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- PDB-1q42: Crystal structure analysis of the Candida albicans Mtr2 -

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Basic information

Entry
Database: PDB / ID: 1q42
TitleCrystal structure analysis of the Candida albicans Mtr2
ComponentsMRNA TRANSPORT REGULATOR Mtr2
KeywordsTRANSLATION / Mtr2 / NTF2-fold / nuclear export
Function / homologyNuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / nucleus / Alpha Beta / mRNA transport regulator MTR2
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSenay, C. / Ferrari, P. / Rocher, C. / Rieger, K.J. / Winter, J. / Platel, D. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The mtr2-mex67 ntf2-like domain complex: Structural insights into a dual role of MTR2 for yeast nuclear export
Authors: Senay, C. / Ferrari, P. / Rocher, C. / Rieger, K.J. / Winter, J. / Platel, D. / Bourne, Y.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA TRANSPORT REGULATOR Mtr2


Theoretical massNumber of molelcules
Total (without water)22,6831
Polymers22,6831
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.489, 54.308, 61.285
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MRNA TRANSPORT REGULATOR Mtr2 / Mtr2


Mass: 22683.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: P84148
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / pH: 7
Details: NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.5 mg/mlprotein1drop
20.8 Msodium potassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 19385 / % possible obs: 94.8 % / Redundancy: 2.3 % / Rsym value: 0.056 / Net I/σ(I): 4.7
Reflection shellResolution: 1.75→1.8 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.36 / % possible all: 84
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 25 Å / Num. obs: 19910 / Redundancy: 2.3 % / Num. measured all: 125926 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q40

1q40


Resolution: 1.75→12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.743 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25434 994 5.1 %RANDOM
Rwork0.22355 ---
obs0.22518 18343 94.37 %-
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: 22.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å21.47 Å2
2---0.47 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.115 Å0.114 Å
Refinement stepCycle: LAST / Resolution: 1.75→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 0 71 1342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211304
X-RAY DIFFRACTIONr_bond_other_d0.0020.021137
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9411774
X-RAY DIFFRACTIONr_angle_other_deg0.7732664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695157
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_restr0.0860.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021449
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02259
X-RAY DIFFRACTIONr_nbd_refined0.1980.2218
X-RAY DIFFRACTIONr_nbd_other0.2250.21198
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.2769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0820.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0380.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.5795
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70821295
X-RAY DIFFRACTIONr_scbond_it1.9623509
X-RAY DIFFRACTIONr_scangle_it3.2724.5479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 64
Rwork0.268 1177
Refinement TLS params.Method: refined / Origin x: 8.0269 Å / Origin y: 0.7072 Å / Origin z: 13.6453 Å
111213212223313233
T0.0294 Å20.0231 Å2-0.0213 Å2-0.0394 Å20.0057 Å2--0.0393 Å2
L0.8198 °2-0.3187 °2-0.5824 °2-0.2613 °2-0.1785 °2--1.2261 °2
S0.0128 Å °-0.0938 Å °0.0592 Å °0.0279 Å °0.0825 Å °-0.0287 Å °-0.0657 Å °0.046 Å °-0.0954 Å °
Refinement
*PLUS
Lowest resolution: 12 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.22
X-RAY DIFFRACTIONr_chiral_restr0.081

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