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- PDB-5acq: W228A-Investigation of the impact from residues W228 and Y233 in ... -

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Basic information

Entry
Database: PDB / ID: 5acq
TitleW228A-Investigation of the impact from residues W228 and Y233 in the metallo-beta-lactamase GIM-1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / GIM-1 / CARBAPENEMASE / ENZYME KINETICS / MIC
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / 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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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 / 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.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: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9705
Polymers54,7742
Non-polymers1963
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-127.5 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.549, 131.796, 40.581
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-LACTAMASE


Mass: 27387.045 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.34 % / 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: 1.7→44 Å / Num. obs: 42445 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 92.5

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Processing

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

2ynt


Resolution: 1.7→24.998 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 2137 5.1 %
Rwork0.1878 --
obs0.1897 42278 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 3 281 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123476
X-RAY DIFFRACTIONf_angle_d1.3784730
X-RAY DIFFRACTIONf_dihedral_angle_d13.8641260
X-RAY DIFFRACTIONf_chiral_restr0.053533
X-RAY DIFFRACTIONf_plane_restr0.007599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73950.29141360.2612575X-RAY DIFFRACTION92
1.7395-1.7830.33391550.2612593X-RAY DIFFRACTION94
1.783-1.83120.2291450.24392685X-RAY DIFFRACTION95
1.8312-1.88510.30251520.23272609X-RAY DIFFRACTION95
1.8851-1.94590.25511480.21242654X-RAY DIFFRACTION95
1.9459-2.01540.26491240.20882639X-RAY DIFFRACTION94
2.0154-2.09610.2321380.20132643X-RAY DIFFRACTION96
2.0961-2.19140.22511440.20062671X-RAY DIFFRACTION96
2.1914-2.30690.21831310.1942691X-RAY DIFFRACTION96
2.3069-2.45130.22531560.19862718X-RAY DIFFRACTION97
2.4513-2.64040.261480.20232679X-RAY DIFFRACTION96
2.6404-2.90570.27441450.20662727X-RAY DIFFRACTION97
2.9057-3.32540.24531230.19542760X-RAY DIFFRACTION98
3.3254-4.18640.21961610.16332726X-RAY DIFFRACTION98
4.1864-25.00020.1741310.16362771X-RAY DIFFRACTION97
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)
14.02480.82320.14067.34652.92516.27540.0759-0.0253-0.3826-0.22720.1455-0.33150.22820.1151-0.19890.14510.00480.02060.25880.01630.217421.8958-3.714116.5236
22.46740.01372.21061.82550.66873.27910.3026-0.5937-0.1951-0.0135-0.149-0.08580.1273-0.0788-0.14630.18510.02040.03090.38570.01670.202920.5325-3.951324.5675
35.4481-0.16241.87374.6421-1.90724.95850.3139-0.7352-0.22190.1921-0.19590.19840.0028-0.0291-0.09590.1956-0.0250.03440.4662-0.0090.14257.7575-2.427929.9423
44.6061.70521.18953.55571.50993.6567-0.00010.28960.2855-0.401-0.10150.2052-0.2409-0.31940.10850.23410.08210.00710.28010.0240.17198.24914.294910.6324
53.72643.48810.06436.43842.68812.7307-0.217-0.05270.8402-1.26780.41871.815-0.1307-0.71760.12520.5688-0.1317-0.37290.42150.150.84792.897-28.86034.7343
67.3242-1.1796-2.18793.2223-1.84222.87060.1312-0.45880.6109-0.2180.27710.60530.0447-0.3188-0.34740.3476-0.0685-0.02980.29240.08820.50725.0799-37.177611.2243
73.1022-0.1838-0.41614.3786-1.01913.2687-0.23860.2790.4226-1.21660.3031-0.41620.24810.1399-0.03380.6819-0.1569-0.01710.28340.0480.444717.6534-35.50421.3135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 39 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 89 THROUGH 124 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 125 THROUGH 175 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 179 THROUGH 295 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 40 THROUGH 76 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 77 THROUGH 124 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 125 THROUGH 295 )

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