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- PDB-1z6u: Np95-like ring finger protein isoform b [Homo sapiens] -

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Basic information

Entry
Database: PDB / ID: 1z6u
TitleNp95-like ring finger protein isoform b [Homo sapiens]
ComponentsNp95-like ring finger protein isoform b
KeywordsLIGASE / STRUCTURAL GENOMICS CONSORTIUM / UBIQUITIN-PROTEIN LIGASE / RING FINGER / CELL CYCLE REGULATION / SGC
Function / homology
Function and homology information


SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / regulation of cell cycle / protein ubiquitination / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain ...: / : / : / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / PUA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: 2.1 Angstrom Crystal Structure of the Human Ubiquitin Liagse NIRF
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Np95-like ring finger protein isoform b
B: Np95-like ring finger protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4596
Polymers34,1972
Non-polymers2624
Water88349
1
A: Np95-like ring finger protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2293
Polymers17,0981
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Np95-like ring finger protein isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2293
Polymers17,0981
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.561, 64.561, 130.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Np95-like ring finger protein isoform b


Mass: 17098.473 Da / Num. of mol.: 2 / Fragment: RING ZINC FINGER, RESIDUES 672-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF2 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PU4, ubiquitin-protein ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.3 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.8 M NA CITRATE, 0.1 M HEPES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.28287
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2005
RadiationMonochromator: CRYOGENICALLY-COOLED SI(111) DOUBLE-CRYSTAL SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28287 Å / Relative weight: 1
ReflectionResolution: 2.1→45.86 Å / Num. obs: 16546 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.37 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→45.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.9 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28274 840 5.1 %RANDOM
Rwork0.22223 ---
obs0.22507 15705 98.76 %-
all-16546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.967 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 4 49 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9452836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3555249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31225.351114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60415377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.824159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2882
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21320
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9181.51301
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5722029
X-RAY DIFFRACTIONr_scbond_it2.1353912
X-RAY DIFFRACTIONr_scangle_it3.2564.5807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 60 -
Rwork0.246 1155 -
obs--99.92 %

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