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

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Basic information

Entry
Database: PDB / ID: 1jje
TitleIMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A BIARYL SUCCINIC ACID INHIBITOR (11)
ComponentsIMP-1 METALLO BETA-LACTAMASE
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE INHIBITOR / SUCCINIC ACID INHIBITOR / IMP-1 METALLO-BETA-LACTAMASE
Function / homology
Function and homology information


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 / 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
ACETATE ION / Chem-BYS / Metallo-beta-lactamase type 2 / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFitzgerald, P.M.D. / Sharma, N.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Succinic acids as potent inhibitors of plasmid-borne IMP-1 metallo-beta-lactamase.
Authors: Toney, J.H. / Hammond, G.G. / Fitzgerald, P.M. / Sharma, N. / Balkovec, J.M. / Rouen, G.P. / Olson, S.H. / Hammond, M.L. / Greenlee, M.L. / Gao, Y.D.
History
DepositionJul 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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

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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)50,26512
Polymers49,0702
Non-polymers1,19510
Water3,315184
1
A: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1336
Polymers24,5351
Non-polymers5985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1336
Polymers24,5351
Non-polymers5985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: IMP-1 METALLO BETA-LACTAMASE
hetero molecules

B: IMP-1 METALLO BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26512
Polymers49,0702
Non-polymers1,19510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4600 Å2
ΔGint-244 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.440, 43.240, 64.230
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IMP-1 METALLO BETA-LACTAMASE


Mass: 24535.006 Da / Num. of mol.: 2 / Fragment: metallo-beta-lactamase
Source method: isolated from a genetically manipulated source
Details: PLEASE NOTE THAT THE PROTEIN CONTAINS POSTRANSLATIONAL MODIFICATION: ATOM CG OF ASN 26 IS BOUND TO ATOM N OF GLY 27. THIS ACCOUNTS FOR MISSING ATOMS LISTED IN REMARK 470 AND DISTORTED ...Details: PLEASE NOTE THAT THE PROTEIN CONTAINS POSTRANSLATIONAL MODIFICATION: ATOM CG OF ASN 26 IS BOUND TO ATOM N OF GLY 27. THIS ACCOUNTS FOR MISSING ATOMS LISTED IN REMARK 470 AND DISTORTED GEOMETRY REPORTED FOR THESE RESIDUES.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P52699, UniProt: Q79MP6*PLUS, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BYS / 2-BENZO[1,3]DIOXOL-5-YLMETHYL-3-BENZYL-SUCCINIC ACID


Mass: 342.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.98 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG MONOMETHYL ETHER 550, ZINC ACETATE, MES PH 6.7-7.1, 310 K, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris1drop
32 mMdithiothreitol1drop
40.1 %beta-octylglucoside1drop
525-32 %PEG5501reservoir
62 mMzinc acetate1reservoir
7100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.8→99 Å / Num. all: 35791 / Num. obs: 35791 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.59 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.0752 / Net I/σ(I): 13.005
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4997 / Mean I/σ(I) obs: 1.336 / Num. unique all: 5910 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 9999 Å
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 5910

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Processing

Software
NameClassification
SHELXL-97refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: ANOTHER INHIBITED COMPLEX IN THE SAME SPACE GROUP

Resolution: 1.8→10 Å / Num. parameters: 14767 / Num. restraintsaints: 14533 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1760 5 %RANDOM
Rwork0.201 ---
all0.201 34043 --
obs0.201 35803 99.7 %-
Solvent computationSolvent model: SHELXL 97 SWAT PARAMETER REFINEMENT
Displacement parametersBiso mean: 35.2 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3688
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 64 184 3688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.087
X-RAY DIFFRACTIONs_from_restr_planes0.337
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): -3 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.337
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / Num. reflection obs: 3653 / Rfactor obs: 0.365

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