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- PDB-1dd6: IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1dd6
TitleIMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A MERCAPTOCARBOXYLATE INHIBITOR
ComponentsIMP-1 METALLO BETA-LACTAMASE
KeywordsHYDROLASE / METALLO BETA-LACTAMASE INHIBITOR / MERCAPTOCARBOXYLATE INHIBITOR / IMP-1 METALLO BETA-LACTAMASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / 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 / 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
Chem-MCI / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsConcha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. ...Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor.
Authors: Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S.
History
DepositionNov 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: IMP-1 METALLO BETA-LACTAMASE
B: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5109
Polymers50,2932
Non-polymers1,2177
Water6,125340
1
A: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8035
Polymers25,1471
Non-polymers6564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7074
Polymers25,1471
Non-polymers5603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.3, 51.2, 203.3
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 IMP-1 METALLO BETA-LACTAMASE


Mass: 25146.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52699, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MCI / (2-MERCAPTOMETHYL-4-PHENYL-BUTYRYLIMINO)-(5-TETRAZOL-1-YLMETHYL-THIOPHEN-2-YL)-ACETIC ACID / MERCAPTOCARBOXYLATE INHIBITOR


Mass: 429.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N5O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: SITTING DROPS WERE PREPARED BY MIXING EQUAL VOLUMES OF PROTEIN WHICH WAS 14 MG/ ML IN 20MM HEPES, PH 7.5 AND TO WHICH AN EXCESS OF SOLID INHIBITOR HAD BEEN ADDED AND RESERVOIR SOLUTION (30% ...Details: SITTING DROPS WERE PREPARED BY MIXING EQUAL VOLUMES OF PROTEIN WHICH WAS 14 MG/ ML IN 20MM HEPES, PH 7.5 AND TO WHICH AN EXCESS OF SOLID INHIBITOR HAD BEEN ADDED AND RESERVOIR SOLUTION (30% PEG 2000 MONOMETHYLETHER, 0.1M SODIUM ACETATE, PH 5.0 AND 0.2M AMMONIUM SULFATE). THIS MIXTURE WAS INCUBATED OVERNIGHT AT 4C AND CENTRIFUGED TO REMOVE PRECIPITATE BEFORE SETTING UP CRYSTALLIZATION DROPS. CO-CRYSTALS WERE GROWN FROM 6 ML SITTING DROPS OF THE PROTEIN-RESERVOIR SOLUTION AND 0.3 ML OF THE RESERVOIR SOLUTION AT EITHER ROOM TEMPERATURE OR 4C, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Temp details: 293-295
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
220 mMHEPES1droppH7.5
330 %PEG MME20001reservoir
40.1 Msodium acetate1reservoirpH5.6
50.2 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU30011.54
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 21, 1997
MARRESEARCH2IMAGE PLATENov 11, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.11
ReflectionResolution: 2→20 Å / Num. all: 35656 / Num. obs: 545270 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 21
Reflection shellResolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.314 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 34187 / % possible obs: 95.9 % / Num. measured all: 545270
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3355 -RANDOM
Rwork0.198 ---
obs0.198 33702 94.1 %-
all-35831 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 72 340 3804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2

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