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- PDB-5acp: W228R-Investigation of the impact from residues W228 and Y233 in ... -

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Basic information

Entry
Database: PDB / ID: 5acp
TitleW228R-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1
ComponentsGIM-1 PROTEIN
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / GIM-1 / CARBAPENEMASE / ENZYME KINETICS / MIC
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: 1.98 Å
AuthorsSkagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.-K.S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Role of Residues W228 and Y233 in the Structure and Activity of Metallo-Beta-Lactamase Gim-1.
Authors: Skagseth, S. / Carlsen, T.J. / Bjerga, G.E.K. / Spencer, J. / Samuelsen, O. / Leiros, H.S.
History
DepositionAug 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: GIM-1 PROTEIN
B: GIM-1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1676
Polymers54,9462
Non-polymers2214
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-136.3 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.757, 133.619, 40.702
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27473.160 Da / Num. of mol.: 2 / Mutation: YES
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 PRARE / References: UniProt: Q704V1
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.91 Å3/Da / Density % sol: 35.6 % / Description: NONE
Crystal growDetails: 19.8% POLYETHYLENE GLYCOL (PEG) 10K AND 0.1 M SODIUM CACODYLATE, PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.98→41 Å / Num. obs: 28430 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 40.36 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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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 2YNT

2ynt


Resolution: 1.98→24.834 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1428 5 %
Rwork0.2017 --
obs0.2033 28382 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→24.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 4 131 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043579
X-RAY DIFFRACTIONf_angle_d0.8544882
X-RAY DIFFRACTIONf_dihedral_angle_d14.0991306
X-RAY DIFFRACTIONf_chiral_restr0.032546
X-RAY DIFFRACTIONf_plane_restr0.004626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.05080.29331510.28282716X-RAY DIFFRACTION99
2.0508-2.13280.30091380.26722664X-RAY DIFFRACTION99
2.1328-2.22980.26591400.24262670X-RAY DIFFRACTION99
2.2298-2.34730.24061470.23872704X-RAY DIFFRACTION99
2.3473-2.49420.25441490.23642665X-RAY DIFFRACTION100
2.4942-2.68660.27171310.22582731X-RAY DIFFRACTION99
2.6866-2.95660.24641260.23872716X-RAY DIFFRACTION99
2.9566-3.38350.23971480.21512689X-RAY DIFFRACTION99
3.3835-4.25940.23511530.18792677X-RAY DIFFRACTION99
4.2594-24.83620.19941450.16232722X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -13.0929 Å / Origin y: -48.9509 Å / Origin z: -11.1348 Å
111213212223313233
T0.3244 Å20.0115 Å2-0.0191 Å2-0.4024 Å2-0.0077 Å2--0.3491 Å2
L0.3828 °2-0.1015 °2-0.051 °2-2.5477 °2-0.0317 °2--0.7828 °2
S0.0688 Å °0.0945 Å °-0.1627 Å °0.453 Å °0.0062 Å °0.0235 Å °0.1077 Å °0.182 Å °-0.0788 Å °
Refinement TLS groupSelection details: ALL

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