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- PDB-6h1w: Crystal Structure of protein MJ1004 from Mathanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 6h1w
TitleCrystal Structure of protein MJ1004 from Mathanocaldococcus jannaschii
ComponentsMJ1004
KeywordsUNKNOWN FUNCTION / CBS domain / DUF / Bateman module / Q58410
Function / homology
Function and homology information


Uncharacterised conserved protein UCP006591, MJ1004 type / : / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MJ1004
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.394 Å
AuthorsAlfonso Martinez-Cruz, L. / Oyenarte, I. / Fernandez-Rodriguez, C.
Funding support Spain, 6items
OrganizationGrant numberCountry
PI2010-17 Spain
ETORTEK IE05-147, IE07-202 Spain
Exp. 7/13/08/2006/11 Spain
Exp. 7/13/08/2005/14 Spain
MICINN BFU2010-17857 Spain
CSD2008-00005 Spain
CitationJournal: To Be Published
Title: Crystal Structure of protein MJ1004 from Mathanocaldococcus jannaschii
Authors: Alfonso Martinez-Cruz, L. / Oyenarte, I. / Fernandez-Rodriguez, C.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MJ1004
B: MJ1004


Theoretical massNumber of molelcules
Total (without water)49,9092
Polymers49,9092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-48 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.899, 80.899, 178.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MJ1004


Mass: 24954.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: MJ1004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58410
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES pH=7.5 25% Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.394→89.475 Å / Num. obs: 24118 / % possible obs: 99.5 % / Redundancy: 27.1 % / Biso Wilson estimate: 55.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.019 / Rrim(I) all: 0.098 / Net I/σ(I): 25.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.394-2.438201.43812000.650.3191.47595.5
6.695-89.47521.80.06911840.9970.0150.07194.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.394→35.24 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.98
RfactorNum. reflection% reflection
Rfree0.2499 1998 8.3 %
Rwork0.2271 --
obs0.229 24084 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 63.3197 Å2 / Biso min: 31.68 Å2
Refinement stepCycle: final / Resolution: 2.394→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 0 0 3284
Num. residues----415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023340
X-RAY DIFFRACTIONf_angle_d0.4414507
X-RAY DIFFRACTIONf_chiral_restr0.04531
X-RAY DIFFRACTIONf_plane_restr0.003556
X-RAY DIFFRACTIONf_dihedral_angle_d14.4862039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3944-2.45430.37311360.34031498163497
2.4543-2.52060.3451400.307215521692100
2.5206-2.59470.32121400.289515451685100
2.5947-2.67850.31941400.280815501690100
2.6785-2.77420.29941410.295315571698100
2.7742-2.88520.33991420.292315651707100
2.8852-3.01640.30361420.293415731715100
3.0164-3.17540.29361420.277215681710100
3.1754-3.37420.29071420.284715831725100
3.3742-3.63440.24321430.244615721715100
3.6344-3.99970.21561440.208715921736100
3.9997-4.57740.21441450.183416151760100
4.5774-5.7630.21490.177316411790100
5.763-35.24410.23841520.1961675182796

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