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- PDB-4z0o: CW-type zinc finger of ZCWPW2 with F78D mutation -

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Basic information

Entry
Database: PDB / ID: 4z0o
TitleCW-type zinc finger of ZCWPW2 with F78D mutation
ComponentsZinc finger CW-type PWWP domain protein 2
KeywordsPROTEIN BINDING / Structural Genomics / zinc finger / cw domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


methylated histone binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger CW-type PWWP domain protein ZCWPW1/ZCWPW2 / Herpes Virus-1 - #100 / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / Herpes Virus-1 / PWWP domain / PWWP domain profile. / PWWP domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger CW-type PWWP domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: CW-type zinc finger of ZCWPW2 with F78D mutation
Authors: Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger CW-type PWWP domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,13512
Polymers7,0471
Non-polymers8811
Water1,02757
1
A: Zinc finger CW-type PWWP domain protein 2
hetero molecules

A: Zinc finger CW-type PWWP domain protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,27024
Polymers14,0932
Non-polymers17722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.569, 47.569, 48.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1002-

NA

21A-1117-

HOH

31A-1156-

HOH

41A-1157-

HOH

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Components

#1: Protein Zinc finger CW-type PWWP domain protein 2 / zcwpw2


Mass: 7046.648 Da / Num. of mol.: 1 / Fragment: CW domain (UNP residues 21-78) / Mutation: F78D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZCWPW2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q504Y3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→31.52 Å / Num. obs: 9271 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.011 / Net I/σ(I): 56.2 / Num. measured all: 93278
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.57-1.69.50.20313.341084340.990.06897.4
8.61-31.527.60.02124.85547310.00797.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4O62

4o62


Resolution: 1.57→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1609 / FOM work R set: 0.9073 / SU B: 1.113 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0752 / SU Rfree: 0.0742 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The protein was crystallized in the presence of a putative peptide ligand not found in the crystal structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 455 4.9 %RANDOM
Rwork0.1637 8813 --
obs0.1648 9268 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.31 Å2 / Biso mean: 16.017 Å2 / Biso min: 7 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms458 0 11 57 526
Biso mean--26.41 23.89 -
Num. residues----55
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019494
X-RAY DIFFRACTIONr_bond_other_d0.0020.02419
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.893677
X-RAY DIFFRACTIONr_angle_other_deg1.0033972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.768562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.11925.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.2681583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.334152
X-RAY DIFFRACTIONr_chiral_restr0.1110.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02585
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02125
X-RAY DIFFRACTIONr_mcbond_it1.6661.39230
X-RAY DIFFRACTIONr_mcbond_other1.6681.38229
X-RAY DIFFRACTIONr_mcangle_it2.5282.072289
LS refinement shellResolution: 1.572→1.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 29 -
Rwork0.143 625 -
all-654 -
obs--98.35 %

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