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- PDB-6jkw: Seleno-methionine PNGM-1 from deep-sea sediment metagenome -

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Entry
Database: PDB / ID: 6jkw
TitleSeleno-methionine PNGM-1 from deep-sea sediment metagenome
ComponentsMetallo-beta-lactamases PNGM-1
KeywordsTRANSFERASE / MBLs / Zinc binding motif / antibiotic resistance / metagenome / Structural Genomics / PSI-Biology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å
AuthorsHong, M.K. / Park, K.S. / Jeon, J.H. / Lee, J.H. / Park, Y.S. / Lee, S.H. / Kang, L.W.
CitationJournal: Journal of Global Antimicrobial Resistance / Year: 2018
Title: PNGM 1 a novel subclass B3 metallo beta lactamase from a deep sea sediment metagenome
Authors: Kang, L.W. / Lee, S.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 2, 2019 / Release: Apr 17, 2019
RevisionDateData content typeProviderType
1.0Apr 17, 2019Structure modelrepositoryInitial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamases PNGM-1
B: Metallo-beta-lactamases PNGM-1
C: Metallo-beta-lactamases PNGM-1
D: Metallo-beta-lactamases PNGM-1
E: Metallo-beta-lactamases PNGM-1
F: Metallo-beta-lactamases PNGM-1
G: Metallo-beta-lactamases PNGM-1
H: Metallo-beta-lactamases PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,03624
Polymers339,9908
Non-polymers1,04716
Water7,746430
1
A: Metallo-beta-lactamases PNGM-1
D: Metallo-beta-lactamases PNGM-1
F: Metallo-beta-lactamases PNGM-1
G: Metallo-beta-lactamases PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,51812
Polymers169,9954
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28900 Å2
ΔGint-463 kcal/mol
Surface area47440 Å2
MethodPISA
2
B: Metallo-beta-lactamases PNGM-1
C: Metallo-beta-lactamases PNGM-1
E: Metallo-beta-lactamases PNGM-1
H: Metallo-beta-lactamases PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,51812
Polymers169,9954
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28910 Å2
ΔGint-466 kcal/mol
Surface area47430 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)121.857, 83.124, 162.833
Angle α, β, γ (deg.)90.000, 110.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Metallo-beta-lactamases PNGM-1


Mass: 42498.727 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Zinc
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7 / Details: 0.1M Tris-HCl, 0.2M MgCl2 and 10% PEG 8000

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Data collection

DiffractionMean temperature: 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: 2.29→34.93 Å / Num. obs: 137843 / % possible obs: 98.1 % / Redundancy: 3.8 % / Net I/σ(I): 4.7
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.29→34.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.994 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.278
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 6795 5 %RANDOM
Rwork0.2111 ---
Obs0.2143 128348 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.57 Å2 / Biso mean: 32.866 Å2 / Biso min: 7.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.07 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.29→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23464 0 16 430 23910
Biso mean--31.36 26.16 -
Num. residues----2976
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0160.01924152
r_bond_other_d0.0010.0221648
r_angle_refined_deg1.7251.93632920
r_angle_other_deg0.874349664
r_dihedral_angle_1_deg7.47852968
r_dihedral_angle_2_deg37.3223.81200
r_dihedral_angle_3_deg17.156153208
r_dihedral_angle_4_deg19.70415152
r_chiral_restr0.10.23400
r_gen_planes_refined0.0080.02128048
r_gen_planes_other0.0010.025960
LS refinement shellResolution: 2.285→2.344 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 423 -
Rwork0.274 7949 -
All-8372 -
Obs--82.18 %

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