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- PDB-5wck: Native FEZ-1 metallo-beta-lactamase from Legionella gormanii -

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Basic information

Entry
Database: PDB / ID: 5wck
TitleNative FEZ-1 metallo-beta-lactamase from Legionella gormanii
ComponentsFEZ-1 protein
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFluoribacter gormanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsGarcia-Saez, I. / Mercuri, P.S. / Kahn, R. / Papamicael, C. / Shabalin, I.G. / Raczynska, J.E. / Jaskolski, M. / Minor, W. / Frere, J.M. / Galleni, M. / Dideberg, O.
Citation
Journal: 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 D-captopril.
Authors: Garcia-Saez, I. / Mercuri, P.S. / Papamicael, C. / Kahn, R. / Frere, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O.
#1: Journal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJun 20, 2018ID: 1K07
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Apr 27, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_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
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FEZ-1 protein
B: FEZ-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03930
Polymers58,6332
Non-polymers1,40628
Water15,439857
1
A: FEZ-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,02015
Polymers29,3161
Non-polymers70314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FEZ-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,02015
Polymers29,3161
Non-polymers70314
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.)90.000, 102.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 20 - 282 / Label seq-ID: 1 - 263

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FEZ-1 protein / Metallo-beta-lactamase L1


Mass: 29316.463 Da / Num. of mol.: 2 / Fragment: residues 20-282 / Mutation: Q248S, A282G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fluoribacter gormanii (bacteria) / Gene: blaFEZ-1, Lgor_2502 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)(PLYSS) / References: UniProt: Q9K578, beta-lactamase

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Non-polymers , 5 types, 885 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.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 45.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1K07.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG4000, 0.2M ammonium sulfate, 0.010MM ZnCl2, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: 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→50 Å / Num. obs: 61308 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 21.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.051 / Num. unique obs: 8838 / Rsym value: 0.037 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1K07

1k07
PDB Unreleased entry


Resolution: 1.65→24.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1687 / WRfactor Rwork: 0.1319 / FOM work R set: 0.9046 / SU B: 1.175 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0814 / SU Rfree: 0.0829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1581 6172 10.1 %RANDOM
Rwork0.1232 ---
obs0.1267 55140 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.03 Å2 / Biso mean: 13.134 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.04 Å2
2--0.12 Å20 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.65→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 78 865 5064
Biso mean--21.89 27.44 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0144319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173893
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6765846
X-RAY DIFFRACTIONr_angle_other_deg0.9681.6489132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9423.909197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94715751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8451512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
X-RAY DIFFRACTIONr_sphericity_bonded2.78554
Refine LS restraints NCS

Ens-ID: 1 / Number: 8757 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 421 -
Rwork0.127 3734 -
all-4155 -
obs--89.9 %

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