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- PDB-4nn2: Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Synd... -

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Basic information

Entry
Database: PDB / ID: 4nn2
TitleProtein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6
ComponentsPHD finger protein 6
KeywordsTRANSCRIPTION / Zinc Finger
Function / homology
Function and homology information


blastocyst hatching / ribonucleoprotein complex binding / tubulin binding / phosphoprotein binding / kinetochore / histone deacetylase binding / histone binding / scaffold protein binding / nucleolus / enzyme binding ...blastocyst hatching / ribonucleoprotein complex binding / tubulin binding / phosphoprotein binding / kinetochore / histone deacetylase binding / histone binding / scaffold protein binding / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
PHD-like zinc-binding domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Herpes Virus-1 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHD finger protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.472 Å
AuthorsLiu, Z. / Li, F. / Zhang, J. / Mei, Y. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the second extended PHD domain of human PHF6 protein
Authors: Liu, Z. / Li, F. / Zhang, J. / Mei, Y. / Wu, J. / Shi, Y.
History
DepositionNov 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: PHD finger protein 6
B: PHD finger protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3709
Polymers28,8852
Non-polymers4857
Water4,756264
1
A: PHD finger protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6394
Polymers14,4431
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHD finger protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7315
Polymers14,4431
Non-polymers2884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.780, 102.780, 51.250
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-541-

HOH

21A-546-

HOH

31A-602-

HOH

41B-579-

HOH

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Components

#1: Protein PHD finger protein 6 / / PHD-like zinc finger protein


Mass: 14442.686 Da / Num. of mol.: 2 / Fragment: unp residues 208-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF6, KIAA1823 / Plasmid: pGEx4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8IWS0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#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.: 264 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M amminium acetate, 0.1M tri-sodium citrate dehydrate, 30% (w/v) PEG4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.472→89.01 Å / Num. all: 52631 / Num. obs: 52631 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.47-1.554.60.5051.33494576450.50599.8
1.55-1.655.10.34823662172350.34899.8
1.65-1.7650.2333.13395067850.23399.5
1.76-1.94.90.1684.33102963280.16899.1
1.9-2.084.80.1324.92795957840.13298.7
2.08-2.334.80.0827.82531752740.08299
2.33-2.6950.0659.62363447140.06599.8
2.69-3.295.30.0777.12115839950.07799.8
3.29-4.655.30.05210.31641531150.05299.6
4.65-36.2895.60.03416.7979617560.03498.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.472→36.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1767 / WRfactor Rwork: 0.1588 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9174 / SU B: 0.877 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0547 / SU Rfree: 0.0553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 2672 5.1 %RANDOM
Rwork0.1588 ---
all0.1588 52630 --
obs0.1597 52630 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.6 Å2 / Biso mean: 14.4839 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.472→36.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 12 264 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191938
X-RAY DIFFRACTIONr_bond_other_d0.0010.021871
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.9472583
X-RAY DIFFRACTIONr_angle_other_deg0.7334325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.39623.17182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.20915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5721511
X-RAY DIFFRACTIONr_chiral_restr0.070.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
X-RAY DIFFRACTIONr_mcbond_it0.7441.215965
X-RAY DIFFRACTIONr_mcbond_other0.7411.214964
X-RAY DIFFRACTIONr_mcangle_it1.2751.8141201
LS refinement shellResolution: 1.472→1.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 197 -
Rwork0.256 3681 -
all-3878 -
obs--99.54 %

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