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- PDB-4ldq: Crystal Structure of the Mediator of Rho Dependent Invasion -

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Basic information

Entry
Database: PDB / ID: 4ldq
TitleCrystal Structure of the Mediator of Rho Dependent Invasion
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 / MOLECULAR REPLACEMENT / Resolution: 2.496 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 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)78,3892
Polymers78,3892
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-39 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.785, 116.591, 136.867
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: 39194.691 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.28 Å3/Da / Density % sol: 46.03 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.496→88.754 Å / Num. all: 25738 / Num. obs: 25486
Reflection shellHighest resolution: 2.496 Å

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.496→26.817 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2114 1296 5.09 %RANDOM
Rwork0.1785 ---
obs0.1801 25482 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.496→26.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 0 162 5444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065362
X-RAY DIFFRACTIONf_angle_d1.0587289
X-RAY DIFFRACTIONf_dihedral_angle_d17.5321947
X-RAY DIFFRACTIONf_chiral_restr0.055872
X-RAY DIFFRACTIONf_plane_restr0.006953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.496-2.59580.25581300.19582574X-RAY DIFFRACTION97
2.5958-2.71390.25021690.20582612X-RAY DIFFRACTION99
2.7139-2.85680.2751270.20232646X-RAY DIFFRACTION99
2.8568-3.03550.23571360.20492686X-RAY DIFFRACTION100
3.0355-3.26950.24161480.20482675X-RAY DIFFRACTION100
3.2695-3.59790.20211330.1872688X-RAY DIFFRACTION100
3.5979-4.11690.1941460.16572718X-RAY DIFFRACTION100
4.1169-5.18070.17691420.14492740X-RAY DIFFRACTION100
5.1807-26.81810.19281650.17262847X-RAY DIFFRACTION99

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