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- PDB-5act: W228S-Investigation of the impact from residues W228 and Y233 in ... -

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Basic information

Entry
Database: PDB / ID: 5act
TitleW228S-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


: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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: 1.81 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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)54,9374
Polymers54,8062
Non-polymers1312
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-86.5 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.644, 133.007, 40.860
Angle α, β, γ (deg.)90.00, 95.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27403.045 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 35.64 % / Description: NONE
Crystal growDetails: 26.8% PEG MME 2K, 0.1 M TRIS, PH 7.0, 0.11 M POTASSIUM PHOSPHATE MONOBASIC (KH2PO4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.81→45 Å / Num. obs: 36990 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.02 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YNT

2ynt


Resolution: 1.81→24.823 Å / SU ML: 0.23 / σ(F): 1.38 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1848 5 %
Rwork0.1794 --
obs0.1819 36939 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→24.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 2 242 3622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133521
X-RAY DIFFRACTIONf_angle_d1.3874793
X-RAY DIFFRACTIONf_dihedral_angle_d15.6041275
X-RAY DIFFRACTIONf_chiral_restr0.06538
X-RAY DIFFRACTIONf_plane_restr0.007609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85890.29211440.25512735X-RAY DIFFRACTION99
1.8589-1.91360.31281420.25432676X-RAY DIFFRACTION99
1.9136-1.97540.28831440.23552633X-RAY DIFFRACTION98
1.9754-2.04590.29931320.21742766X-RAY DIFFRACTION100
2.0459-2.12780.27471330.21492680X-RAY DIFFRACTION99
2.1278-2.22460.27391350.20672676X-RAY DIFFRACTION99
2.2246-2.34180.2571450.19622705X-RAY DIFFRACTION99
2.3418-2.48840.25231410.19652692X-RAY DIFFRACTION99
2.4884-2.68030.24581480.19362721X-RAY DIFFRACTION99
2.6803-2.94960.24161530.20152691X-RAY DIFFRACTION99
2.9496-3.37560.22621490.18732681X-RAY DIFFRACTION99
3.3756-4.24940.21541290.15392722X-RAY DIFFRACTION99
4.2494-24.82490.18611530.14422713X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5253-0.2344-0.13270.4607-0.66781.1072-0.14470.0213-0.1726-0.24770.3695-0.0391-0.05680.31510.00050.2107-0.01260.03790.2506-0.04350.3099-58.842117.872354.7884
20.3571-0.3906-0.00440.35090.22220.63810.0836-0.2412-0.0855-0.0269-0.0362-0.09050.02220.012-0.00010.1902-0.00680.00190.3693-0.00880.2341-60.897320.373865.2324
32.19090.1472-0.52360.5642-0.08521.45340.06010.03850.0443-0.1493-0.06880.0505-0.1763-0.2194-0.00130.2310.03290.01040.2366-0.01050.1747-73.407625.740556.5476
40.49770.1038-0.10030.6027-0.28681.14660.0114-0.25340.1728-0.19950.12330.14770.1256-0.28710.00840.2925-0.0746-0.08430.26310.04280.4918-76.9943-10.086549.5581
52.4343-0.1529-0.31721.1213-0.00921.87110.03530.04420.2578-0.41120.1157-0.07520.1430.12060.01280.3993-0.0683-0.02470.18620.03670.3313-63.3622-12.302242.6381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 39 THROUGH 76 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 77 THROUGH 124 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 125 THROUGH 295 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 38 THROUGH 122 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 123 THROUGH 295 )

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