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- PDB-2xoz: C-terminal cysteine rich domain of human CHFR bound to AMP -

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Basic information

Entry
Database: PDB / ID: 2xoz
TitleC-terminal cysteine rich domain of human CHFR bound to AMP
ComponentsE3 UBIQUITIN-PROTEIN LIGASE CHFR
KeywordsLIGASE / ZINC-BINDING / PBZ / POLY(ADP-RIBOSE) BINDING / MITOSIS / ANTEPHASE CHECKPOINT
Function / homology
Function and homology information


meiotic spindle checkpoint signaling / mitotic G2/M transition checkpoint / positive regulation of protein ubiquitination / protein destabilization / RING-type E3 ubiquitin transferase / PML body / 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 / protein destabilization / RING-type E3 ubiquitin transferase / PML body / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / protein ubiquitination / cell division / nucleotide binding / metal 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 / SMAD/FHA domain superfamily ...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
ADENOSINE MONOPHOSPHATE / E3 ubiquitin-protein ligase CHFR
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.374 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 1.1Mar 7, 2012Group: Non-polymer description / Source and taxonomy / Version format compliance
Revision 1.2Dec 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

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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)59,88514
Polymers58,5372
Non-polymers1,34912
Water3,639202
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)30,2908
Polymers29,2681
Non-polymers1,0217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.810, 51.560, 82.490
Angle α, β, γ (deg.)90.00, 105.93, 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): BL21(DE3) / Variant (production host): CODONPLUS RIL
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 / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 'GAM' SEQUENCE FROM VECTOR. GENBANK AAF91084.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 % / Description: NONE
Crystal growDetails: 12% PEG 20000, 0.1M MES PH 6.5, 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: 2.37→65.41 Å / Num. obs: 26821 / % possible obs: 99.6 % / Observed criterion σ(I): 6 / Redundancy: 3.5 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5

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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: 2.374→39.687 Å / SU ML: 0.28 / σ(F): 0.03 / Phase error: 21.08 / Stereochemistry target values: ML / Details: AMP LIGAND WAS MODELED AS ADENINE
RfactorNum. reflection% reflection
Rfree0.2315 2273 8.7 %
Rwork0.1793 --
obs0.1838 26036 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.755 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4997 Å20 Å21.5329 Å2
2--0.7942 Å20 Å2
3----0.2945 Å2
Refinement stepCycle: LAST / Resolution: 2.374→39.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 30 202 3623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083533
X-RAY DIFFRACTIONf_angle_d1.0434801
X-RAY DIFFRACTIONf_dihedral_angle_d18.5861294
X-RAY DIFFRACTIONf_chiral_restr0.069506
X-RAY DIFFRACTIONf_plane_restr0.005632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3742-2.45910.28082110.21622235X-RAY DIFFRACTION92
2.4591-2.55750.24012380.20392253X-RAY DIFFRACTION93
2.5575-2.67390.24652130.19122312X-RAY DIFFRACTION95
2.6739-2.81480.25932240.18392349X-RAY DIFFRACTION97
2.8148-2.99110.2642280.20222359X-RAY DIFFRACTION97
2.9911-3.2220.28262200.20282431X-RAY DIFFRACTION98
3.222-3.5460.23662360.18112414X-RAY DIFFRACTION99
3.546-4.05870.19312310.14822451X-RAY DIFFRACTION99
4.0587-5.11180.18712320.14422448X-RAY DIFFRACTION99
5.1118-39.69220.19362400.15832511X-RAY DIFFRACTION99

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