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- PDB-4fit: FHIT-APO -

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Basic information

Entry
Database: PDB / ID: 4fit
TitleFHIT-APO
ComponentsFRAGILE HISTIDINE TRIAD PROTEINFHIT
KeywordsHYDROLASE / FRAGILE HISTIDINE TRIAD PROTEIN / FHIT / PUTATIVE TUMOR SUPPRESSOR / HIT PROTEIN FAMILY / HISTIDINE TRIAD PROTEIN FAMILY / NUCLEOTIDYL HYDROLASE / NUCLEOTIDYL TRANSFERASE
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 / cytosol / cytoplasm
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bis(5'-adenosyl)-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLima, C.D. / Klein, M.G. / Hendrickson, W.A.
Citation
Journal: Science / Year: 1997
Title: Structure-based analysis of catalysis and substrate definition in the HIT protein family.
Authors: Lima, C.D. / Klein, M.G. / Hendrickson, W.A.
#1: Journal: 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
DepositionSep 25, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRAGILE HISTIDINE TRIAD PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,8861
Polymers16,8861
Non-polymers00
Water1,20767
1
A: FRAGILE HISTIDINE TRIAD PROTEIN

A: FRAGILE HISTIDINE TRIAD PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,7722
Polymers33,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)50.500, 50.500, 268.900
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 TRIAD PROTEIN / FHIT / FHIT


Mass: 16886.203 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 IN ESCHERICHIA COLI
Gene: FHIT / Plasmid: PGEX-2T / Gene (production host): FHIT / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA
References: UniProt: P49789, bis(5'-adenosyl)-triphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growpH: 6.5 / Details: GROWN FROM AMMONIUM SULFATE, PH 6.5
Crystal grow
*PLUS
Method: unknown / Details: Lima, C.D., (1997) Structure (London), 5, 763.
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 sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 16, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16062 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Num. measured all: 100846

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.251 -5 %
Rwork0.216 --
obs0.216 12031 97.3 %
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 67 1054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.04
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.78
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.827
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_deg25.783
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.827

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