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- PDB-2ynw: GIM-1-2Mol native. Crystal structures of Pseudomonas aeruginosa G... -

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Basic information

Entry
Database: PDB / ID: 2ynw
TitleGIM-1-2Mol native. Crystal structures of Pseudomonas aeruginosa GIM- 1: active site plasticity in metallo-beta-lactamases
ComponentsGIM-1 PROTEIN
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / RESIDUE DETERMINANTS / LOOP DYNAMICS
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBorra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases.
Authors: Borra, P.S. / Samuelsen, O. / Spencer, J. / Walsh, T.R. / Lorentzen, M.S. / Leiros, H.-K.S.
History
DepositionOct 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_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.ptnr1_auth_asym_id / _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_asym_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: GIM-1 PROTEIN
B: GIM-1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6898
Polymers51,2402
Non-polymers4506
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-187.2 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.160, 135.534, 38.541
Angle α, β, γ (deg.)90.00, 90.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1


Mass: 25619.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A ...RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A SERINE FROM THE TEV SITE IS THEN THE FIRST RESIDUE FOLLOWED BY GLN19 IN THE GENE.

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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: 2.05 Å3/Da / Density % sol: 39.91 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 7.1, 21% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 (PEG MME 2K), 4% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 45053 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.25 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 0
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDK

1ddk


Resolution: 1.7→19.861 Å / SU ML: 0.19 / σ(F): 1.38 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 2269 5.1 %
Rwork0.1669 --
obs0.1685 44969 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 15 202 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133574
X-RAY DIFFRACTIONf_angle_d1.3184871
X-RAY DIFFRACTIONf_dihedral_angle_d13.8781284
X-RAY DIFFRACTIONf_chiral_restr0.085539
X-RAY DIFFRACTIONf_plane_restr0.007617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7370.29321380.23892650X-RAY DIFFRACTION99
1.737-1.77730.30621430.24332606X-RAY DIFFRACTION99
1.7773-1.82180.28041510.22412719X-RAY DIFFRACTION100
1.8218-1.8710.26061430.20172621X-RAY DIFFRACTION100
1.871-1.9260.21131580.18922703X-RAY DIFFRACTION100
1.926-1.98810.24971200.19562638X-RAY DIFFRACTION100
1.9881-2.05910.24991360.18192680X-RAY DIFFRACTION100
2.0591-2.14140.22641340.17912668X-RAY DIFFRACTION99
2.1414-2.23880.20551320.17492663X-RAY DIFFRACTION100
2.2388-2.35660.21791430.17262667X-RAY DIFFRACTION100
2.3566-2.5040.20471580.16762645X-RAY DIFFRACTION100
2.504-2.69690.20771370.16932684X-RAY DIFFRACTION100
2.6969-2.96750.22391600.17492666X-RAY DIFFRACTION100
2.9675-3.39510.1641250.15752683X-RAY DIFFRACTION100
3.3951-4.27040.15511240.14232721X-RAY DIFFRACTION100
4.2704-19.86250.16751670.14482686X-RAY DIFFRACTION100

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