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- PDB-5jj6: Fic-1 (aa134 - 508) from C. elegans -

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Basic information

Entry
Database: PDB / ID: 5jj6
TitleFic-1 (aa134 - 508) from C. elegans
ComponentsAdenosine monophosphate-protein transferase FICD homolog
KeywordsTRANSFERASE / AMPylase
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / nuclear envelope / nuclear membrane / defense response to Gram-negative bacterium / hydrolase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / cytoplasm
Similarity search - Function
Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. ...Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein adenylyltransferase fic-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.907 Å
AuthorsCruz, V.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5R01AR065484-02 United States
CitationJournal: To be published
Title: Fic-1 dimer
Authors: Truttman, M.C. / Cruz, V.E. / Guo, X. / Engert, C. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase FICD homolog
B: Adenosine monophosphate-protein transferase FICD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5494
Polymers86,3572
Non-polymers1922
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-39 kcal/mol
Surface area32000 Å2
2
A: Adenosine monophosphate-protein transferase FICD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2742
Polymers43,1781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Adenosine monophosphate-protein transferase FICD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2742
Polymers43,1781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.152, 192.152, 182.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Adenosine monophosphate-protein transferase FICD homolog


Mass: 43178.250 Da / Num. of mol.: 2 / Fragment: Fido domain, residues 134-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ZK593.8 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LOBSTR
References: UniProt: Q23544, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.1M Ammonium Sulfate, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.907→122.97 Å / Num. obs: 28518 / % possible obs: 97.6 % / Redundancy: 6.3 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ED8

5ed8


Resolution: 2.907→122.97 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2546 1999 7.16 %
Rwork0.2063 --
obs0.2097 27914 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.907→122.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 10 6 5100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095174
X-RAY DIFFRACTIONf_angle_d1.3217021
X-RAY DIFFRACTIONf_dihedral_angle_d15.7161910
X-RAY DIFFRACTIONf_chiral_restr0.054822
X-RAY DIFFRACTIONf_plane_restr0.007909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9068-2.97950.37671360.30591751X-RAY DIFFRACTION94
2.9795-3.060.30141430.27011869X-RAY DIFFRACTION98
3.06-3.15010.31721350.25741760X-RAY DIFFRACTION94
3.1501-3.25170.3181440.25211860X-RAY DIFFRACTION99
3.2517-3.3680.29241440.23861859X-RAY DIFFRACTION99
3.368-3.50280.26591440.22751874X-RAY DIFFRACTION100
3.5028-3.66230.26321450.21511878X-RAY DIFFRACTION99
3.6623-3.85540.26771450.20661870X-RAY DIFFRACTION99
3.8554-4.09690.24611390.19561809X-RAY DIFFRACTION96
4.0969-4.41330.21641420.1881845X-RAY DIFFRACTION98
4.4133-4.85740.24061460.17981891X-RAY DIFFRACTION100
4.8574-5.56030.22861460.20791896X-RAY DIFFRACTION99
5.5603-7.00530.27391410.21641825X-RAY DIFFRACTION95
7.0053-123.07970.21811490.16521928X-RAY DIFFRACTION97

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