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- PDB-1k07: Native FEZ-1 metallo-beta-lactamase from Legionella gormanii -

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Basic information

Entry
Database: PDB / ID: 1k07
TitleNative FEZ-1 metallo-beta-lactamase from Legionella gormanii
ComponentsFEZ-1 beta-lactamase
KeywordsHYDROLASE / monomer with alpha-beta/beta-alpha fold. Two monomers per assymmetric unit.
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
ACETATE ION / FEZ-1 protein
Similarity search - Component
Biological speciesFluoribacter gormanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionSep 18, 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 1.3Oct 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FEZ-1 beta-lactamase
B: FEZ-1 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,82417
Polymers58,6332
Non-polymers1,19115
Water8,989499
1
A: FEZ-1 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9429
Polymers29,3161
Non-polymers6258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FEZ-1 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8838
Polymers29,3161
Non-polymers5667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.860, 76.850, 78.890
Angle α, β, γ (deg.)90.00, 102.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FEZ-1 beta-lactamase


Mass: 29316.463 Da / Num. of mol.: 2 / 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 , 5 types, 514 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG4000, 0.2M ammonium sulfate, 0.010MM ZnCl2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.5 mg/mlprotein1drop
215 mMsodium cacodylate1droppH6.0
320 %(w/v)PEG40001reservoir
40.2 Mammonium sulfate1reservoir
520000 mM1reservoirZnCl2
60.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å
DetectorDetector: CCD / Date: Apr 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. all: 61458 / Num. obs: 61308 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.775 Å2 / Rmerge(I) obs: 0.029 / Rsym value: 0.021 / Net I/σ(I): 21.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.051 / Num. unique all: 8838 / Rsym value: 0.037 / % possible all: 96.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 61458 / Num. measured all: 217456 / Rmerge(I) obs: 0.021
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.037

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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 1JT1

1jt1


Resolution: 1.65→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
Details: Refinement of double conformation of residues 221 and 255 in A and B chains (two monomers per assym/unit), double conformation of hetero-atoms 502A and 503B and two different positions for waters 127 and 178.
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 6030 9.8 %RANDOM
Rwork0.1737 ---
all-62989 --
obs-61308 97.3 %-
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 60 499 4673
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014067
X-RAY DIFFRACTIONc_angle_deg1.61547
X-RAY DIFFRACTIONc_angle_d0.016
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.65-6.050.25441230.2371X-RAY DIFFRACTION1029
2.08-2.110.21571100.1674X-RAY DIFFRACTION1135
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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