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- PDB-7byq: The mutant variant of PNGM-1. H279A was substituted for alanine t... -

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Basic information

Entry
Database: PDB / ID: 7byq
TitleThe mutant variant of PNGM-1. H279A was substituted for alanine to study metal coordination.
ComponentsMetallo-beta-lactamase PNGM-1
KeywordsANTIBIOTIC / RNase Z / MBLs / Zinc binding motif
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: 1.96 Å
Model detailsPNGM-1 residue H91 was substituted to 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 24, 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 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)166,7998
Polymers166,5384
Non-polymers2624
Water10,196566
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 area28320 Å2
ΔGint-298 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.380, 83.057, 163.581
Angle α, β, γ (deg.)90.000, 110.690, 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: H279A
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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 4.63 Å3/Da / Density % sol: 73.45 % / Mosaicity: 0.804 °
Crystal growTemperature: 287 K / Method: evaporation / pH: 5.4
Details: 0.1 M Sodium acetate, 1.5 M Sodium formate, 0.08 M CaCl2 and 10% PEG 3350

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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: 1.94→50 Å / Num. obs: 211626 / % possible obs: 96.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Χ2: 1.16 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.96-1.994.10.397104320.7160.2090.4520.51595.6
1.99-2.0340.378101900.7260.2020.4310.5493.8
2.03-2.0740.354101720.6860.1880.4030.57693.1
2.07-2.114.60.345105040.8340.1710.3870.65896.1
2.11-2.164.70.308104440.880.150.3440.62896.3
2.16-2.214.80.287105320.9060.1390.320.66196.5
2.21-2.264.90.275105530.9160.1320.3070.8396.4
2.26-2.324.80.249105190.9390.120.2780.77196.9
2.32-2.394.90.234106160.9450.1120.260.79897.4
2.39-2.474.90.211106270.9590.10.2340.88497.2
2.47-2.564.90.193106410.9610.0920.2150.93197.1
2.56-2.664.70.169102650.9670.0820.1891.05793.7
2.66-2.785.50.165106760.9760.0740.1821.10497.7
2.78-2.935.50.148106680.9790.0660.1631.17697.8
2.93-3.115.60.133106700.9840.0590.1461.35797.4
3.11-3.355.70.118107540.9890.0510.1291.64998
3.35-3.695.60.106108050.9910.0470.1161.88398.1
3.69-4.225.90.093106170.9930.040.1012.01996.5
4.22-5.326.50.084109830.9950.0350.0911.97499.2
5.32-506.30.076109580.9960.0320.0831.56897.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6j4n

6j4n


Resolution: 1.96→49.04 Å / Cor.coef. Fo:Fc: 0.523 / Cor.coef. Fo:Fc free: 0.434 / SU B: 18.309 / SU ML: 0.546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.5568 10778 5 %RANDOM
Rwork0.5186 ---
obs0.5205 204033 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.5 Å2 / Biso mean: 20.693 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.96→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 4 566 11914
Biso mean--38.19 14.2 -
Num. residues----1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01311690
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710380
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6415924
X-RAY DIFFRACTIONr_angle_other_deg1.1281.57723826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.48451436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71822.39636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.775151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3141567
X-RAY DIFFRACTIONr_chiral_restr0.0540.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022854
LS refinement shellResolution: 1.96→1.989 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.443 578 -
Rwork0.403 10842 -
obs--68.68 %

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