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- PDB-4ldr: Structure of the S283Y mutant of MRDI -

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Basic information

Entry
Database: PDB / ID: 4ldr
TitleStructure of the S283Y mutant of MRDI
ComponentsMethylthioribose-1-phosphate isomerase
KeywordsISOMERASE / CELL INVASION / Helix bundle / Rossmann-like fold
Function / homology
Function and homology information


S-methyl-5-thioribose-1-phosphate isomerase / S-methyl-5-thioribose-1-phosphate isomerase activity / Methionine salvage pathway / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / cell projection / fibrillar center / nucleoplasm / identical protein binding / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.292 Å
AuthorsSousa, M.C. / Templeton, P.D. / Metzner, S.I.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of Mediator of RhoA-Dependent Invasion (MRDI) Explains Its Dual Function as a Metabolic Enzyme and a Mediator of Cell Invasion.
Authors: Templeton, P.D. / Litman, E.S. / Metzner, S.I. / Ahn, N.G. / Sousa, M.C.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylthioribose-1-phosphate isomerase
B: Methylthioribose-1-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)78,5422
Polymers78,5422
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-39 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.518, 115.970, 135.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methylthioribose-1-phosphate isomerase / MRDI / M1Pi / MTR-1-P isomerase / Mediator of RhoA-dependent invasion / S-methyl-5-thioribose-1- ...MRDI / M1Pi / MTR-1-P isomerase / Mediator of RhoA-dependent invasion / S-methyl-5-thioribose-1-phosphate isomerase / Translation initiation factor eIF-2B subunit alpha/beta/delta-like protein


Mass: 39270.785 Da / Num. of mol.: 2 / Mutation: S283Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRI1, MRDI, UNQ6390/PRO21135
References: UniProt: Q9BV20, S-methyl-5-thioribose-1-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.76 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.292→88.107 Å / Num. all: 32430 / Num. obs: 32107
Reflection shellHighest resolution: 2.292 Å

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.292→44.053 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 20.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 1629 5.07 %
Rwork0.1799 --
obs0.1813 32101 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.292→44.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 0 313 5607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055376
X-RAY DIFFRACTIONf_angle_d0.9587309
X-RAY DIFFRACTIONf_dihedral_angle_d15.1281951
X-RAY DIFFRACTIONf_chiral_restr0.048872
X-RAY DIFFRACTIONf_plane_restr0.005955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.292-2.35890.2561250.20582364X-RAY DIFFRACTION93
2.3589-2.43510.22031340.1922491X-RAY DIFFRACTION99
2.4351-2.52210.26061410.19872502X-RAY DIFFRACTION99
2.5221-2.62310.25161430.1972503X-RAY DIFFRACTION99
2.6231-2.74240.23991170.17722522X-RAY DIFFRACTION100
2.7424-2.8870.23021310.18882515X-RAY DIFFRACTION99
2.887-3.06780.20411380.19392527X-RAY DIFFRACTION99
3.0678-3.30460.22471530.18262521X-RAY DIFFRACTION99
3.3046-3.6370.20771460.16992551X-RAY DIFFRACTION100
3.637-4.1630.19381100.16042609X-RAY DIFFRACTION100
4.163-5.24350.16221540.15322599X-RAY DIFFRACTION100
5.2435-44.06140.20921370.20282768X-RAY DIFFRACTION100

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