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- PDB-3q4n: Crystal structure of hypothetical protein MJ0754 from Methanococc... -

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Basic information

Entry
Database: PDB / ID: 3q4n
TitleCrystal structure of hypothetical protein MJ0754 from Methanococcus jannaschii DSM 2661
ComponentsUncharacterized protein MJ0754
KeywordsUNKNOWN FUNCTION / ferritin-like protein / four-helix bundle / metal binding / dinuclear center
Function / homologyDomain of unknown function DUF2202 / Uncharacterized protein domain (DUF2202) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / Uncharacterized protein MJ0754
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Proteins / Year: 2011
Title: Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii.
Authors: Lee, E.H. / Kim, H.S. / Kim, H.Y. / Jeon, Y.H. / Hwang, K.Y.
History
DepositionDec 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MJ0754
B: Uncharacterized protein MJ0754


Theoretical massNumber of molelcules
Total (without water)45,7322
Polymers45,7322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.015, 127.015, 48.929
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Uncharacterized protein MJ0754


Mass: 22865.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0754 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58164

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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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris, 22% PEG 3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 20, 2008
RadiationMonochromator: TCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 9543 / % possible obs: 91.8 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.88-2.982.30.413504150.2
2.98-3.13.60.406769173.7
3.1-3.245.80.392961193.4
3.24-3.4190.3661016199.5
3.41-3.63120.3131033199.7
3.63-3.9114.90.25110321100
3.91-4.317.20.19110331100
4.3-4.9218.70.1371053199.9
4.92-6.218.50.1341052199.9
6.2-5019.40.111090199.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.88→31.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.195 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 454 4.8 %RANDOM
Rwork0.2037 ---
obs0.2064 9511 91.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 75.9443 Å2 / Biso min: 51.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.88→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 0 0 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222890
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9753887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.98726.107149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.9515574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6241510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212156
X-RAY DIFFRACTIONr_mcbond_it0.521.51717
X-RAY DIFFRACTIONr_mcangle_it1.02722784
X-RAY DIFFRACTIONr_scbond_it1.50631173
X-RAY DIFFRACTIONr_scangle_it2.6344.51103
LS refinement shellResolution: 2.884→2.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 17 -
Rwork0.277 321 -
all-338 -
obs--45.37 %

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