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- PDB-3qb5: Human C3PO complex in the presence of MnSO4 -

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Basic information

Entry
Database: PDB / ID: 3qb5
TitleHuman C3PO complex in the presence of MnSO4
Components
  • Translin
  • Translin-associated protein X
KeywordsHYDROLASE / 7 alpha helical bundle / ribonuclease
Function / homology
Function and homology information


A2A adenosine receptor binding / endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / RNA endonuclease activity / male germ cell nucleus / single-stranded DNA binding / spermatogenesis / endonuclease activity ...A2A adenosine receptor binding / endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / RNA endonuclease activity / male germ cell nucleus / single-stranded DNA binding / spermatogenesis / endonuclease activity / DNA recombination / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / cell differentiation / mRNA binding / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Translin; domain 2 / Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Translin / Translin-associated protein X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYe, X. / Huang, N. / Liu, Y. / Paroo, Z. / Chen, S. / Zhang, H. / Liu, Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structure of C3PO and mechanism of human RISC activation.
Authors: Ye, X. / Huang, N. / Liu, Y. / Paroo, Z. / Huerta, C. / Li, P. / Chen, S. / Liu, Q. / Zhang, H.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: Translin
B: Translin
C: Translin
K: Translin-associated protein X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,31511
Polymers111,8194
Non-polymers4957
Water36020
1
A: Translin
B: Translin
C: Translin
K: Translin-associated protein X
hetero molecules

A: Translin
B: Translin
C: Translin
K: Translin-associated protein X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,63022
Polymers223,6398
Non-polymers99114
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area32840 Å2
ΔGint-248 kcal/mol
Surface area69360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.166, 98.166, 446.466
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 4 molecules ABCK

#1: Protein Translin


Mass: 26219.967 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSN / Plasmid: PETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15631
#2: Protein Translin-associated protein X


Mass: 33159.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSNAX, TRAX / Plasmid: PETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3) / References: UniProt: Q99598

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Non-polymers , 6 types, 27 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 1.2 M ammonium sulfate, 0.1 M phosphate citrate, 0.4 M lithium sulfate, soaked in 50 mM MnSO4, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.17712
DetectorDetector: CCD / Date: Jun 21, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.17712 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 28514 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PJA

3pja


Resolution: 2.95→29.859 Å / SU ML: 0.37 / σ(F): 0.14 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1448 5.19 %RANDOM
Rwork0.2235 ---
obs0.226 27903 99.45 %-
all-27903 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.301 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1326 Å2-0 Å20 Å2
2---6.1326 Å2-0 Å2
3---12.2651 Å2
Refinement stepCycle: LAST / Resolution: 2.95→29.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 23 20 7062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037159
X-RAY DIFFRACTIONf_angle_d0.619657
X-RAY DIFFRACTIONf_dihedral_angle_d12.9352670
X-RAY DIFFRACTIONf_chiral_restr0.0451104
X-RAY DIFFRACTIONf_plane_restr0.0021223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.05540.37761610.32292557X-RAY DIFFRACTION100
3.0554-3.17770.37591440.29722543X-RAY DIFFRACTION99
3.1777-3.32210.32481480.28572564X-RAY DIFFRACTION99
3.3221-3.4970.33261330.26892605X-RAY DIFFRACTION99
3.497-3.71570.2751550.22712585X-RAY DIFFRACTION99
3.7157-4.0020.25371460.21162590X-RAY DIFFRACTION99
4.002-4.40360.2211480.1842653X-RAY DIFFRACTION100
4.4036-5.03810.23451270.18842684X-RAY DIFFRACTION100
5.0381-6.33750.30391420.24262727X-RAY DIFFRACTION99
6.3375-29.86030.241440.19912947X-RAY DIFFRACTION100
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)
10.9590.9240.31981.65860.87811.10980.0171-0.03870.0913-0.1180.02640.0147-0.10530.0124-0.02030.68010.0888-0.02270.487-0.06950.629368.5324-23.77680.6054
20.36080.12610.00153.64360.67250.3017-0.06730.10580.0506-0.1380.1982-0.0032-0.02190.1067-0.11320.888-0.1111-0.01530.6999-0.11630.586460.2939-3.5001-26.0638
30.3097-0.0953-0.36861.22550.40290.967-0.0893-0.0246-0.03850.14630.10120.08560.15620.0090.03580.7397-0.0645-0.0240.5560.01560.694835.9551-30.4725.4989
40.47060.002-0.36862.7321.11511.2256-0.06630.07320.0232-0.44950.06770.419-0.1117-0.1341-0.01210.6425-0.0171-0.18110.56140.0050.673227.8284-6.7878-17.48
50000000000000001.3924-0.0977-0.41460.5772-0.03560.89331.024-11.887-12.624
65.0125-0.4709-0.1554.283.97563.7085-0.33770.99430.3948-0.0196-0.48470.58870.0254-0.14470.68711.2841-0.2180.27730.8078-0.040.988433.5763-14.5133-7.4112
71.91451.92111.94229.33781.58981.9877-0.173-0.1514-0.0276-0.350.1220.1280.28170.02170.00151.4377-0.3961-0.04730.99360.02841.560133.3829-11.292-10.7166
80.2313-0.0019-0.20050.26830.26510.2784-0.04030.02190.07190.06720.1348-0.10220.2232-0.0483-0.05360.41230.0137-0.11220.3644-0.03550.353147.2885-12.0165-11.6803
90000000000000001.34210.1516-0.35011.654-0.78771.211250.216-45.347-25.967
100000000000000002.01760.2678-0.29291.061-0.51411.115966.291-23.89415.811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain K
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain D
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain F
9X-RAY DIFFRACTION9chain H
10X-RAY DIFFRACTION10chain I

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