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- PDB-8ztb: Crystal Structure of Active Site Influencing Variant (F218Y) of I... -

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Basic information

Entry
Database: PDB / ID: 8ztb
TitleCrystal Structure of Active Site Influencing Variant (F218Y) of Imp-1 Metallo-beta-lactamase.
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / Carbapenemase / Metallo-Hydrolase / Antimicrobial Resistance.
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Metallo-beta-lactamase IMP-1
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBaidya, S. / Dhankhar, K. / Hazra, S.
Funding support India, 1items
OrganizationGrant numberCountry
Board of Research in Nuclear Sciences (BRNS)54/14/03/2023-BRNS/12162 India
CitationJournal: To Be Published
Title: Crystal Structure of Active Site Influencing Variant (F218Y) of Imp-1 Metallo-beta-lactamase.
Authors: Baidya, S. / Dhankhar, K. / Hazra, S.
History
DepositionJun 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Metallo-beta-lactamase type 2
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,74418
Polymers48,7022
Non-polymers1,04316
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-231 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.418, 49.301, 110.696
Angle α, β, γ (deg.)90, 92.348, 90
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / BLA-IMP / IMP-1 / Beta-lactamase type II / Metallo-beta-lactamase type II


Mass: 24350.750 Da / Num. of mol.: 2 / Mutation: F218Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52699, beta-lactamase

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Non-polymers , 8 types, 41 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Sodium Acetate, 0.1M Sodium Citrate, 34% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→24.682 Å / Num. obs: 12578 / % possible obs: 99.7 % / Redundancy: 16.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.047 / Rrim(I) all: 0.14 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.7-24.6712.50.0394430.9990.0150.042
2.9-3.0813.90.54724720.9740.2180.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→24.682 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.867 / SU B: 46.148 / SU ML: 0.395 / Cross valid method: FREE R-VALUE / ESU R Free: 0.438 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2715 550 4.451 %
Rwork0.2095 11807 -
all0.212 --
obs-12357 97.932 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.772 Å2
Baniso -1Baniso -2Baniso -3
1-1.956 Å2-0 Å21.202 Å2
2---8.027 Å20 Å2
3---5.952 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 46 25 3496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123545
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.8284809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9065440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.10956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60410603
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.50210138
X-RAY DIFFRACTIONr_chiral_restr0.1320.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022682
X-RAY DIFFRACTIONr_nbd_refined0.2590.21927
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2164
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5360.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.214
X-RAY DIFFRACTIONr_mcbond_it5.1912.7651762
X-RAY DIFFRACTIONr_mcangle_it8.474.962197
X-RAY DIFFRACTIONr_scbond_it6.0462.9021783
X-RAY DIFFRACTIONr_scangle_it9.3965.312611
X-RAY DIFFRACTIONr_lrange_it23.09132.6965661
X-RAY DIFFRACTIONr_rigid_bond_restr3.38533545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.9-2.9740.474390.3128410.3188840.8860.95999.54750.289
2.974-3.0550.353410.2418330.2468740.9110.971000.21
3.055-3.1420.291380.2188310.2218730.9560.97699.54180.187
3.142-3.2370.296350.1668210.1718570.9610.98599.88330.141
3.237-3.3410.203360.1697720.1718090.9820.98799.87640.153
3.341-3.4560.271450.1797400.1847860.9430.98399.87280.159
3.456-3.5840.277450.2357170.2377670.9440.96999.34810.213
3.584-3.7270.349140.3176520.3177420.9190.9489.75740.282
3.727-3.8890.377160.3276410.3297030.8860.95193.45660.312
3.889-4.0740.226250.2096280.2096880.9760.97494.91280.174
4.074-4.2870.195310.1646020.1666350.9750.98299.6850.147
4.287-4.5390.29210.1735840.1766260.9350.9896.64540.155
4.539-4.8410.319290.2035270.2095810.9470.97595.69710.183
4.841-5.2120.197320.1915040.1925380.9630.97899.62830.18
5.212-5.6840.18240.1774770.1775010.980.981000.169
5.684-6.3130.323230.1964370.2014640.9340.97799.13790.187
6.313-7.2120.33190.1813970.1894160.9520.981000.169
7.212-8.650.432160.1543400.1633580.8980.98699.44130.154
8.65-11.5440.136100.1452770.1442900.9930.98798.96550.149
11.544-24.6820.397110.2391860.2462000.8680.96598.50.235
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)
13.5994-0.51160.06836.10360.20522.2310.06870.264-0.0721-0.6373-0.21750.7896-0.0131-0.36450.14880.0779-0.001-0.08870.1872-0.03040.113165.739512.25720.5779
23.435-0.1899-0.21876.1556-0.20722.00720.01380.2827-0.015-0.598-0.1908-0.88330.06350.40390.17710.06020.03520.08830.16980.04920.138135.28330.059720.5578
Refinement TLS groupSelection: ALL

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