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- PDB-1t9k: X-ray crystal structure of aIF-2B alpha subunit-related translati... -

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Basic information

Entry
Database: PDB / ID: 1t9k
TitleX-ray crystal structure of aIF-2B alpha subunit-related translation initiation factor [Thermotoga maritima]
ComponentsProbable methylthioribose-1-phosphate isomerase
KeywordsISOMERASE / structural genomics / translation initiation factor / aIF-2B subunit / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


S-methyl-5-thioribose-1-phosphate isomerase / S-methyl-5-thioribose-1-phosphate isomerase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine
Similarity search - Function
Methylthioribose-1-phosphate isomerase / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Translation initiation factor eif-2b; domain 2 / Methylthioribose-1-phosphate isomerase, N-terminal / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Methylthioribose-1-phosphate isomerase / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Translation initiation factor eif-2b; domain 2 / Methylthioribose-1-phosphate isomerase, N-terminal / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methylthioribose-1-phosphate isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsOsipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of aIF-2B translation initiation factor from Thermotoga maritima
Authors: Osipiuk, J. / Skarina, T. / Savchenko, A. / Edwards, A. / Cymborowski, M. / Minor, W. / Joachimiak, A.
History
DepositionMay 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable methylthioribose-1-phosphate isomerase
B: Probable methylthioribose-1-phosphate isomerase
C: Probable methylthioribose-1-phosphate isomerase
D: Probable methylthioribose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,89210
Polymers155,4374
Non-polymers4556
Water3,567198
1
A: Probable methylthioribose-1-phosphate isomerase
B: Probable methylthioribose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9826
Polymers77,7192
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-91 kcal/mol
Surface area25330 Å2
MethodPISA
2
C: Probable methylthioribose-1-phosphate isomerase
D: Probable methylthioribose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9114
Polymers77,7192
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-79 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.885, 103.885, 259.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is unknown. There are 4 protomers in the assymetric unit. Two chains missing from this deposition file are generated by noncrystallographic symmetry. ncs_matrix=( 0.49986 0.86611 0.00066 ) ( 0.86611 -0.49986 0.00008 ) ( 0.00040 0.00053 -1.00000 ); ncs_vector=(-52.00523 89.95369 216.56924);

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Components

#1: Protein
Probable methylthioribose-1-phosphate isomerase / MTR-1-P isomerase


Mass: 38859.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: MTNA, TM0911 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X013, S-methyl-5-thioribose-1-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
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: 2.664 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Lithium Sulfate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: SBC-2 / Detector: CCD / Date: Oct 17, 2003
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 96655 / Num. obs: 96655 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 27.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 5.28 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→34.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1338418.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 4627 4.9 %RANDOM
Rwork0.239 ---
obs0.239 93958 97.4 %-
all-96437 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0153 Å2 / ksol: 0.328025 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å24.87 Å20 Å2
2--4.33 Å20 Å2
3----9.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10634 0 22 198 10854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 773 5.2 %
Rwork0.311 14069 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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