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- PDB-4ubq: Crystal Structure of IMP-2 Metallo-beta-Lactamase from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 4ubq
TitleCrystal Structure of IMP-2 Metallo-beta-Lactamase from Acinetobacter spp.
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / beta-lactam antibiotics / metallo-beta-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 2. / 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 ...Beta-lactamases class B signature 2. / 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
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYamaguchi, Y. / Matsueda, S. / Matsunaga, K. / Takashio, N. / Toma-Fukai, S. / Yamagata, Y. / Shibata, N. / Wachino, J. / Shibayama, K. / Arakawa, Y. / Kurosaki, H.
CitationJournal: Biol.Pharm.Bull. / Year: 2015
Title: Crystal structure of IMP-2 metallo-beta-lactamase from Acinetobacter spp.: comparison of active-site loop structures between IMP-1 and IMP-2.
Authors: Yamaguchi, Y. / Matsueda, S. / Matsunaga, K. / Takashio, N. / Toma-Fukai, S. / Yamagata, Y. / Shibata, N. / Wachino, J. / Shibayama, K. / Arakawa, Y. / Kurosaki, H.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5024
Polymers25,3121
Non-polymers1903
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-80 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.942, 68.488, 88.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase / Metallo-beta-lactamase IMP-2


Mass: 25311.742 Da / Num. of mol.: 1 / Fragment: UNP residues 18-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaIMP-2 / Plasmid: pBCSK(+) / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: Q9KVZ2, 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M citric acid/sodium citrate buffer, 0.2M sodium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→44.2 Å / Num. obs: 10767 / % possible obs: 99.8 % / Redundancy: 6.81 % / Rsym value: 0.095 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.62 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata scaling
MOLREPphasing
REFMAC5.5refinement
Coot0.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DD6

1dd6


Resolution: 2.3→44.16 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.334 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29864 514 4.9 %RANDOM
Rwork0.23239 ---
obs0.23548 9994 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 6 113 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221766
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.9522394
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81125.49371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.172152
X-RAY DIFFRACTIONr_chiral_restr0.080.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211308
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4981.51090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94521757
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2213676
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0794.5637
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 38 -
Rwork0.276 751 -
obs--99.87 %

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