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- PDB-8dot: Structure of a methane clathrate binding protein -

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Basic information

Entry
Database: PDB / ID: 8dot
TitleStructure of a methane clathrate binding protein
Componentsmethane clathrate binding protein
KeywordsANTIFREEZE PROTEIN / methane / clathrate / subsurface / metagenome
Function / homologyStreptococcal non-M secreted SibA / cytoskeleton / Uncharacterized protein
Function and homology information
Biological speciesmarine sediment metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsHuard, D.J.E. / Lieberman, R.L. / Glass, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)80NSSC19K0477 United States
CitationJournal: Pnas Nexus / Year: 2023
Title: Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.
Authors: Huard, D.J.E. / Johnson, A.M. / Fan, Z. / Kenney, L.G. / Xu, M. / Drori, R. / Gumbart, J.C. / Dai, S. / Lieberman, R.L. / Glass, J.B.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methane clathrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3772
Polymers47,1831
Non-polymers1941
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.050, 79.050, 109.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein methane clathrate binding protein


Mass: 47183.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine sediment metagenome (others) / Gene: S12H4_00347 / Production host: Escherichia coli (E. coli) / References: UniProt: X1QJA1
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
Has ligand of interestN

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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: 1.81 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.16 M sodium acetate trihydrate, 7.5% PEG 8,000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→39.05 Å / Num. obs: 7012 / % possible obs: 99.72 % / Redundancy: 25 % / Biso Wilson estimate: 76.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.17
Reflection shellResolution: 3.05→3.159 Å / Mean I/σ(I) obs: 7.27 / Num. unique obs: 675 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 3.05→39.05 Å / SU ML: 0.4425 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 1243 9.91 %
Rwork0.1915 11303 -
obs0.1955 7012 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.12 Å2
Refinement stepCycle: LAST / Resolution: 3.05→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 13 0 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891334
X-RAY DIFFRACTIONf_angle_d1.12561809
X-RAY DIFFRACTIONf_chiral_restr0.0576204
X-RAY DIFFRACTIONf_plane_restr0.0109237
X-RAY DIFFRACTIONf_dihedral_angle_d18.0528486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.170.37281380.32081230X-RAY DIFFRACTION99.56
3.17-3.320.37771410.25741266X-RAY DIFFRACTION99.93
3.32-3.490.26591390.24681252X-RAY DIFFRACTION99.43
3.49-3.710.25021410.21331255X-RAY DIFFRACTION99.93
3.71-40.24671410.21261262X-RAY DIFFRACTION99.86
4-4.390.28751410.18211245X-RAY DIFFRACTION99.86
4.4-5.030.20341350.17161269X-RAY DIFFRACTION100
5.03-6.330.20871340.20851252X-RAY DIFFRACTION99.78
6.34-39.050.14841330.13161272X-RAY DIFFRACTION99.86

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