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- PDB-2fhi: SUBSTRATE ANALOG (IB2) COMPLEX WITH THE HIS 96 ASN SUBSTITUTION O... -

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Basic information

Entry
Database: PDB / ID: 2fhi
TitleSUBSTRATE ANALOG (IB2) COMPLEX WITH THE HIS 96 ASN SUBSTITUTION OF THE FRAGILE HISTIDINE TRIAD PROTEIN, FHIT
ComponentsFRAGILE HISTIDINE TRIAD PROTEIN
KeywordsNUCLEOTIDE-BINDING PROTEIN / CANCER / DIADENOSINE TRIPHOSPHATE HYDROLASE / ACTIVE SITE SUBSTITUTION / HISTIDINE TRIAD / TUMOR SUPPRESSOR
Function / homology
Function and homology information


adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity ...adenylylsulfate-ammonia adenylyltransferase / adenylylsulfatase / diadenosine triphosphate catabolic process / adenylylsulfate-ammonia adenylyltransferase activity / bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / purine nucleotide metabolic process / adenylylsulfatase activity / 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 / 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: 2.6 Å
AuthorsPace, H.C. / Garrison, P.N. / Robinson, A.K. / Barnes, L.D. / Draganescu, A. / Rosler, A. / Blackburn, G.M. / Siprashvili, Z. / Croce, C.M. / Heubner, 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: 1997
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
DepositionApr 1, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)17,6332
Polymers16,8621
Non-polymers7711
Water57632
1
A: FRAGILE HISTIDINE TRIAD PROTEIN
hetero molecules

A: FRAGILE HISTIDINE TRIAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2654
Polymers33,7242
Non-polymers1,5412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area11200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.460, 50.460, 268.950
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


Mass: 16862.158 Da / Num. of mol.: 1 / Mutation: H96N
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


Mass: 18.015 Da / Num. of mol.: 32 / 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 growpH: 7.5
Details: FHIT H96N WAS COCRYSTALLIZED WITH 2.9 MOLAR EQUIVALENTS OF IB2 BY VAPOR DIFFUSION WITH 2 M AMMONIUM SULFATE, 4% PEG 400, AND 0.1M NA HEPES PH 7.5.
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: 0.9188
DetectorType: ADSC / Detector: CCD / Date: Dec 22, 1997
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2→21.8 Å / Num. obs: 12563 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 3
Reflection shellResolution: 2→2.12 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2 / Rsym value: 0.267 / % possible all: 80
Reflection
*PLUS
Num. measured all: 36336
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: REFINEMENT
Starting model: PDB ENTRY 1FIT

1fit


Resolution: 2.6→6 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.278 428 8 %RANDOM
Rwork0.241 ---
obs0.241 5718 84 %-
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 49 32 1072
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
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: 2.6→2.71 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.436 51 6.76 %
Rwork0.356 553 -
obs--83.4 %
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_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor obs: 0.356

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