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- PDB-2bjn: X-ray Structure of human TPC6 -

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Basic information

Entry
Database: PDB / ID: 2bjn
TitleX-ray Structure of human TPC6
ComponentsTRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
KeywordsTRANSPORT PROTEIN / TPC6 / TRAPP COMPLEX / TETHERING
Function / homology
Function and homology information


vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPP complex / cis-Golgi network / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of GTPase activity / trans-Golgi network ...vesicle coating / vesicle tethering / TRAPPII protein complex / TRAPP complex / cis-Golgi network / RAB GEFs exchange GTP for GDP on RABs / COPII-mediated vesicle transport / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of GTPase activity / trans-Golgi network / nervous system development / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
Trafficking protein particle complex subunit 3 / TRAPP complex, Trs33 subunit / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / NO signalling/Golgi transport ligand-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Trafficking protein particle complex subunit 6B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKummel, D. / Mueller, J.J. / Roske, Y. / Misselwitz, R. / Bussow, K. / Heinemann, U.
CitationJournal: Embo Rep. / Year: 2005
Title: The Structure of the Trapp Subunit Tpc6 Suggests a Model for a Trapp Subcomplex.
Authors: Kummel, D. / Mueller, J.J. / Roske, Y. / Misselwitz, R. / Bussow, K. / Heinemann, U.
History
DepositionFeb 4, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
B: TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,15111
Polymers36,3022
Non-polymers8499
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.423, 57.005, 60.406
Angle α, β, γ (deg.)90.00, 117.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 6B / TPC6


Mass: 18151.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: RZPD, GERMAN RESOURCE CENTRE / Plasmid: PQTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 ROSETTA / References: UniProt: Q86SZ2
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5
Details: 22-23%PEG3350,0.1M HEPES PH7.5, 0.3M(NH4)2SO4, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 6, 2004 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→23 Å / Num. obs: 32829 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.05 / Net I/σ(I): 22.81
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.27 / Rsym value: 0.48 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→22.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.902 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1697 5.2 %RANDOM
Rwork0.175 ---
obs0.177 31019 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.35 Å2
2--0.91 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 49 126 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222401
X-RAY DIFFRACTIONr_bond_other_d0.0020.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9753207
X-RAY DIFFRACTIONr_angle_other_deg1.52535213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4055285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72324.167108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2071515
X-RAY DIFFRACTIONr_chiral_restr0.10.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
X-RAY DIFFRACTIONr_nbd_refined0.2680.3524
X-RAY DIFFRACTIONr_nbd_other0.2090.32275
X-RAY DIFFRACTIONr_nbtor_refined0.1920.51167
X-RAY DIFFRACTIONr_nbtor_other0.0940.51370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.326
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1251.51468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44922298
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27431028
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.224.5909
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 90
Rwork0.241 2072
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
126.5561-5.04140.91932.8033-0.23591.55750.04470.18560.0051-0.0997-0.00160.08240.07860.1573-0.043-0.16080.02020.0206-0.15630.0276-0.181519.3264-4.799522.6044
29.1193-1.85922.746924.2155-5.96142.9390.0353-0.5744-1.02660.20110.36962.30210.4106-1.1576-0.4049-0.0596-0.05270.0020.02540.03810.2269-1.4868-0.03320.7058
318.58464.44723.2076.14210.74424.0472-0.102-0.07060.15290.0576-0.17-0.1333-0.09650.34080.2721-0.16520.0306-0.0232-0.21220.0495-0.177314.94739.591219.9343
41.49210.46930.224814.7611-6.1310.41910.03820.89440.441-0.3646-0.375-0.6498-0.41991.42090.3368-0.0992-0.04930.05150.36790.19830.024326.43359.524410.2818
54.789-4.79234.210911.6221-6.49111.47040.31791.16180.2514-1.0454-0.5954-0.26390.09611.1150.27750.0290.05330.08690.47370.1364-0.004523.267.08792.0783
66.5216-0.9664-0.846812.1799-5.24178.8341-0.00280.8971-0.5769-0.7239-0.2238-0.28110.87870.67310.2266-0.00410.13940.03870.1955-0.0278-0.075420.9677-2.91298.9685
73.82292.042-0.595914.5580.24333.0901-0.07860.4127-0.0361-0.53530.03650.11140.08030.18010.0421-0.16670.029-0.0275-0.09650.0456-0.180114.8486.655313.6607
86.12952.74061.26276.71271.83914.4638-0.14040.6742-0.4014-1.61630.17460.38190.01970.254-0.0342-0.01570.03950.00580.07320.0389-0.119814.7294.83126.4165
97.4438-9.49641.826626.83990.32696.03250.21330.8940.1931-0.998-0.5525-0.1489-0.10970.48520.33910.01580.04140.00530.20320.1389-0.114815.68528.73024.0684
1017.7471-0.0228-6.62555.5048-1.45649.28330.11610.09170.2586-0.0973-0.354-0.4005-0.31710.68820.2379-0.10110.0221-0.039-0.11020.0882-0.103620.48225.929527.7738
115.4031-0.7506-0.567922.6546-12.52514.69510.2247-0.15990.47260.54610.62892.4915-0.6517-2.0182-0.8536-0.00380.130.08570.1389-0.01780.24541.70621.571736.6248
1210.0117-4.4971-5.54278.82143.04496.25810.2082-0.06210.16990.0086-0.12430.3452-0.1332-0.1664-0.0839-0.2007-0.0063-0.015-0.22870.0029-0.188315.0783-7.408333.1756
130.08050.32820.14551.60032.566915.10280.1606-0.0832-0.6336-0.03670.031-0.43461.76681.0233-0.19160.05650.09810.00730.09630.06390.05532.4817-17.065333.7634
143.1693-2.61483.15788.8814-4.05057.89340.07120.0391-0.04820.1617-0.0186-0.19870.05220.2334-0.0525-0.1972-0.0056-0.0008-0.1423-0.0019-0.180830.2917-6.990935.9604
154.01882.2861-0.740310.4135-9.762215.74440.154-0.41360.03820.4962-0.4245-0.3217-0.09090.71160.2705-0.05060.0168-0.0557-0.12150.001-0.135131.1589-5.970945.6695
166.2461-1.27834.021711.5341-8.170114.4803-0.28170.11270.6790.6627-0.1137-0.2474-1.14840.30660.39540.0191-0.037-0.0322-0.1563-0.0311-0.112126.65724.158740.5298
173.9111-1.99940.978511.7373-1.12223.2851-0.0434-0.22260.09320.549-0.00740.4604-0.3336-0.18890.0507-0.1636-0.00510.0012-0.1785-0.0093-0.206618.6439-4.403938.2049
183.41831.8270.393815.6573.81154.02540.2486-0.38520.34480.8556-0.41930.2883-0.2258-0.22280.1707-0.0346-0.0012-0.0084-0.1073-0.0091-0.164822.0378-2.675745.128
198.04619.87192.691945.34733.7586.12040.3848-0.6929-0.30960.615-0.34190.31590.7872-0.8041-0.04290.1073-0.0506-0.0801-0.11380.0457-0.170921.9587-12.057447.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 33
3X-RAY DIFFRACTION3A34 - 53
4X-RAY DIFFRACTION4A63 - 79
5X-RAY DIFFRACTION5A80 - 94
6X-RAY DIFFRACTION6A95 - 105
7X-RAY DIFFRACTION7A117 - 135
8X-RAY DIFFRACTION8A136 - 150
9X-RAY DIFFRACTION9A151 - 158
10X-RAY DIFFRACTION10B1 - 20
11X-RAY DIFFRACTION11B21 - 34
12X-RAY DIFFRACTION12B35 - 50
13X-RAY DIFFRACTION13B51 - 65
14X-RAY DIFFRACTION14B66 - 79
15X-RAY DIFFRACTION15B80 - 94
16X-RAY DIFFRACTION16B95 - 105
17X-RAY DIFFRACTION17B116 - 135
18X-RAY DIFFRACTION18B136 - 153
19X-RAY DIFFRACTION19B154 - 158

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