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- PDB-1ems: CRYSTAL STRUCTURE OF THE C. ELEGANS NITFHIT PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1ems
TitleCRYSTAL STRUCTURE OF THE C. ELEGANS NITFHIT PROTEIN
ComponentsNIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
KeywordsANTITUMOR PROTEIN / WORM / NITRILASE / FHIT / NUCLEOTIDE-BINDING PROTEIN / CANCER / DIADENOSINE POLYPHOSPHATE HYDROLASE / HISTIDINE TRIAD / TUMOR SUPPRESSOR / ROSETTA STONE
Function / homology
Function and homology information


bis(5'-adenosyl)-triphosphatase / bis(5'-adenosyl)-triphosphatase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / nucleobase-containing compound metabolic process / nucleotide binding
Similarity search - Function
Uncharacterised protein family UPF0012, conserved site / Uncharacterized protein family UPF0012 signature. / FHIT family / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. ...Uncharacterised protein family UPF0012, conserved site / Uncharacterized protein family UPF0012 signature. / FHIT family / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HIT-like / HIT family, subunit A / HIT-like superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHYL MERCURY ION / Nitrilase and fragile histidine triad fusion protein NitFhit
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / TWO WAVELENGTH ANOMALOUS DIFFRACTION / Resolution: 2.8 Å
AuthorsPace, H.C. / Hodawadekar, S.C. / Draganescu, A. / Huang, J. / Bieganowski, P. / Pekarsky, Y. / Croce, C.M. / Brenner, C.
Citation
Journal: Curr.Biol. / Year: 2000
Title: Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers.
Authors: Pace, H.C. / Hodawadekar, S.C. / Draganescu, A. / Huang, J. / Bieganowski, P. / Pekarsky, Y. / Croce, C.M. / Brenner, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Nitrilase and Fhit homologs are encoded as fusion proteins in Drosophila melanogaster and Caenorhabditis elegans
Authors: Pekarsky, Y. / Campiglio, M. / Siprashvili, Z. / Druck, T. / Sedkov, Y. / Tillib, S. / Draganescu, A. / Wermuth, P. / Rothman, J.H. / Huebner, K. / Buchberg, A.M. / Mazo, A. / Brenner, C. / Croce, C.M.
#2: 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.
#3: Journal: J.CELL PHYSIOL. / Year: 1999
Title: The Histidine Triad Superfamily of Nucleotide-Binding Proteins
Authors: Brenner, C. / Bieganowski, P. / Pace, H.C. / Huebner, K.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
B: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,37412
Polymers100,0162
Non-polymers1,35810
Water2,900161
1
A: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
B: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
hetero molecules

A: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
B: NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,74924
Polymers200,0324
Non-polymers2,71720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area21730 Å2
ΔGint-179 kcal/mol
Surface area58720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.750, 100.440, 158.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer constructed from the crystallographic symmetry partners of chains A and B

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Components

#1: Protein NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN / NITFHIT


Mass: 50007.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PSGA02 / Production host: Escherichia coli (E. coli) / References: UniProt: O76463
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: methylpentanediol, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
25 mMNa+-HEPES1drop
325 mM1dropNaCl
42.5 mMdithiothreitol1drop
519 %MPD1drop
638 %MPD1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0090, 0.9928
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 1999
RadiationProtocol: TWO WAVELENGTH ANOMALOUS DIFFRACTION / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
20.99281
ReflectionResolution: 2.8→40 Å / Num. all: 49928 / Num. obs: 49928 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.088 / Num. unique all: 3897
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 97.9 %
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: TWO WAVELENGTH ANOMALOUS DIFFRACTION
Resolution: 2.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5410833.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: mlhl target and bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3315 6.7 %random
Rwork0.19 ---
all0.181 49386 --
obs0.181 49386 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.7963 Å2 / ksol: 0.343798 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å20 Å20 Å2
2---0.55 Å20 Å2
3----5.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6520 0 27 161 6708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 271 6.5 %
Rwork0.256 3897 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion2.paramion2.top
X-RAY DIFFRACTION4mpd2.parmpd2.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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