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- PDB-7bz3: The mutant variant of PNGM-1. H257 was substituted for alanine to... -

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Basic information

Entry
Database: PDB / ID: 7bz3
TitleThe mutant variant of PNGM-1. H257 was substituted for alanine to study substrate binding.
ComponentsMetallo-beta-lactamase PNGM-1
KeywordsANTIBIOTIC / RNase Z / MBLs / carbapenemase
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase PNGM-1
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Model detailsPNGM-1 residue H96 was substitued for alanine
AuthorsPark, Y.S. / Kang, L.W. / Lee, J.H.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants.
Authors: Park, Y.S. / Kim, T.Y. / Park, H. / Lee, J.H. / Nguyen, D.Q. / Hong, M.K. / Lee, S.H. / Kang, L.W.
History
DepositionApr 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase PNGM-1
B: Metallo-beta-lactamase PNGM-1
C: Metallo-beta-lactamase PNGM-1
D: Metallo-beta-lactamase PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,06112
Polymers166,5384
Non-polymers5238
Water16,952941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SuperoseTM 12 10/300 was used for the experiment. Buffer composition was 0.05 M Tris-HCl pH 7.0, 150mM NaCl, 3 mM Mercaptoethanol.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21020 Å2
ΔGint-420 kcal/mol
Surface area43710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.787, 143.741, 79.760
Angle α, β, γ (deg.)90.000, 111.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Metallo-beta-lactamase PNGM-1


Mass: 41634.457 Da / Num. of mol.: 4 / Mutation: H257A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U8UYM6, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.76 % / Mosaicity: 0.5 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 4.6
Details: 0.1 M Sodium acetate, 20% glycerol, 0.2 M MgCl2 and 7.5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: steady flow of liquid nitrogen was used to maintain 100 K.
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 103806 / % possible obs: 97.6 % / Redundancy: 6.2 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.097 / Rsym value: 0.089 / Χ2: 3.751 / Net I/av σ(I): 37.603 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.086.20.20349910.980.0880.2221.48296
2.08-2.116.20.18549830.9820.080.2021.54996.2
2.11-2.156.20.16850790.9840.0730.1841.62796.4
2.15-2.26.20.15449440.9850.0660.1681.7496.6
2.2-2.256.20.14350740.9870.0620.1561.8996.8
2.25-2.36.10.13950130.9870.060.1521.98696.8
2.3-2.356.10.13750820.9860.060.152.04196.8
2.35-2.426.10.12850420.9880.0560.142.16197.4
2.42-2.496.10.11750680.990.0510.1282.33596.8
2.49-2.576.10.11150750.9910.0480.1212.46597.8
2.57-2.666.10.10351090.9910.0450.1132.64697.7
2.66-2.776.10.10450950.990.0450.1132.93797.9
2.77-2.896.10.09751140.990.0420.1063.2398
2.89-3.056.10.09251570.9910.040.1013.90698.3
3.05-3.246.20.08551100.9920.0370.0924.1498.4
3.24-3.496.20.08151830.9930.0350.0885.02398.7
3.49-3.846.20.07951710.9930.0340.0865.43498.9
3.84-4.396.30.07551770.9910.0320.0817.20198.6
4.39-5.546.20.07251620.9890.0310.0798.31698.6
5.54-506.30.07352850.9910.0320.07911.81299

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.69 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 5.999 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 5529 5.1 %RANDOM
Rwork0.2291 ---
obs0.2321 103806 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.97 Å2 / Biso mean: 24.755 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10640 0 8 941 11589
Biso mean--19.72 32.2 -
Num. residues----1347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310953
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179533
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.63914932
X-RAY DIFFRACTIONr_angle_other_deg1.3261.57322023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.57251339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49422.023618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.113151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0811572
X-RAY DIFFRACTIONr_chiral_restr0.0790.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022511
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.329 350 -
Rwork0.276 7020 -
obs--88.7 %

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