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- PDB-4bhx: Crystal structure of the SCAN domain from human paternally expres... -

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Basic information

Entry
Database: PDB / ID: 4bhx
TitleCrystal structure of the SCAN domain from human paternally expressed gene 3 protein
ComponentsPATERNALLY-EXPRESSED GENE 3 PROTEIN
KeywordsDNA BINDING PROTEIN / PEG3
Function / homology
Function and homology information


autophagosome / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...DNA breaking-rejoining enzymes fold / DNA breaking-rejoining enzymes / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Paternally-expressed gene 3 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRimsa, V. / Eadsforth, T.C. / Hunter, W.N.
CitationJournal: Plos One / Year: 2013
Title: Structure of the Scan Domain of Human Paternally Expressed Gene 3 Protein.
Authors: Rimsa, V. / Eadsforth, T.C. / Hunter, W.N.
History
DepositionApr 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PATERNALLY-EXPRESSED GENE 3 PROTEIN
B: PATERNALLY-EXPRESSED GENE 3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,93129
Polymers22,9032
Non-polymers2,02827
Water2,792155
1
A: PATERNALLY-EXPRESSED GENE 3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,60316
Polymers11,4511
Non-polymers1,15115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PATERNALLY-EXPRESSED GENE 3 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,32813
Polymers11,4511
Non-polymers87712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.615, 83.615, 55.233
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 PATERNALLY-EXPRESSED GENE 3 PROTEIN / ZINC FINGER AND SCAN DOMAIN-CONTAINING PROTEIN 24


Mass: 11451.426 Da / Num. of mol.: 2 / Fragment: SCAN DOMAIN, RESIDUES 40-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q9GZU2
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST THREE RESIDUES AT THE N-TERMINUS (GHM) ARE FROM THE HISTIDINE TAG AND REMAINED AFTER TEV DIGESTION.

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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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: CRYSTALLIZATION WAS OBSERVED DURING PROTEIN CONCENTRATION USING VIVASPIN 20 CONCENTRATORS (SARTORIUS STEDIM BIOTECH) IN 50 MM TRIS-HCL PH 7.5, 150 MM NACL.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→13.8 Å / Num. obs: 16090 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 28 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 38
Reflection shellResolution: 1.95→2 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 9.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E6S

4e6s


Resolution: 1.95→13.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.489 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22383 806 5 %RANDOM
Rwork0.17151 ---
obs0.17412 15239 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.167 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å20 Å20 Å2
2--3.11 Å20 Å2
3----6.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→13.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 132 155 1854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021765
X-RAY DIFFRACTIONr_bond_other_d0.0020.021832
X-RAY DIFFRACTIONr_angle_refined_deg2.0172.0232332
X-RAY DIFFRACTIONr_angle_other_deg0.96134230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02523.97683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32815340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7971513
X-RAY DIFFRACTIONr_chiral_restr0.120.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 64 -
Rwork0.19 1133 -
obs--99.67 %

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