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- PDB-3fit: FHIT (FRAGILE HISTIDINE TRIAD PROTEIN) IN COMPLEX WITH ADENOSINE/... -

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Basic information

Entry
Database: PDB / ID: 3fit
TitleFHIT (FRAGILE HISTIDINE TRIAD PROTEIN) IN COMPLEX WITH ADENOSINE/SULFATE AMP ANALOG
ComponentsFRAGILE HISTIDINE PROTEIN
KeywordsCOMPLEX (CHROMOSOMAL TRANSLOCATION/ADE) / FHIT / FRAGILE HISTIDINE TRIAD PROTEIN / PUTATIVE HUMAN TUMOR SUPPRESSOR / ADVANCED PHOTON SOURCE / APS / HIT PROTEIN FAMILY / PKCI / COMPLEX (CHROMOSOMAL TRANSLOCATION-ADE) / COMPLEX (CHROMOSOMAL TRANSLOCATION-ADE) complex
Function / homology
Function and homology information


adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / adenylylsulfatase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity ...adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / adenylylsulfatase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / fibrillar center / nucleotide binding / ubiquitin protein ligase binding / mitochondrion / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / FHIT family / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily ...: / FHIT family / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / beta-D-fructofuranose / Bis(5'-adenosyl)-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsLima, C.D. / D'Amico, K.L. / Naday, I. / Rosenbaum, G. / Westbrook, E.M. / Hendrickson, W.A.
CitationJournal: Structure / Year: 1997
Title: MAD analysis of FHIT, a putative human tumor suppressor from the HIT protein family.
Authors: Lima, C.D. / D'Amico, K.L. / Naday, I. / Rosenbaum, G. / Westbrook, E.M. / Hendrickson, W.A.
History
DepositionMay 17, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRAGILE HISTIDINE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6995
Polymers16,9801
Non-polymers7204
Water1,820101
1
A: FRAGILE HISTIDINE PROTEIN
hetero molecules

A: FRAGILE HISTIDINE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,39910
Polymers33,9602
Non-polymers1,4398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)50.600, 50.600, 268.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein FRAGILE HISTIDINE PROTEIN / FHIT / FRAGILE HISTIDINE TRIAD PROTEIN


Mass: 16979.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: EXPRESSED AS FUSION PROTEIN WITH GLUTATHIONE-S-TRANSFERASE;
Gene: FHIT / Plasmid: PGEX-2T / Gene (production host): FHIT / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P49789
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.8 %
Description: DATA WERE COLLECTED USING 2.0 DEGREE OSCILLATIONS WITH 0.5 DEGREE OVERLAP.
Crystal growpH: 6.5 / Details: 1.25-1.35M AMSO4, 100MM SODIUM CACODYLATE PH6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
21.25-1.35 MAmSO411
3100 mMsodium cacodylate11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9551
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 23, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9551 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 19709 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.097
Reflection
*PLUS
Num. measured all: 81943
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.457

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.249 -5 %
Rwork0.201 --
obs0.201 13969 96.2 %
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 41 101 1130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.106
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.882
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.702
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.882

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