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- PDB-5acr: W228Y-Investigation of the impact from residues W228 and Y233 in ... -

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Basic information

Entry
Database: PDB / ID: 5acr
TitleW228Y-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: 1.9 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)55,1295
Polymers54,9582
Non-polymers1713
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-100.2 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.532, 129.732, 40.396
Angle α, β, γ (deg.)90.00, 96.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27479.141 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.83 Å3/Da / Density % sol: 32.61 % / Description: NONE
Crystal growDetails: 24% PEG 5000 MONOMETHYL ETHER (PEG 5K MME), 0.1 M SODIUM ACETATE, PH 5.5 AND 0.12 POTASSIUM THIOCYANATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97972
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 1.81→45 Å / Num. obs: 30606 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 26.55 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

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

2ynt


Resolution: 1.9→24.747 Å / SU ML: 0.28 / σ(F): 1.38 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 1545 5.1 %
Rwork0.2017 --
obs0.2039 30556 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→24.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 3 270 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083460
X-RAY DIFFRACTIONf_angle_d1.2714704
X-RAY DIFFRACTIONf_dihedral_angle_d15.7521250
X-RAY DIFFRACTIONf_chiral_restr0.091528
X-RAY DIFFRACTIONf_plane_restr0.006594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96130.38641310.3152573X-RAY DIFFRACTION97
1.9613-2.03140.29211500.26492641X-RAY DIFFRACTION98
2.0314-2.11270.32891250.24642605X-RAY DIFFRACTION98
2.1127-2.20880.2641520.21782571X-RAY DIFFRACTION99
2.2088-2.32510.29361460.22182634X-RAY DIFFRACTION99
2.3251-2.47070.30131310.21882660X-RAY DIFFRACTION99
2.4707-2.66120.27571420.21772638X-RAY DIFFRACTION99
2.6612-2.92870.31011380.21972672X-RAY DIFFRACTION99
2.9287-3.35160.24951560.19112637X-RAY DIFFRACTION100
3.3516-4.21920.19031290.16922693X-RAY DIFFRACTION100
4.2192-24.74880.18791450.17832687X-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)
12.1461.0540.31494.92551.29872.6049-0.03640.2985-0.411-0.14490.181-0.37420.22330.0138-0.25390.2450.01290.00280.2908-0.12290.246322.524-6.027414.8439
23.82560.49630.49744.9156-0.3432.93720.2641-0.063-0.45040.1597-0.14830.02230.12010.16-0.14430.1210.0277-0.0220.2631-0.06020.213322.89-3.888525.3268
35.27261.18790.34181.73660.14641.28580.1245-0.4845-0.28860.0925-0.1015-0.0226-0.01870.0520.01670.16670.02530.00640.2692-0.01620.157213.0816-3.228228.0993
43.2612-0.6619-0.06724.70630.1152.39960.0151-0.5296-0.3248-0.3592-0.21320.2178-0.0511-0.41970.11860.19480.02280.07450.3644-0.04190.24425.2374-1.695330.7292
52.72870.8838-0.01261.97260.74992.40320.0360.36370.0415-0.3634-0.09810.2369-0.2001-0.35410.06010.25080.0763-0.04220.2839-0.06360.16887.34213.14613.8147
62.78330.80880.13056.06590.51413.0709-0.04040.78710.0548-0.574-0.1565-0.1827-0.50950.31540.13510.26040.0669-0.03080.3926-0.03070.180215.44325.57799.3224
72.80811.16960.54425.7090.55452.4043-0.07230.8091-0.1298-0.98750.0810.4928-0.4866-0.12350.01520.42520.0987-0.09320.6251-0.07890.20094.93941.59941.8072
82.65660.2277-0.5973.73741.23182.9197-0.09980.06340.5919-0.59280.20140.69650.4841-0.2744-0.17170.6682-0.0389-0.17530.29870.11930.73171.8213-27.21434.7006
93.8597-0.9073-0.02673.1798-0.96381.9779-0.3162-0.17210.5299-0.61810.2547-0.13130.1837-0.01240.03490.3746-0.0506-0.00940.21720.07170.411611.4197-38.97378.9985
102.631.19650.28461.4480.2161.7382-0.4570.74360.1782-0.943-0.074-0.22750.634-0.12890.35250.9235-0.17250.04830.37540.1020.561310.7214-35.7515-4.477
113.9607-0.73272.75140.8037-0.60273.08980.0042-0.11370.1143-0.09190.1846-0.33650.0072-0.1296-0.0470.5794-0.1006-0.24370.47950.19071.436419.3134-21.6039-0.0503
121.5674-1.04510.6513.7707-0.15921.9660.41740.62440.4151-0.9869-0.324-0.92820.67930.43120.21781.2055-0.14320.13010.44710.29950.573916.031-33.228-7.6434
131.05710.0138-0.24122.72-1.89231.58850.17440.03230.2111-0.19450.20460.013-0.11110.01860.20361.537-0.0410.49760.21490.52380.918820.2192-25.1627-10.1767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 40 THROUGH 76 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 77 THROUGH 102 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 104 THROUGH 148 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 149 THROUGH 175 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 179 THROUGH 252 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 253 THROUGH 279 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 280 THROUGH 295 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 40 THROUGH 66 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 67 THROUGH 201 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 202 THROUGH 226 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 227 THROUGH 238 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 239 THROUGH 279 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 280 THROUGH 295 )

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