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- PDB-2xoy: C-terminal cysteine-rich domain of human CHFR bound to P(1),P(2)-... -

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Basic information

Entry
Database: PDB / ID: 2xoy
TitleC-terminal cysteine-rich domain of human CHFR bound to P(1),P(2)- Diadenosine-5'-pyrophosphate
ComponentsE3 UBIQUITIN-PROTEIN LIGASE CHFR
KeywordsLIGASE / ZINC-BINDING / PBZ / MITOSIS / ANTEPHASE CHECKPOINT
Function / homology
Function and homology information


meiotic spindle checkpoint signaling / mitotic G2/M transition checkpoint / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / PML body / protein destabilization / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process ...meiotic spindle checkpoint signaling / mitotic G2/M transition checkpoint / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / PML body / protein destabilization / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / cell division / nucleotide binding / zinc ion binding / nucleus
Similarity search - Function
Herpes Virus-1 - #140 / E3 ubiquitin-protein ligase CHFR, cysteine rich domain with multizinc binding / : / Cysteine rich domain with multizinc binding regions / PBZ domain / Zinc finger, C3HC4 type (RING finger) / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain ...Herpes Virus-1 - #140 / E3 ubiquitin-protein ligase CHFR, cysteine rich domain with multizinc binding / : / Cysteine rich domain with multizinc binding regions / PBZ domain / Zinc finger, C3HC4 type (RING finger) / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / ADENOSINE MONOPHOSPHATE / E3 ubiquitin-protein ligase CHFR
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOberoi, J. / Bayliss, R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis of Poly(Adp-Ribose) Recognition by the Multizinc Binding Domain of Checkpoint with Forkhead-Associated and Ring Domains (Chfr).
Authors: Oberoi, J. / Richards, M.W. / Crumpler, S. / Brown, N. / Blagg, J. / Bayliss, R.
History
DepositionAug 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE CHFR
B: E3 UBIQUITIN-PROTEIN LIGASE CHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,67314
Polymers58,5372
Non-polymers1,13612
Water1,54986
1
A: E3 UBIQUITIN-PROTEIN LIGASE CHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5956
Polymers29,2681
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E3 UBIQUITIN-PROTEIN LIGASE CHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0788
Polymers29,2681
Non-polymers8097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.050, 52.120, 83.610
Angle α, β, γ (deg.)90.00, 105.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE CHFR / CHFR / CHECKPOINT WITH FORKHEAD AND RING FINGER DOMAINS PROTEIN / RING FINGER PROTEIN 196


Mass: 29268.252 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH REGION, RESIDUES 407-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CODONPLUS RIL BL21-DE3
References: UniProt: Q96EP1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL SEQUENCE 'GAM' FROM VECTOR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 % / Description: NONE
Crystal growDetails: 12% PEG 20000, 0.1M MES PH6.5, 0.1M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→65.63 Å / Num. obs: 21061 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 3.4 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOC

2xoc


Resolution: 2.6→36.256 Å / SU ML: 0.36 / σ(F): 0.01 / Phase error: 24.37 / Stereochemistry target values: ML
Details: P(1),P(2)-DIADENOSINE-5'- PYROPHOSPHATE MODELED AS AMP AND ADENINE.
RfactorNum. reflection% reflection
Rfree0.246 1752 8.6 %
Rwork0.1947 --
obs0.199 20279 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.63 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.6415 Å20 Å2-1.4189 Å2
2--8.0374 Å20 Å2
3---0.6041 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 43 86 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093507
X-RAY DIFFRACTIONf_angle_d1.144767
X-RAY DIFFRACTIONf_dihedral_angle_d18.8111272
X-RAY DIFFRACTIONf_chiral_restr0.075507
X-RAY DIFFRACTIONf_plane_restr0.006623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.6930.32981600.26761716X-RAY DIFFRACTION90
2.693-2.80080.33341680.23391738X-RAY DIFFRACTION91
2.8008-2.92820.27451660.24481801X-RAY DIFFRACTION94
2.9282-3.08250.31031760.24111846X-RAY DIFFRACTION96
3.0825-3.27550.28341800.22141872X-RAY DIFFRACTION97
3.2755-3.52820.24941770.19691870X-RAY DIFFRACTION98
3.5282-3.88290.26051700.19431862X-RAY DIFFRACTION96
3.8829-4.44390.2181830.15811911X-RAY DIFFRACTION99
4.4439-5.59550.16961820.14091917X-RAY DIFFRACTION98
5.5955-36.25950.20451900.16041994X-RAY DIFFRACTION99

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