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- PDB-1ddk: CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONA... -

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Basic information

Entry
Database: PDB / ID: 1ddk
TitleCRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA
ComponentsIMP-1 METALLO BETA-LACTAMASE
KeywordsHYDROLASE / IMP-1 METALLO BETA-LACTAMASE / BINUCLEAR METAL CENTER / ZN 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 / 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
ACETIC ACID / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.1 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 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection / Derived calculations
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5264
Polymers24,3351
Non-polymers1913
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 105.800, 112.300
Angle α, β, γ (deg.)90.00, 93.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.99995, -0.0094, 0.0029), (-0.00933, 0.99966, 0.02423), (-0.00313, 0.0242, -0.9997)21.18934, 3.135, 56.24181
3generate(-0.99992, 0.00296, 0.0119), (-0.00303, -0.99998, -0.00525), (0.01188, -0.00528, 0.99992)16.96566, 29.75573, -0.4844
4generate(0.99988, 0.00967, 0.01236), (0.00949, -0.99985, 0.01465), (0.0125, -0.01453, -0.99982)3.12039, 32.94323, 56.37651

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Components

#1: Protein IMP-1 METALLO BETA-LACTAMASE


Mass: 24334.750 Da / Num. of mol.: 1
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: Q932P5, UniProt: Q79MP6*PLUS, 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: drop contained 5 uL protein (14mg/mL in 20mM HEPES, pH 7.5) with 5 uL reservoir (0.2M sodium acetate, 30% PEG4000, 0.1M sodium citrate pH 5.6). Crystal grew as plates after 2 weeks., pH 6.5, ...Details: drop contained 5 uL protein (14mg/mL in 20mM HEPES, pH 7.5) with 5 uL reservoir (0.2M sodium acetate, 30% PEG4000, 0.1M sodium citrate pH 5.6). Crystal grew as plates after 2 weeks., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Temp details: 293-295
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
220 mMHEPES1droppH7.5
30.2 Msodium acetate1reservoir
430 %PEG40001reservoir
50.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Feb 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 19288 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.14
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.249 / Num. unique all: 0 / % possible all: 56.6
Reflection
*PLUS
Num. measured all: 31781 / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.19 Å / % possible obs: 56.6 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.5refinement
FRAMBOdata collection
XDSdata scaling
CCP4phasing
RefinementResolution: 3.1→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 784186.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1898 9.9 %RANDOM
Rwork0.255 ---
obs0.255 19263 90.2 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.13 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.64 Å20 Å2-2.41 Å2
2---0.99 Å20 Å2
3---7.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 6 1 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it2.681.5
X-RAY DIFFRACTIONc_mcangle_it4.42
X-RAY DIFFRACTIONc_scbond_it3.642
X-RAY DIFFRACTIONc_scangle_it5.632.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 226 9.2 %
Rwork0.346 2221 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2ACE.PARACE.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.383 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.346

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