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- PDB-1fhi: SUBSTRATE ANALOG (IB2) COMPLEX WITH THE FRAGILE HISTIDINE TRIAD P... -

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Basic information

Entry
Database: PDB / ID: 1fhi
TitleSUBSTRATE ANALOG (IB2) COMPLEX WITH THE FRAGILE HISTIDINE TRIAD PROTEIN, FHIT
ComponentsFRAGILE HISTIDINE TRIAD PROTEINFHIT
KeywordsNUCLEOTIDE-BINDING PROTEIN / CANCER / DIADENOSINE TRIPHOSPHATE HYDROLASE / HISTIDINE TRIAD / TUMOR SUPPRESSOR
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
P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE / Bis(5'-adenosyl)-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT / Resolution: 3.1 Å
AuthorsPace, H.C. / Garrison, P.N. / Barnes, L.D. / Draganescu, A. / Rosler, A. / Blackburn, G.M. / Siprashvili, Z. / Croce, C.M. / Huebner, K. / Brenner, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Genetic, biochemical, and crystallographic characterization of Fhit-substrate complexes as the active signaling form of Fhit.
Authors: Pace, H.C. / Garrison, P.N. / Robinson, A.K. / Barnes, L.D. / Draganescu, A. / Rosler, A. / Blackburn, G.M. / Siprashvili, Z. / Croce, C.M. / Huebner, K. / Brenner, C.
#1: Journal: Protein Eng. / Year: 1998
Title: Purification and Crystallization of Complexes Modeling the Active State of the Fragile Histidine Triad Protein
Authors: Brenner, C. / Pace, H.C. / Garrison, P.N. / Robinson, A.K. / Rosler, A. / Liu, X.H. / Blackburn, G.M. / Croce, C.M. / Huebner, K. / Barnes, L.D.
History
DepositionDec 11, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: FRAGILE HISTIDINE TRIAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6572
Polymers16,8861
Non-polymers7711
Water543
1
A: FRAGILE HISTIDINE TRIAD PROTEIN
hetero molecules

A: FRAGILE HISTIDINE TRIAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3134
Polymers33,7722
Non-polymers1,5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)50.728, 50.728, 268.513
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) / Gene: FHIT / Plasmid: PSGA02 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109/DE3/LACIQ
References: UniProt: P49789, bis(5'-adenosyl)-triphosphatase
#2: Chemical ChemComp-IB2 / P1-P2-METHYLENE-P3-THIO-DIADENOSINE TRIPHOSPHATE / ADO-P-CH2-P-PS-ADO


Mass: 770.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N10O14P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.83 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: FHIT PROTEIN (13.4 MG/ML) WAS COCRYSTALLIZED WITH 2.5 MOLAR EQUIVALENTS OF IB2 BY MIXING WITH AN EQUAL VOLUME (2.5 - 4 MICROLITERS) OF 2 M AMMONIUM SULFATE, 4% PEG 400 0.1 M NA HEPES PH 7.5 ...Details: FHIT PROTEIN (13.4 MG/ML) WAS COCRYSTALLIZED WITH 2.5 MOLAR EQUIVALENTS OF IB2 BY MIXING WITH AN EQUAL VOLUME (2.5 - 4 MICROLITERS) OF 2 M AMMONIUM SULFATE, 4% PEG 400 0.1 M NA HEPES PH 7.5 ON A SILICONIZED COVERSLIP WHICH WAS SEALED OVER A 0.8 ML VOLUME OF THE SAME SOLUTION FOR 1 - 4 WEEKS AT ROOM TEMPERATURE., vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate11
24 %PEG40011
30.1 MNa HEPES11

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: CCD / Date: Mar 10, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.1→43.9 Å / Num. obs: 2965 / % possible obs: 68.3 % / Observed criterion σ(I): 0 / Rsym value: 0.097 / Net I/σ(I): 10.2
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 8.5 / Rsym value: 0.084 / % possible all: 39.1
Reflection
*PLUS
Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 39.1 % / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB ENTRY 1FIT

1fit


Resolution: 3.1→8 Å / Rfactor Rfree error: 0.028 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3.5
RfactorNum. reflection% reflectionSelection details
Rfree0.314 125 5 %RANDOM
Rwork0.241 ---
obs0.241 2535 61 %-
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 49 3 1262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.854
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
LS refinement shellResolution: 3.1→3.23 Å / Rfactor Rfree error: 0.156 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.516 11 7 %
Rwork0.284 157 -
obs--33 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION3WATER.PARAMWATER2.TOPH
X-RAY DIFFRACTION4IB2.PARIB2.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.854
LS refinement shell
*PLUS
Rfactor obs: 0.284

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