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- PDB-2hqe: Crystal structure of human P100 Tudor domain: Large fragment -

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Basic information

Entry
Database: PDB / ID: 2hqe
TitleCrystal structure of human P100 Tudor domain: Large fragment
ComponentsP100 Co-activator tudor domain
KeywordsTRANSCRIPTION / P100 Tudor domain / Large fragment / Human / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process ...regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / melanosome / Signaling by BRAF and RAF1 fusions / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. ...: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShah, N. / Zhao, M. / Cheng, C. / Xu, H. / Yang, J. / Silvennoinen, O. / Liu, Z.J. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of a large fragment of the Human P100 Tudor Domain
Authors: Shah, N. / Zhao, M. / Cheng, C. / Xu, H. / Yang, J. / Silvennoinen, O. / Wang, B.C. / Liu, Z.J.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P100 Co-activator tudor domain
B: P100 Co-activator tudor domain


Theoretical massNumber of molelcules
Total (without water)55,8832
Polymers55,8832
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.931, 93.413, 95.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein P100 Co-activator tudor domain / p100 co- activator / 100 kDa coactivator / EBNA2 coactivator p100


Mass: 27941.320 Da / Num. of mol.: 2 / Fragment: Large fragment, residues 665-910
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SND1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7KZF4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2 micor liter drops containing equal volumes of protein solution (10.0 mg/ml) and precipitate solution (20% PEG 8000, 100.0 MM Phosphate, 0.1M Hepes), pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2006 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9791
ReflectionResolution: 1.8→44 Å / Num. all: 38197 / Num. obs: 29102 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rsym value: 0.078 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 12.1 / Num. unique all: 1624 / Rsym value: 0.816 / % possible all: 100

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Processing

Software
NameVersionClassification
SCA2STRUCTUREmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQX

2hqx


Resolution: 2→44.24 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.794 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24919 1701 5.5 %RANDOM
Rwork0.23338 ---
all0.23427 29102 --
obs0.23427 29102 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.84 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 0 156 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222493
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9523381
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12323.52125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8981521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021933
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.31062
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.51708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.329
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.15921572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83732465
X-RAY DIFFRACTIONr_scbond_it1.12821049
X-RAY DIFFRACTIONr_scangle_it1.7283916
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 126 -
Rwork0.295 2060 -
obs--100 %

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