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- PDB-7bz1: The mutant variant of PNGM-1. H96 was substituted for alanine to ... -

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Basic information

Entry
Database: PDB / ID: 7bz1
TitleThe mutant variant of PNGM-1. H96 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Metallo-beta-lactamase PNGM-1
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Nov 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)164,3938
Polymers164,1314
Non-polymers2624
Water5,549308
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 area26570 Å2
ΔGint-297 kcal/mol
Surface area47540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.638, 82.545, 163.716
Angle α, β, γ (deg.)90.000, 110.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41032.785 Da / Num. of mol.: 4 / Mutation: H96A
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.: 308 / 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: 2.31 Å3/Da / Density % sol: 46.69 % / Mosaicity: 1.995 °
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: 2.44→50 Å / Num. obs: 50546 / % possible obs: 90.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.06 / Rrim(I) all: 0.139 / Χ2: 1.611 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.46-2.550.41425360.8970.2020.4630.80792.6
2.5-2.555.10.40625030.9130.1960.4530.76490.2
2.55-2.65.10.34125410.9370.1670.3810.90591.5
2.6-2.655.10.31725460.940.1540.3550.94492
2.65-2.7150.30525580.9350.1510.3420.97492.6
2.71-2.7750.28225080.9410.1390.3160.9990.8
2.77-2.8450.25925550.9540.1280.291.02191.1
2.84-2.924.70.23124760.9530.1190.2611.17590.7
2.92-34.70.20122920.9620.1030.2281.28182.6
3-3.15.20.17525130.9740.0840.1961.3790.9
3.1-3.215.20.15525750.9780.0750.1731.5590.8
3.21-3.345.20.13725030.9820.0660.1531.75991.4
3.34-3.495.20.12525420.9850.060.1391.89691.3
3.49-3.675.20.11425350.9860.0550.1272.00290.8
3.67-3.95.10.10325290.9880.050.1152.17490.7
3.9-4.214.80.09525150.9880.0470.1062.3190.6
4.21-4.634.90.08524200.9920.0410.0952.37285.9
4.63-5.35.20.08526000.9920.040.0952.29392.6
5.3-6.675.10.08626080.9890.0410.0962.07792.9
6.67-505.10.08926910.9920.0420.0993.32493.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6j4n

6j4n


Resolution: 2.45→48.08 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.633 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.102 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 2485 4.9 %RANDOM
Rwork0.1862 ---
obs0.1898 48014 89.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.17 Å2 / Biso mean: 28.766 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.45→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11537 0 4 308 11849
Biso mean--26.08 23 -
Num. residues----1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311877
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710308
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.64116195
X-RAY DIFFRACTIONr_angle_other_deg1.2681.57323855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.61751456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90822.239670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.507151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7731576
X-RAY DIFFRACTIONr_chiral_restr0.070.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022684
LS refinement shellResolution: 2.45→2.511 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.34 188 -
Rwork0.247 3202 -
obs--82.84 %

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