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- PDB-1jt1: FEZ-1 metallo-beta-lactamase from Legionella gormanii modelled wi... -

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Basic information

Entry
Database: PDB / ID: 1jt1
TitleFEZ-1 metallo-beta-lactamase from Legionella gormanii modelled with D-captopril
ComponentsFEZ-1, class B3 metallo-beta-lactamase
KeywordsHYDROLASE / monomer with alpha-beta/beta-alpha fold
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MCO / FEZ-1 protein
Similarity search - Component
Biological speciesFluoribacter gormanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGarcia-Saez, I. / Mercuri, P.S. / Kahn, R. / Papamicael, C. / Frere, J.M. / Galleni, M. / Dideberg, O.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Three-dimensional Structure of FEZ-1, a Monomeric Subclass B3 Metallo-[beta]-lactamase from Fluoribacter gormanii, in Native Form and in Complex with -Captopril
Authors: Garcia-Saez, I. / Mercuri, P.S. / Papamicael, C. / Kahn, R. / Frere, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O.
History
DepositionAug 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 8, 2013Group: Advisory
Revision 1.4Oct 25, 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_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.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_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: FEZ-1, class B3 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,17610
Polymers29,3161
Non-polymers8609
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.120, 76.775, 44.841
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FEZ-1, class B3 metallo-beta-lactamase


Mass: 29316.463 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fluoribacter gormanii (bacteria) / Gene: blaFEZ-1 / Plasmid: pDML1810 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pLysS) / References: UniProt: Q9K578, beta-lactamase

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Non-polymers , 6 types, 264 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MCO / 1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG MME5000, 0.2M ammonium sulfate, 0.1M HEPES 7.0, 0.010MM Zn chloride, 0.0108MM D-CAPTOPRIL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.5 mg/mlprotein1drop
215 mMsodium cacodylate1droppH6.0
318 %PEG5000 MME1reservoir
40.2 Mammonium sulfate1reservoir
50.1 MHEPES1reservoirpH7.0
60.1 mM1reservoirZnCl2
736 mMD-captopril1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODEENRAF-NONIUS FR59111.5418
SYNCHROTRONESRF BM30A21.28276
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEApr 2, 2001mirrors
2CCDApr 29, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.282761
ReflectionResolution: 1.78→42.258 Å / Num. all: 49235 / Num. obs: 45143 / % possible obs: 92.4 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.038 / Net I/σ(I): 14.3
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 8.4 / Num. unique all: 2221 / Rsym value: 0.076 / % possible all: 61
Reflection
*PLUS
Num. obs: 46214 / Num. measured all: 74560 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 61 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 1.78→38.08 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1880532.45 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
Details: refinement target: maximum likelihood, using amplitudes from single wavelength experiment and phase probability distribution from SAD experiment
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4472 9.91 %random
Rwork0.161 ---
all-24162 --
obs-23107 91.7 %-
Displacement parametersBiso mean: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20.28 Å2
2--1.15 Å20 Å2
3----2.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.78→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 43 255 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it0.411.5
X-RAY DIFFRACTIONc_mcangle_it0.72
X-RAY DIFFRACTIONc_scbond_it0.572
X-RAY DIFFRACTIONc_scangle_it0.872.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.78-1.890.2152480.1840.014231261.9
2.09-2.110.1782940.1626869
2.55-2.60.2181960.1719867
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4sulfcaprr.paramsulfcaprr.top
X-RAY DIFFRACTION5glyc.paramglyc.top
Refinement
*PLUS
Num. reflection obs: 45143 / % reflection Rfree: 10 % / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.1678
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
LS refinement shell
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 1.89 Å / Rfactor Rfree: 0.222 / Num. reflection Rfree: 248 / Rfactor Rwork: 0.18 / Num. reflection Rwork: 9.7 / Num. reflection obs: 2310

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