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- PDB-2efv: Crystal Structure of a Hypothetical Protein(MJ0366) from Methanoc... -

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Basic information

Entry
Database: PDB / ID: 2efv
TitleCrystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus jannaschii
ComponentsHypothetical protein MJ0366Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical Protein / Methanocaldococcus jannaschii DSM 2661 / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Uncharacterised protein PF10802, DUF2540 / MJ0366-like / Protein of unknown function (DUF2540) / Ribbon-helix-helix / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein MJ0366
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold
Authors: Thiruselvam, V. / Kumarevel, T. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / Ponnuswamy, M.N.
History
DepositionFeb 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MJ0366
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9692
Polymers10,8741
Non-polymers951
Water1,22568
1
A: Hypothetical protein MJ0366
hetero molecules

A: Hypothetical protein MJ0366
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9374
Polymers21,7472
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)78.846, 78.846, 35.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Hypothetical protein MJ0366 / Hypothesis


Mass: 10873.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Species: Methanocaldococcus jannaschii / Strain: DSM2661 / Gene: mj0366 / Plasmid: pET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codonplus-RIL-X / References: UniProt: Q57812
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.97 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5
Details: 2% PEG400, 2M Ammonium Sulfate, 0.1M HEPES pH7.5, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97884, 0.9000, 0.97973
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 16, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.91
30.979731
ReflectionResolution: 1.9→50 Å / Num. obs: 16670 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.4 / Num. unique all: 894 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 306925.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.231 498 3.1 %RANDOM
Rwork0.219 ---
obs0.219 16177 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.4893 Å2 / ksol: 0.398351 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2---3.66 Å20 Å2
3---7.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 5 68 762
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.682.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 87 3.4 %
Rwork0.268 2438 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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