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- PDB-7wi1: The mutant variant of PNGM-1, H93 was substituuted for alanine to... -

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Basic information

Entry
Database: PDB / ID: 7wi1
TitleThe mutant variant of PNGM-1, H93 was substituuted for alanine to study metal coordination
ComponentsMetallo-beta-lactamase PNGM-1
KeywordsHYDROLASE / RNase Z / MBLs / Zinc binding motif / ANTIBIOTIC
Function / homologyBeta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / beta-lactamase / Metallo-beta-lactamase PNGM-1
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
Model detailsPNGM-1 residue H91 was substituted to Alanine
AuthorsPark, Y.S. / Kang, L.W. / Lee, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionJan 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model / struct
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 / _struct.title

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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
G: Metallo-beta-lactamase PNGM-1
C: Metallo-beta-lactamase PNGM-1
E: Metallo-beta-lactamase PNGM-1
D: Metallo-beta-lactamase PNGM-1
F: Metallo-beta-lactamase PNGM-1
B: Metallo-beta-lactamase PNGM-1
H: Metallo-beta-lactamase PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,59916
Polymers333,0768
Non-polymers5238
Water19,9971110
1
A: Metallo-beta-lactamase PNGM-1
C: Metallo-beta-lactamase PNGM-1
D: Metallo-beta-lactamase PNGM-1
B: Metallo-beta-lactamase PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7998
Polymers166,5384
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28060 Å2
ΔGint-303 kcal/mol
Surface area47440 Å2
MethodPISA
2
G: Metallo-beta-lactamase PNGM-1
E: Metallo-beta-lactamase PNGM-1
F: Metallo-beta-lactamase PNGM-1
H: Metallo-beta-lactamase PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7998
Polymers166,5384
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28120 Å2
ΔGint-304 kcal/mol
Surface area47540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.755, 82.792, 164.047
Angle α, β, γ (deg.)90.000, 111.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41634.453 Da / Num. of mol.: 8 / Mutation: H93A
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 / Water


Mass: 18.015 Da / Num. of mol.: 1110 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.1
Details: 50 mM HEPES pH 7.1, 10% PEG 4000, 150 mM Magnesium acetate, 200 mM Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: steady flow of liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 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: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 388155 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 1.477 / Net I/σ(I): 8.6 / Num. measured all: 2483252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.61-1.6460.31190480.960.1350.3390.55797.5
1.64-1.675.90.275190890.9680.1220.3020.56897.9
1.67-1.75.80.255190710.9690.1130.280.58598.1
1.7-1.735.60.228191160.9740.1050.2520.62997.9
1.73-1.775.50.203191480.9770.0940.2250.67898.1
1.77-1.815.80.182192240.9820.0810.20.72698.6
1.81-1.8660.168192360.9850.0740.1840.77898.8
1.86-1.916.60.152193920.9880.0630.1650.85599.1
1.91-1.976.70.133194450.990.0550.1440.9999.4
1.97-2.036.70.122193590.9920.050.1321.10199.3
2.03-2.16.70.113194600.9930.0470.1221.21699.5
2.1-2.196.70.104194800.9940.0430.1131.35999.6
2.19-2.286.70.096195010.9950.040.1041.5499.7
2.28-2.46.80.094195060.9940.0390.1011.64399.8
2.4-2.566.90.088195620.9940.0360.0951.83699.8
2.56-2.756.70.082196380.9950.0350.0892.04999.9
2.75-3.036.20.078195560.9950.0350.0862.34599.9
3.03-3.4760.068195550.9950.0310.0752.80499.3
3.47-4.377.30.063197630.9970.0250.0683.058100
4.37-507.30.062200060.9970.0250.0673.04899.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
DENZOdata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6j4n

6j4n


Resolution: 1.61→41.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.688 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 19534 5 %RANDOM
Rwork0.1963 ---
obs0.1977 368596 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.02 Å2 / Biso mean: 13.337 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.61→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23424 0 8 1110 24542
Biso mean--9.31 17.02 -
Num. residues----2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01324104
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521455
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.64132856
X-RAY DIFFRACTIONr_angle_other_deg1.5191.57849270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68352968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92322.2621344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.959153608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.45115152
X-RAY DIFFRACTIONr_chiral_restr0.0920.23048
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0228000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025911
LS refinement shellResolution: 1.611→1.653 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 1373 -
Rwork0.207 26425 -
all-27798 -
obs--96.02 %

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