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- PDB-2ynv: Cys221 oxidized, Mono zinc GIM-1 - GIM-1-Ox. Crystal structures o... -

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Basic information

Entry
Database: PDB / ID: 2ynv
TitleCys221 oxidized, Mono zinc GIM-1 - GIM-1-Ox. Crystal structures of Pseudomonas aeruginosa GIM-1: active site plasticity in metallo-beta- lactamases
Components(GIM-1 PROTEIN) x 2
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
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: 2.05 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 2.0Jun 20, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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_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_type.id
Revision 2.1Apr 9, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_entry_details.has_protein_modification / _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_conn_type.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)51,4435
Polymers51,2882
Non-polymers1553
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-95.5 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.648, 131.712, 40.721
Angle α, β, γ (deg.)90.00, 94.78, 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 / METALLO-BETA-LACTAMASE


Mass: 25667.756 Da / Num. of mol.: 1
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: Protein GIM-1 PROTEIN / METALLO-BETA-LACTAMASE GIM-1 / METALLO-BETA-LACTAMASE


Mass: 25619.758 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.92 % / Description: SOLVED USING ANOTHER GIM-1 STRUCTURE
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 CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.05→41 Å / Num. obs: 24869 / % possible obs: 87.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.552 Å / SU ML: 0.29 / σ(F): 1.44 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1261 5.1 %
Rwork0.1967 --
obs0.1994 24810 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→19.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 3 58 3444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153528
X-RAY DIFFRACTIONf_angle_d1.6454809
X-RAY DIFFRACTIONf_dihedral_angle_d15.8151274
X-RAY DIFFRACTIONf_chiral_restr0.117539
X-RAY DIFFRACTIONf_plane_restr0.008610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1320.31131360.26062653X-RAY DIFFRACTION99
2.132-2.22890.31551610.24652602X-RAY DIFFRACTION99
2.2289-2.34620.32671380.24352600X-RAY DIFFRACTION98
2.3462-2.4930.27511280.22642652X-RAY DIFFRACTION99
2.493-2.6850.31081200.2152655X-RAY DIFFRACTION98
2.685-2.95440.2681350.22122613X-RAY DIFFRACTION98
2.9544-3.380.24071220.20582627X-RAY DIFFRACTION97
3.38-4.25120.22911580.17962562X-RAY DIFFRACTION96
4.2512-19.55270.22031630.1682585X-RAY DIFFRACTION96
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)
11.2133-0.498-0.3981.0769-0.05061.67630.03150.1446-0.1483-0.16210.0091-0.03160.1673-0.00140.06260.08060.02190.01990.0748-0.06270.087122.7059-4.24516.2779
23.2635-0.14580.72680.2505-0.21040.48930.0595-0.0726-0.16680.0655-0.0574-0.04770.05170.0259-0.04330.053-0.0121-0.02410.1427-0.03580.123923.7916-3.620525.5462
33.2125-0.66672.03851.8262-0.06047.65850.0859-0.075-0.2458-0.0314-0.00990.12150.243-0.1044-0.07530.0818-0.0147-0.0030.16490.10380.190215.3629-8.403326.7899
42.46790.54850.95020.77610.26860.69620.0871-0.241-0.08020.0563-0.01310.05830.0468-0.10930.01570.0388-0.0050.00220.16240.01540.04496.675-2.878429.0988
51.9189-0.14460.61152.1066-1.71562.17730.0871-0.1413-0.0633-0.00070.00520.2148-0.0968-0.0991-0.07360.09060.01170.03160.2038-0.03480.10726.7146-0.725430.4096
60.26930.15130.06480.38480.21690.26150.0597-0.00430.0869-0.027-0.0033-0.0091-0.0733-0.00330.05190.12360.05110.03280.0991-0.04120.083310.90446.613417.9653
70.8670.3095-0.8711.110.30941.6227-0.12280.0573-0.0782-0.10060.0757-0.03150.1975-0.09390.09930.21370.1146-0.01590.4095-0.07110.12364.5973-1.09246.7951
80.16670.0957-0.19580.56530.08341.43090.02010.17480.0446-0.1380.01530.0367-0.044-0.2217-0.00240.20070.10150.03480.33450.03650.099810.81663.96634.5994
91.3206-0.02680.02791.72480.02592.03730.0885-0.22290.2778-0.02310.01360.0714-0.13630.0812-0.040.2903-0.124-0.13560.22590.01020.37683.512-32.445.985
103.5272-0.298-0.6170.3505-0.05111.13440.107-0.12760.42620.03280.05320.0777-0.2459-0.0002-0.17230.233-0.0846-0.04580.22250.11780.33933.9031-37.906411.2924
113.221-1.24650.51812.3657-0.72239.1806-0.0151-0.16950.05080.31750.08040.1459-0.1538-0.2377-0.05830.1550.0250.00580.25880.10780.13248.2803-41.051118.9748
125.69283.48731.99762.92972.55042.91950.1271-0.1252-0.28050.2594-0.0127-0.37890.1850.2049-0.12920.1705-0.0314-0.05480.10260.04250.157321.9368-41.077113.0527
131.238-0.955-1.39460.84130.58274.92060.0059-0.06030.1828-0.15160.0663-0.3191-0.08470.0846-0.07790.2045-0.0176-0.08920.09380.05780.301819.8951-42.819714.3614
141.72370.27430.36811.9751-0.24431.138-0.0056-0.0164-0.0699-0.11810.0133-0.0110.0894-0.0489-0.00650.3404-0.1232-0.03050.16060.04810.23715.456-41.436-0.3033
151.5027-0.5402-1.15554.10990.03110.9262-0.2153-0.15570.47980.03410.0193-0.1712-0.42020.07910.20030.7686-0.0232-0.09750.42790.12080.520917.8537-23.0746-1.0488
163.57940.6104-0.76734.98460.58324.0493-0.00690.06950.0426-0.25240.0526-0.4614-0.16820.2949-0.04380.4377-0.09690.11090.23480.10080.39525.3344-33.6927-6.4994
170.8438-0.7678-0.39324.01761.02492.6964-0.00480.0352-0.0102-0.25160.00730.1873-0.0375-0.0581-0.00970.3405-0.1537-0.14070.23560.12170.242910.2493-34.3688-6.9558
184.97853.9752-1.00996.1543-0.21691.56350.02660.06180.1499-0.0646-0.0488-0.4237-0.3390.408-0.00560.6887-0.13330.09920.43470.09850.369821.1839-26.0979-9.8524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 40 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 89 THROUGH 118 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 119 THROUGH 131 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 133 THROUGH 149 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 150 THROUGH 175 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 179 THROUGH 222 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 223 THROUGH 252 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 253 THROUGH 295 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 40 THROUGH 89 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 90 THROUGH 122 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 123 THROUGH 136 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 137 THROUGH 148 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 149 THROUGH 175 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 179 THROUGH 222 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 223 THROUGH 238 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 239 THROUGH 252 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 253 THROUGH 279 )
18X-RAY DIFFRACTION18CHAIN B AND (RESID 280 THROUGH 295 )

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