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- PDB-1w2w: Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphat... -

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Basic information

Entry
Database: PDB / ID: 1w2w
TitleCrystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits
Components(5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE) x 2
KeywordsISOMERASE / EIF2B / METHIONINE SALVAGE PATHWAY / TRANSLATION INITIATION / OXIDOREDUCTASE
Function / homology
Function and homology information


Methionine salvage pathway / S-methyl-5-thioribose-1-phosphate isomerase / S-methyl-5-thioribose-1-phosphate isomerase activity / L-methionine salvage from methylthioadenosine / nucleus / cytoplasm
Similarity search - Function
Methylthioribose-1-phosphate isomerase / Initiation factor 2B alpha/beta/delta / translation initiation factor eif-2b, domain 1 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / 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 / Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eif-2b; domain 2 / 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 speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsBumann, M. / Djafarzadeh, S. / Oberholzer, A.E. / Bigler, P. / Altmann, M. / Trachsel, H. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Yeast Ypr118W, a Methylthioribose-1-Phosphate Isomerase Related to Regulatory Eif2B Subunits
Authors: Bumann, M. / Djafarzadeh, S. / Oberholzer, A.E. / Bigler, P. / Altmann, M. / Trachsel, H. / Baumann, U.
History
DepositionJul 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD, FD" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD, FD" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 4-STRANDED BARRELS WHICH ARE REPRESENTED BY 5-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
B: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
E: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
F: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
I: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
J: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
M: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
N: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,92312
Polymers177,5398
Non-polymers3844
Water16,610922
1
A: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
B: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
M: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
N: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9626
Polymers88,7704
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
F: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
I: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
J: 5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9626
Polymers88,7704
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.620, 105.450, 263.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
31I
12B
22F
32J
42N

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSELYSLYSAA1 - 2111 - 211
21MSEMSELYSLYSEC1 - 2111 - 211
31MSEMSELYSLYSIE1 - 2111 - 211
12CYSCYSPHEPHEBB221 - 4111 - 191
22CYSCYSPHEPHEFD221 - 4111 - 191
32CYSCYSPHEPHEJF221 - 4111 - 191
42CYSCYSPHEPHENH221 - 4111 - 191

NCS ensembles :
ID
1
2

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Components

#1: Protein
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE


Mass: 23353.072 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q06489, S-methyl-5-thioribose-1-phosphate isomerase
#2: Protein
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE


Mass: 21031.689 Da / Num. of mol.: 4 / Fragment: RESIDUES 221-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q06489, S-methyl-5-thioribose-1-phosphate isomerase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 922 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K
Details: 0.2 M AMMONIUM SULPHATE, 25 % PEG3350, 0.1 M BISTRIS, PH 5.5, 20 DEG C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9879
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 169966 / % possible obs: 99.6 % / Observed criterion σ(I): 4.1 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 1.75→1.87 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.977 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2208 1.3 %RANDOM
Rwork0.174 ---
obs0.174 167734 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12408 0 20 922 13350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.97217186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22151599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.22063
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.26264
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2841
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4660.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9883.58003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.515313060
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10244637
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3315.54126
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1625loose positional0.365
12E1625loose positional0.265
13I1625loose positional0.395
21B1479loose positional0.345
22F1479loose positional0.285
23J1479loose positional0.375
24N1479loose positional0.315
11A1625loose thermal1.9310
12E1625loose thermal1.8210
13I1625loose thermal2.8510
21B1479loose thermal5.0710
22F1479loose thermal3.4610
23J1479loose thermal4.610
24N1479loose thermal3.8910
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 150
Rwork0.24 11969
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67271.18036.53254.73420.54189.3868-0.17160.5159-0.2156-0.21460.1887-0.3844-0.06160.622-0.0170.1222-0.012-0.01690.1313-0.04450.142825.247633.847527.2311
25.2956-8.71810.93048.405-1.78484.2237-0.20230.0019-0.83320.20060.03430.69310.3069-0.35990.16790.1193-0.0020.02490.0629-0.0570.231433.96431.7932-17.4689
31.0362-0.19360.06230.96580.16830.72980.00070.11130.04-0.0838-0.01440.0054-0.0585-0.00060.01380.0208-0.0068-0.00120.0181-0.00760.00416.99670.3983-18.5347
41.2145-0.22860.56151.12840.08471.2453-0.0248-0.06-0.01230.18850.0216-0.06910.0221-0.01960.00320.09690.0154-0.01390.0786-0.00620.031752.307145.944763.8326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION1B22 - 41
3X-RAY DIFFRACTION2E1 - 21
4X-RAY DIFFRACTION2F22 - 41
5X-RAY DIFFRACTION3I1 - 21
6X-RAY DIFFRACTION3J22 - 411
7X-RAY DIFFRACTION4M2 - 21
8X-RAY DIFFRACTION4N22 - 411

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