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- PDB-4ldg: Crystal Structure of CpSET8 from Cryptosporidium, cgd4_370 -

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Basic information

Entry
Database: PDB / ID: 4ldg
TitleCrystal Structure of CpSET8 from Cryptosporidium, cgd4_370
ComponentsProtein with a SET domain within carboxy region
KeywordsUNKNOWN FUNCTION / set domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H4K20 methyltransferase activity / polytene chromosome / regulation of DNA damage response, signal transduction by p53 class mediator / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / : / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / Protein with a SET domain within carboxy region
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsWernimont, A.K. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / El Bakkouri, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of CpSET8 from Cryptosporidium, cgd4_370
Authors: Wernimont, A.K. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / El Bakkouri, M.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Protein with a SET domain within carboxy region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7862
Polymers32,6841
Non-polymers1021
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.229, 68.229, 142.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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Components

#1: Protein Protein with a SET domain within carboxy region


Mass: 32684.168 Da / Num. of mol.: 1 / Fragment: UNP residues 280-556
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd4_370 / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5CQK4
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.8 M Na Malonate, 20 % PEG 3350, 7% butanol, 20 glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15687 / Num. obs: 15678 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.144 / Χ2: 3.465 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.3410.60.9793.217701.213100
2.34-2.3810.60.7927551.179100
2.38-2.4310.50.7427791.174100
2.43-2.4810.60.6147441.23100
2.48-2.5310.50.67821.176100
2.53-2.5910.60.4317451.306100
2.59-2.6610.50.4917661.6100
2.66-2.7310.40.5037822.394100
2.73-2.8110.60.3367501.519100
2.81-2.910.50.2667771.736100
2.9-310.40.2117792.034100
3-3.1210.40.1797792.417100
3.12-3.2610.40.1517742.639100
3.26-3.4410.40.137813.081100
3.44-3.6510.40.117824.001100
3.65-3.9310.30.147885.83100
3.93-4.3310.20.1038006.927100
4.33-4.9510.10.0938098.122100
4.95-6.249.80.0928268.05999.9
6.24-5090.09591011.58799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→49.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1845 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8466 / SU B: 11.677 / SU ML: 0.142 / SU R Cruickshank DPI: 0.2307 / SU Rfree: 0.1901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 777 5 %RANDOM
Rwork0.1936 ---
obs0.1953 15482 99.67 %-
all-15533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.76 Å2 / Biso mean: 53.777 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å20 Å2
2--2.12 Å2-0 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 7 68 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191836
X-RAY DIFFRACTIONr_bond_other_d0.0010.021723
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9722486
X-RAY DIFFRACTIONr_angle_other_deg0.77533977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2424.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.609159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
LS refinement shellResolution: 2.31→2.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 54 -
Rwork0.267 1025 -
all-1079 -
obs--96.51 %
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)
111.3819-1.93833.47721.2733-0.40043.6978-0.17780.54950.9152-0.14760.0254-0.3895-1.03881.04510.15240.387-0.33010.06970.37660.04020.182917.908339.578-15.5061
215.51419.75752.00576.141.26340.2623-0.080.11870.0674-0.11890.05550.0135-0.0856-0.01920.02451.7560.91030.32070.70130.41150.321418.709940.6381-11.3295
30.46550.01070.97921.97410.07773.8181-0.0466-0.0703-0.0330.09650.0025-0.1055-0.12720.26630.04420.0858-0.0316-0.01420.14270.01350.041512.976427.12151.2245
41.0151-0.27670.77451.52692.63476.4336-0.0831-0.0696-0.0907-0.08230.00960.1338-0.4546-0.17620.07360.17050.03760.03680.09480.03540.05096.679730.7082-2.5393
53.65060.7355.11810.6076-1.501421.3822-0.37230.47840.1484-0.04270.06190.0323-0.56490.74790.31040.1433-0.08930.01550.1273-0.01310.085410.640234.5605-24.6122
63.5102-0.94521.77860.9585-0.71292.62240.005-0.0878-0.06110.08310.03650.0952-0.3329-0.1709-0.04150.12130.03330.0280.0802-0.00370.0199-3.463230.5953-17.6155
73.20121.22661.70932.9998-1.6095.90950.1645-0.37310.0835-0.1009-0.27010.0997-0.1285-0.61530.10560.15580.08650.00390.2249-0.03550.0343-6.927329.5756-14.9425
81.42150.1371.11480.3909-0.85183.85790.18480.1097-0.0185-0.0348-0.03130.00140.13880.114-0.15350.10990.02450.01170.09280.00010.04695.372924.3613-16.6068
98.65426.91874.86978.4837-3.224620.13761.2731-0.9045-0.48350.718-0.4611-0.10951.3119-0.9762-0.8120.3148-0.1296-0.09930.35760.17510.2806-3.058117.9545-17.3072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 41
2X-RAY DIFFRACTION2A42 - 85
3X-RAY DIFFRACTION3A86 - 127
4X-RAY DIFFRACTION4A128 - 136
5X-RAY DIFFRACTION5A137 - 152
6X-RAY DIFFRACTION6A153 - 191
7X-RAY DIFFRACTION7A192 - 216
8X-RAY DIFFRACTION8A217 - 260
9X-RAY DIFFRACTION9A261 - 267

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