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- PDB-1lgp: Crystal structure of the FHA domain of the Chfr mitotic checkpoin... -

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Basic information

Entry
Database: PDB / ID: 1lgp
TitleCrystal structure of the FHA domain of the Chfr mitotic checkpoint protein complexed with tungstate
Componentscell cycle checkpoint protein CHFR
KeywordsCELL CYCLE / Chfr / FHA / Tungstate / Domain Swapping / 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 / nucleus / metal ion binding
Similarity search - Function
E3 ubiquitin-protein ligase CHFR, cysteine rich domain with multizinc binding / Cysteine rich domain with multizinc binding regions / Tumour Suppressor Smad4 - #20 / Zinc finger, C3HC4 type (RING finger) / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...E3 ubiquitin-protein ligase CHFR, cysteine rich domain with multizinc binding / Cysteine rich domain with multizinc binding regions / Tumour Suppressor Smad4 - #20 / Zinc finger, C3HC4 type (RING finger) / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / E3 ubiquitin-protein ligase CHFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStavridi, E.S. / Huyen, Y. / Loreto, I.R. / Scolnick, D.M. / Halazonetis, T.D. / Pavletich, N.P. / Jeffrey, P.D.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of the FHA domain of the Chfr mitotic checkpoint protein and its complex with tungstate.
Authors: Stavridi, E.S. / Huyen, Y. / Loreto, I.R. / Scolnick, D.M. / Halazonetis, T.D. / Pavletich, N.P. / Jeffrey, P.D.
History
DepositionApr 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cell cycle checkpoint protein CHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4512
Polymers13,2031
Non-polymers2481
Water1,13563
1
A: cell cycle checkpoint protein CHFR
hetero molecules

A: cell cycle checkpoint protein CHFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9024
Polymers26,4062
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6770 Å2
ΔGint-35 kcal/mol
Surface area13690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.210, 62.210, 54.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein cell cycle checkpoint protein CHFR


Mass: 13203.084 Da / Num. of mol.: 1 / Fragment: fha domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96EP1
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277.16 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Bis-Tris 6.5, DTT, Tungstate, VAPOR DIFFUSION, HANGING DROP, temperature 277.16K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMbis-Tris1droppH6.5
2150 mM1dropKCl
35 mMdithiothreitol1drop
414-18 %PEG80001reservoir
5100 mMBis-Tris1reservoirpH6.5
65 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 23, 2001
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 8015 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 35.2 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 37545 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 354428.62 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 720 10.7 %RANDOM
Rwork0.232 ---
all-8468 --
obs-6719 81.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4503 Å2 / ksol: 0.317249 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å23.27 Å20 Å2
2---1.35 Å20 Å2
3---2.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-18 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms903 0 5 63 971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.463
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 52 9.7 %
Rwork0.268 483 -
obs--38.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.268 / Rfactor obs: 0.268

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