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- PDB-3r90: Crystal structure of Malignant T cell-amplified sequence 1 protein -

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Basic information

Entry
Database: PDB / ID: 3r90
TitleCrystal structure of Malignant T cell-amplified sequence 1 protein
ComponentsMalignant T cell-amplified sequence 1
KeywordsRNA BINDING PROTEIN / structural genomics consortium / surface entropy reduction / SGC
Function / homology
Function and homology information


IRES-dependent viral translational initiation / formation of translation preinitiation complex / ribosome disassembly / translation initiation factor activity / cell cycle / DNA damage response / positive regulation of cell population proliferation / RNA binding / cytoplasm
Similarity search - Function
Sulfate adenylyltransferase - #20 / MCT-1/Tma20 / Pre-PUA domain / Pre-PUA-like domain / Sulfate adenylyltransferase / Uncharacterised domain CHP00451 / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. ...Sulfate adenylyltransferase - #20 / MCT-1/Tma20 / Pre-PUA domain / Pre-PUA-like domain / Sulfate adenylyltransferase / Uncharacterised domain CHP00451 / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Malignant T-cell-amplified sequence 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHong, B. / Dimov, S. / Tempel, W. / Tong, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
Citation
Journal: to be published
Title: Crystal structure of Malignant T cell-amplified sequence 1 protein
Authors: Hong, B. / Dimov, S. / Tempel, W. / Tong, Y. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Protein crystallization by surface entropy reduction: optimization of the SER strategy.
Authors: Cooper, D.R. / Boczek, T. / Grelewska, K. / Pinkowska, M. / Sikorska, M. / Zawadzki, M. / Derewenda, Z.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Malignant T cell-amplified sequence 1
B: Malignant T cell-amplified sequence 1
C: Malignant T cell-amplified sequence 1
D: Malignant T cell-amplified sequence 1
E: Malignant T cell-amplified sequence 1
F: Malignant T cell-amplified sequence 1
G: Malignant T cell-amplified sequence 1
H: Malignant T cell-amplified sequence 1
I: Malignant T cell-amplified sequence 1
J: Malignant T cell-amplified sequence 1
K: Malignant T cell-amplified sequence 1
L: Malignant T cell-amplified sequence 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,239212
Polymers255,74512
Non-polymers2,494200
Water24,7531374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33300 Å2
ΔGint-552 kcal/mol
Surface area85590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.590, 115.590, 157.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsAS PER AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein
Malignant T cell-amplified sequence 1 / MCT-1 / Multiple copies T-cell malignancies


Mass: 21312.076 Da / Num. of mol.: 12 / Mutation: E137A, K139A, Q140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCTS1, MCT1 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULC4
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 174 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1374 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.449
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion72.5M ammonium sulfate, 0.1M Bis-Tris propane, pH 7, VAPOR DIFFUSION, temperature 293K
2932vapor diffusion7Se-Met derivative. 2.5M ammonium sulfate, 0.1M Bis-Tris propane, 2% PEG-3350, pH 7, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97901
SYNCHROTRONAPS 23-ID-D20.97944
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 25, 2011
MARMOSAIC 300 mm CCD2CCDMar 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979441
ReflectionResolution: 1.7→40 Å / Num. obs: 259245 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.989 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.8691.910756519130100
1.74-1.790.7182.310550218723100
1.79-1.840.5463.110285318224100
1.84-1.90.4343.89995217672100
1.9-1.960.3195.29722517170100
1.96-2.030.2297.39364216527100
2.03-2.110.189.19084816004100
2.11-2.190.14910.98727815374100
2.19-2.290.1312.38390714740100
2.29-2.40.1114.28020414108100
2.4-2.530.09715.97631113391100
2.53-2.690.08617.67266512749100
2.69-2.870.07419.86777511900100
2.87-3.10.05824.66278011063100
3.1-3.40.0528.4575231024199.9
3.4-3.80.04432.250656913799.8
3.8-4.390.04134.544470812699.6
4.39-5.380.0435.838201683999.4
5.38-7.60.04134.629919528599.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
XDSdata reduction
SCALEPACKdata scaling
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY STRUCTURE WAS SOLVED WITH SELENOMETHIONYL DERIVATIVE (RADIATION WAVELENGTH 0.97944A) IN PRIMITIVE TRICLINIC ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY STRUCTURE WAS SOLVED WITH SELENOMETHIONYL DERIVATIVE (RADIATION WAVELENGTH 0.97944A) IN PRIMITIVE TRICLINIC CRYSTAL FORM (A=78.58,B=87.17,92.19,ALPHA=80.36,BETA=85.03,GAMMA=89.12). ORIGINAL MODEL WAS GENERATED BY BUCCANEER. MOLECULAR REPLACEMENT INTO TRIGONAL CRYSTAL FORM WAS DONE WITH MOLREP. DIFFERENCE PEAKS IN ELECTRON DENSITY SUGGEST SOME MODIFICATION OF LYS-103-NZ. MODEL TRACE IN POOR ELECTRON DENSITY, PARTICULARLY CHAIN L, RESIDUES 23-25, 45-51 IS BASED ON NCS-RELATED MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 5105 1.97 %THIN SHELLS (SFTOOLS)
Rwork0.2015 ---
obs0.202 259167 99.924 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 63.88 Å2 / Biso mean: 16.874 Å2 / Biso min: 2.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.535 Å2-0.267 Å20 Å2
2---0.535 Å20 Å2
3---0.802 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17050 0 305 1374 18729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02218249
X-RAY DIFFRACTIONr_bond_other_d00.0212106
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.95924932
X-RAY DIFFRACTIONr_angle_other_deg4.225329987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91552390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25224.892740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.929153144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8311537
X-RAY DIFFRACTIONr_chiral_restr0.0820.22803
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120161
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023408
X-RAY DIFFRACTIONr_mcbond_it0.9511.511313
X-RAY DIFFRACTIONr_mcbond_other01.54535
X-RAY DIFFRACTIONr_mcangle_it1.678218433
X-RAY DIFFRACTIONr_scbond_it2.59636936
X-RAY DIFFRACTIONr_scangle_it4.2934.56406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7920.2967750.292369913776999.992
1.792-1.90.2787160.252351513586999.994
1.9-2.0310.2545390.218330583359999.994
2.031-2.1930.2424840.202308783136499.994
2.193-2.4020.2424880.1972833028818100
2.402-2.6840.2287540.202253472610399.992
2.684-3.0970.2445580.207223942295599.987
3.097-3.7880.233200.182191001944299.887
3.788-5.3330.1882640.157147131504999.522
5.333-400.2212070.2098100839798.928

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