Lactamase Reveals Gatekeeper Residue that Regulates Antibiotic Resistance and Catalytic Efficiency.
Authors: Feiler, C. / Fisher, A.C. / Boock, J.T. / Marrichi, M.J. / Wright, L. / Schmidpeter, P.A.M. / Blankenfeldt, W. / Pavelka, M. / Delisa, M.P.
History
DepositionDec 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: BETA-LACTAMASE
C: BETA-LACTAMASE
D: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,82121
Polymers117,1874
Non-polymers1,63317
Water1,838102
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7776
Polymers29,2971
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6815
Polymers29,2971
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5854
Polymers29,2971
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7776
Polymers29,2971
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.737, 96.438, 111.005
Angle α, β, γ (deg.)90.00, 108.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BETA-LACTAMASE / / PENICILLINASE / BLAC


Mass: 29296.867 Da / Num. of mol.: 4 / Fragment: RESIDUES 32-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.33 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7.8 / Details: 100MM TRIS PH 7.8 2.1 M (NH4)2SO4 (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→19.87 Å / Num. obs: 36698 / % possible obs: 99.7 % / Observed criterion σ(I): 4.07 / Redundancy: 3.2 % / Biso Wilson estimate: 33.26 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.52
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.07 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GDN

2gdn


Resolution: 2.85→19.872 Å / SU ML: 0.34 / σ(F): 2 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1780 4.8 %
Rwork0.1675 --
obs0.17 36691 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7945 0 85 102 8132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158171
X-RAY DIFFRACTIONf_angle_d1.55411165
X-RAY DIFFRACTIONf_dihedral_angle_d13.4562903
X-RAY DIFFRACTIONf_chiral_restr0.0771276
X-RAY DIFFRACTIONf_plane_restr0.0091468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.92690.31291540.23892664X-RAY DIFFRACTION100
2.9269-3.01270.28391380.2262650X-RAY DIFFRACTION100
3.0127-3.10960.30241210.2032696X-RAY DIFFRACTION100
3.1096-3.22030.25341340.2042639X-RAY DIFFRACTION100
3.2203-3.34860.26331520.19312685X-RAY DIFFRACTION100
3.3486-3.50030.23321320.17772657X-RAY DIFFRACTION100
3.5003-3.68370.21511410.16042697X-RAY DIFFRACTION100
3.6837-3.91290.19581160.15452706X-RAY DIFFRACTION100
3.9129-4.21230.19411360.14282677X-RAY DIFFRACTION100
4.2123-4.63140.17221560.12952677X-RAY DIFFRACTION99
4.6314-5.29040.20151240.13472699X-RAY DIFFRACTION100
5.2904-6.62410.18631390.16752719X-RAY DIFFRACTION100
6.6241-19.87220.19631370.15972745X-RAY DIFFRACTION99

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