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- PDB-1l9y: FEZ-1-Y228A, A Mutant of the Metallo-beta-lactamase from Legionel... -

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Basic information

Entry
Database: PDB / ID: 1l9y
TitleFEZ-1-Y228A, A Mutant of the Metallo-beta-lactamase from Legionella gormanii
ComponentsFEZ-1 b-lactamase
KeywordsHYDROLASE / monomer with alpha-beta/beta-alpha fold / Two monomers per assymmetric unit
Function / homology
Function and homology information


beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesFluoribacter gormanii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGarcia-Saez, I. / Mercuri, P.S. / 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. / Frre, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O.
History
DepositionMar 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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_alt_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 SEQUENCE THERE IS A CONFLICT BETWEEN SEQRES(SER277 AND GLY311) AND SEQUENCE DATABASE(GB8980430). ... SEQUENCE THERE IS A CONFLICT BETWEEN SEQRES(SER277 AND GLY311) AND SEQUENCE DATABASE(GB8980430). THE AUTHORS BELIEVE THAT SER277 AND GLY311 ARE CORRECT AND ARE THE TRUE IDENTITIES OF THESE RESIDUES, RESPECTIVELY. RESIDUES ARE NUMBERED FOLLOWING THE STANDARD NUMBERING FOR CLASS B BETA-LACTAMASES, (BBL NUMBERING). (GALLENI M. ET AL. . 2001. "STANDARD NUMBERING SCHEME FOR CLASS B BETA-LACTAMASES". ANTIMICROB.AGENTS CHEMOTHER. MARCH, P. 660-663).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,82219
Polymers58,4492
Non-polymers1,37317
Water5,711317
1
A: FEZ-1 b-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,95910
Polymers29,2241
Non-polymers7359
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FEZ-1 b-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8639
Polymers29,2241
Non-polymers6398
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.761, 77.430, 78.499
Angle α, β, γ (deg.)90.00, 101.70, 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 b-lactamase / FEZ-1 protein


Mass: 29224.369 Da / Num. of mol.: 2 / Mutation: Y228A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fluoribacter gormanii (bacteria) / Gene: blaFEZ-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K578, beta-lactamase

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Non-polymers , 5 types, 334 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20%PEG MME 5000, 0.2M amm.sulfate, 0.1M Cacod.acid/Na Cacodylate, 10microM Zn acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→54.233 Å / Num. all: 34214 / Num. obs: 33715 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.16 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.063 / Net I/σ(I): 8.3
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 6 / Num. unique all: 4475 / Rsym value: 0.118 / % possible all: 88.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K07

1k07


Resolution: 2.01→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
Details: Refinement of double conformation of residues 168 and 255 in monomer A, and residues 38, 168 and 255 in monomer B. Refinement of two different positions of water molecules 89 and 126.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3304 -RANDOM
Rwork0.1865 ---
all-34797 --
obs-33305 96 %-
Solvent computationBsol: 56.5017 Å2 / ksol: 0.383607 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å2-1.768 Å2
2---1.562 Å20 Å2
3---0.093 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.01→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 65 317 4492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.5571.5
X-RAY DIFFRACTIONc_scbond_it0.8262
X-RAY DIFFRACTIONc_mcangle_it0.8962
X-RAY DIFFRACTIONc_scangle_it1.1632.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.01-2.030.2321440.2093X-RAY DIFFRACTION384
2.5-2.540.2106760.1874X-RAY DIFFRACTION592
3.08-3.150.2106820.1896X-RAY DIFFRACTION618
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4sulf.param
X-RAY DIFFRACTION5glyc.param

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