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- PDB-2h6a: Crystal structure of the zinc-beta-lactamase L1 from Stenotrophom... -

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Basic information

Entry
Database: PDB / ID: 2h6a
TitleCrystal structure of the zinc-beta-lactamase L1 from Stenotrophomonas maltophilia (mono zinc form)
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / METALLO / ZN / LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia.
Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O.
#1: Journal: Embo J. / Year: 1995
Title: The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: A Metallo-Beta-Lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase Cpha and its Complex with Biapenem
Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_validate_polymer_linkage / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 999SEQUENCE THESE COORDINATES CONTAIN NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY ...SEQUENCE THESE COORDINATES CONTAIN NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY (SEE REFERENCE 1). Residue B THR 57 and Residue B GLU 67 are not linked. The length of the C-N(B) bond is 1.77A. Also, residue B ARG 276 and residue B ALA 289 are not linked. The C(A)-N bond is 2.42A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,18810
Polymers57,4812
Non-polymers7078
Water12,142674
1
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1906
Polymers28,7401
Non-polymers4505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9984
Polymers28,7401
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.220, 104.220, 195.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1352-

HOH

21B-1380-

HOH

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Components

#1: Protein Metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28740.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P52700, beta-lactamase
#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.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY (SEE REFEREN

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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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AS, SOAKED CRYSTAL IN 5 ML DROP WITH CRYSTALLIZATION CONDITIONS AND 0.005 M EDTA FOR 30 MINUTES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: Xenocs multilayers
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.8→19.74 Å / Num. obs: 57235 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 5.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.372 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.2.0019refinement
XDSdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.254 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue B THR 57 and Residue B GLU 67 are not linked. The bond length of the C-N(B) bond is 1.77. Also, residue B ARG 276 and residue B ALA ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residue B THR 57 and Residue B GLU 67 are not linked. The bond length of the C-N(B) bond is 1.77. Also, residue B ARG 276 and residue B ALA 289 are not linked. The C(A)-N bond is 2.42.
RfactorNum. reflection% reflectionSelection details
Rfree0.20981 2909 5.1 %RANDOM
Rwork0.17158 ---
obs0.1735 54307 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 32 674 4755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214163
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9595666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39623.408179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6515617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2211531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023169
X-RAY DIFFRACTIONr_nbd_refined0.2910.22315
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2613
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.282
X-RAY DIFFRACTIONr_mcbond_it0.7531.52706
X-RAY DIFFRACTIONr_mcangle_it1.21124220
X-RAY DIFFRACTIONr_scbond_it2.09131632
X-RAY DIFFRACTIONr_scangle_it3.3434.51446
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 202 -
Rwork0.223 3796 -
obs--94.67 %

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