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- PDB-3kpd: Crystal Structure of the CBS domain pair of protein MJ0100 in com... -

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Basic information

Entry
Database: PDB / ID: 3kpd
TitleCrystal Structure of the CBS domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L-methionine.
ComponentsUncharacterized protein MJ0100
KeywordsUNKNOWN FUNCTION / CBS domain / s-adenosylmethionine / conformational change
Function / homology
Function and homology information


L-aspartate semialdehyde sulfurtransferase / methionine biosynthetic process / transferase activity
Similarity search - Function
Homocysteine biosynthesis enzyme, sulfur-incorporation / L-aspartate semialdehyde sulfurtransferase MA1821-like / Homocysteine biosynthesis enzyme, sulfur-incorporation / CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. ...Homocysteine biosynthesis enzyme, sulfur-incorporation / L-aspartate semialdehyde sulfurtransferase MA1821-like / Homocysteine biosynthesis enzyme, sulfur-incorporation / CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / S-ADENOSYLMETHIONINE / L-aspartate semialdehyde sulfurtransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsLucas, M. / Oyenarte, I. / Garcia, I.G. / Arribas, E.A. / Encinar, J.A. / Kortazar, D. / Fernandez, J.A. / Mato, J.M. / Martinez-Chantar, M.L. / Martinez-Cruz, L.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Binding of S-Methyl-5'-Thioadenosine and S-Adenosyl-l-Methionine to Protein MJ0100 Triggers an Open-to-Closed Conformational Change in Its CBS Motif Pair.
Authors: Lucas, M. / Encinar, J.A. / Arribas, E.A. / Oyenarte, I. / Garcia, I.G. / Kortazar, D. / Fernandez, J.A. / Mato, J.M. / Martinez-Chantar, M.L. / Martinez-Cruz, L.A.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0100
B: Uncharacterized protein MJ0100
C: Uncharacterized protein MJ0100
D: Uncharacterized protein MJ0100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,42711
Polymers54,1434
Non-polymers2,2847
Water0
1
A: Uncharacterized protein MJ0100
hetero molecules

A: Uncharacterized protein MJ0100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2616
Polymers27,0722
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area4280 Å2
ΔGint-20 kcal/mol
Surface area12360 Å2
MethodPISA
2
B: Uncharacterized protein MJ0100
C: Uncharacterized protein MJ0100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1665
Polymers27,0722
Non-polymers1,0943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area11330 Å2
MethodPISA
3
D: Uncharacterized protein MJ0100
hetero molecules

D: Uncharacterized protein MJ0100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2616
Polymers27,0722
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4250 Å2
ΔGint-13 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.671, 165.794, 122.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Uncharacterized protein MJ0100


Mass: 13535.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0100 / Plasmid: pET101D / Production host: Escherichia coli (E. coli) / References: UniProt: Q57564
#2: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 10% PEG 6000, 0.1 M TRIS pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorDate: Sep 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. all: 13555 / Num. obs: 12845

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.827 / Highest resolution: 2.91 Å / SU B: 21.163 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3343 670 5 %RANDOM
Rwork0.2341 ---
obs0.2388 12845 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.955 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å20 Å2
2---4.08 Å20 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Highest resolution: 2.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 154 0 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6072.0065400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97625144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.09615720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5731516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212785
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.52407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26523963
X-RAY DIFFRACTIONr_scbond_it1.56231558
X-RAY DIFFRACTIONr_scangle_it2.8024.51433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.909→2.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 41 -
Rwork0.251 888 -
obs--95.18 %

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