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- PDB-2hq6: Structure of the Cyclophilin_CeCYP16-Like Domain of the Serologic... -

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Basic information

Entry
Database: PDB / ID: 2hq6
TitleStructure of the Cyclophilin_CeCYP16-Like Domain of the Serologically Defined Colon Cancer Antigen 10 from Homo Sapiens
ComponentsSerologically defined colon cancer antigen 10
KeywordsISOMERASE / PROTEIN FOLDING / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


U2-type precatalytic spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / protein folding / nucleoplasm
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Spliceosome-associated protein CWC27 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWalker, J.R. / Davis, T. / Paramanathan, R. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Davis, T. / Paramanathan, R. / Newman, E.M. / Finerty Jr., P.J. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: PLoS Biol. / Year: 2010
Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S.
#1: Journal: Nat.Biotechnol. / Year: 2001
Title: Creation of genome-wide protein expression libraries using random activation of gene expression
Authors: Harrington, J.J. / Sherf, B. / Rundlett, S. / Jackson, P.D. / Perry, R. / Cain, S. / Leventhal, C. / Thornton, M. / Ramachandran, R. / Whittington, J. / Lerner, L. / Costanzo, D. / ...Authors: Harrington, J.J. / Sherf, B. / Rundlett, S. / Jackson, P.D. / Perry, R. / Cain, S. / Leventhal, C. / Thornton, M. / Ramachandran, R. / Whittington, J. / Lerner, L. / Costanzo, D. / McElligott, K. / Boozer, S. / Mays, R. / Smith, E. / Veloso, N. / Klika, A. / Hess, J. / Cothren, K. / Lo, K. / Offenbacher, J. / Danzig, J. / Ducar, M.
#2: Journal: Int.J.Cancer / Year: 1998
Title: Characterization of human colon cancer antigens recognized by autologous antibodies
Authors: Scanlan, M.J. / Chen, Y.T. / Williamson, B. / Gure, A.O. / Stockert, E. / Gordan, J.D. / Tureci, O. / Sahin, U. / Pfreundschuh, M. / Old, L.J.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4Aug 30, 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 / 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

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Assembly

Deposited unit
A: Serologically defined colon cancer antigen 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9254
Polymers20,5791
Non-polymers3463
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.433, 84.433, 55.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serologically defined colon cancer antigen 10


Mass: 20578.904 Da / Num. of mol.: 1 / Fragment: Cyclophilin_CeCYP16-Like Domain (residues 8-173)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCCAG10 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6UX04
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 298 K
Details: Protein is 20 mg/mL, in buffer containing 50 mM Tris pH 8.0, 500 mM NaCl, 5 mM BME; hanging drop, 1+1; precipitant is 20% Peg 3350, 0.2M NaI (no buffer); cryo was 20% glycerol, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→24.7 Å / Num. all: 22463 / Num. obs: 22463 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.136 / Net I/σ(I): 9.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2241 / Rsym value: 0.61 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZKC

1zkc


Resolution: 1.75→24.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.708 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18093 1162 5.2 %RANDOM
Rwork0.16671 ---
obs0.16744 21296 98.62 %-
all-22773 --
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: 25.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å20 Å2
2--0.65 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 8 175 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221372
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9481855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86323.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9681510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021076
X-RAY DIFFRACTIONr_nbd_refined0.1960.2659
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.211
X-RAY DIFFRACTIONr_mcbond_it0.8551.5851
X-RAY DIFFRACTIONr_mcangle_it1.28921356
X-RAY DIFFRACTIONr_scbond_it2.3683561
X-RAY DIFFRACTIONr_scangle_it3.5954.5499
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 85 -
Rwork0.235 1574 -
obs--97.7 %
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)
114.6359-7.4785-9.66277.73623.29087.0718-1.20820.3226-0.47580.40450.8643-0.20250.2180.29780.34390.0919-0.00820.03750.243-0.04820.10942.543213.214622.8834
20.59190.37440.21750.4921-0.69472.7932-0.0139-0.07470.03310.0818-0.0922-0.0762-0.06130.19430.1060.1166-0.0037-0.00510.1083-0.00080.144854.555416.12374.9808
33.3221-1.2661-2.06913.2766-2.50178.9082-0.0609-0.24670.10750.3910.0188-0.4237-0.22610.25760.04210.1244-0.007-0.01860.1494-0.00540.147253.43417.997812.9654
42.68420.9995-4.23222.1419-2.614412.2681-0.1564-0.127-0.1288-0.076-0.0043-0.21010.51050.35520.16070.11140.0363-0.00560.1068-0.00180.145555.99492.48795.1764
54.6537-1.36921.30955.1596-0.00816.6867-0.06320.19010.0874-0.22020.0857-0.26170.11620.1987-0.02250.1019-0.00070.0360.1041-0.0140.127958.24248.2133-5.9342
62.4821-0.5522-1.75561.61660.84144.6968-0.0720.0829-0.0661-0.08570.07910.1544-0.0149-0.1905-0.00710.1217-0.0118-0.00510.0849-0.00470.144342.482311.3054-5.1723
75.79970.76421.25814.7414-0.42044.2172-0.171-0.1078-0.0268-0.18670.08130.04790.1165-0.10540.08960.1852-0.0010.0020.0587-0.0380.127647.45772.7033-11.0289
811.4785-1.647-2.26383.43061.66826.6246-0.2139-0.0714-0.25890.19740.0638-0.09880.52430.20.15020.21530.06110.02130.04470.01330.084853.0444-4.72040.5029
92.2019-2.1631-4.08726.40531.17069.47750.1313-0.188-0.02270.0419-0.0748-0.24020.1425-0.1043-0.05650.0966-0.0119-0.01060.0905-0.01160.115945.2172-0.392312.5218
106.3157-2.4610.90725.8924-1.92890.8872-0.0453-0.21580.10720.4790.08-0.1165-0.16880.031-0.03470.16660.00240.0060.1096-0.01050.134441.26818.886714.4086
110.9416-0.6059-0.4111.0480.19442.0711-0.00470.02950.00700.0837-0.00220.243-0.0662-0.0790.1467-0.01170.00430.10280.00540.132544.55095.21051.9754
122.36180.1362-0.24891.9971-0.94660.4631-0.07070.0006-0.047-0.19550.14440.22560.0967-0.184-0.07360.1669-0.0103-0.00840.09130.00820.094535.122711.02318.0198
134.7676-2.058-5.87068.9303-1.09158.8633-0.08410.21940.0231-0.04870.18630.45490.2681-0.1839-0.10220.1754-0.0268-0.01710.09010.00440.133338.14731.87597.9107
141.10132.0265-0.471314.1162-0.23950.89420.0601-0.110.05580.1691-0.10160.033-0.05160.12210.04150.1081-0.01-0.00260.1035-0.00210.133248.952613.0188.7446
155.3038-0.7173-0.3792.01952.84674.09180.0860.05210.1835-0.07510.0036-0.0752-0.1767-0.0403-0.08960.118-0.01080.01860.08710.0240.135745.333122.47841.0406
1649.411925.909730.887123.083813.34235.84960.24980.34670.0072-0.055-0.19670.63140.198-0.3711-0.05310.0970.0183-0.02880.09350.01150.154137.239220.1353-9.8763
1712.97824.2013-8.078313.4782-12.180821.9312-0.3360.86660.1646-0.97510.76190.87681.2802-1.0524-0.42590.186-0.1001-0.07180.13220.00920.120137.040913.4182-13.0222
1811.5305-5.50626.59535.1942-5.10725.31370.34470.3003-0.1134-0.5839-0.1348-0.01530.31570.2495-0.20990.15950.0031-0.01050.0968-0.00960.121447.802717.9772-10.0938
196.8285-2.737515.38811.0975-6.169134.6774-0.29610.26080.39070.0779-0.265-0.3153-0.71841.08110.56120.1010.01420.00670.16940.00390.133160.279615.3555-0.7567
208.44762.99331.766840.00162.62312.41470.201-0.1496-0.6440.5233-0.3303-1.35160.09250.51720.12930.04810.0282-0.0260.14910.04170.116663.53946.67539.7425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 815 - 20
2X-RAY DIFFRACTION2AA9 - 2621 - 38
3X-RAY DIFFRACTION3AA27 - 3139 - 43
4X-RAY DIFFRACTION4AA32 - 4344 - 55
5X-RAY DIFFRACTION5AA44 - 5156 - 63
6X-RAY DIFFRACTION6AA52 - 6864 - 80
7X-RAY DIFFRACTION7AA69 - 7681 - 88
8X-RAY DIFFRACTION8AA77 - 8489 - 96
9X-RAY DIFFRACTION9AA85 - 8997 - 101
10X-RAY DIFFRACTION10AA90 - 95102 - 107
11X-RAY DIFFRACTION11AA96 - 116108 - 128
12X-RAY DIFFRACTION12AA117 - 122129 - 134
13X-RAY DIFFRACTION13AA123 - 127135 - 139
14X-RAY DIFFRACTION14AA128 - 136140 - 148
15X-RAY DIFFRACTION15AA137 - 145149 - 157
16X-RAY DIFFRACTION16AA146 - 150158 - 162
17X-RAY DIFFRACTION17AA151 - 156163 - 168
18X-RAY DIFFRACTION18AA157 - 161169 - 173
19X-RAY DIFFRACTION19AA162 - 167174 - 179
20X-RAY DIFFRACTION20AA168 - 172180 - 184

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