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- PDB-4u0z: Eukaryotic Fic Domain containing protein with bound APCPP -

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Basic information

Entry
Database: PDB / ID: 4u0z
TitleEukaryotic Fic Domain containing protein with bound APCPP
ComponentsAdenosine monophosphate-protein transferase FICD
KeywordsTRANSFERASE / TPR / FIC / APCPP / adenylation
Function / homology
Function and homology information


protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylylation / regulation of IRE1-mediated unfolded protein response / protein adenylyltransferase / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP binding / identical protein binding
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Protein adenylyltransferase FICD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsCole, A.R. / Bunney, T.D. / Katan, M.
CitationJournal: Structure / Year: 2014
Title: Crystal structure of the human, FIC-domain containing protein HYPE and implications for its functions.
Authors: Bunney, T.D. / Cole, A.R. / Broncel, M. / Esposito, D. / Tate, E.W. / Katan, M.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase FICD
B: Adenosine monophosphate-protein transferase FICD
C: Adenosine monophosphate-protein transferase FICD
D: Adenosine monophosphate-protein transferase FICD
E: Adenosine monophosphate-protein transferase FICD
F: Adenosine monophosphate-protein transferase FICD
G: Adenosine monophosphate-protein transferase FICD
H: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,62224
Polymers316,3868
Non-polymers4,23616
Water14,700816
1
G: Adenosine monophosphate-protein transferase FICD
hetero molecules

A: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
MethodPISA
2
A: Adenosine monophosphate-protein transferase FICD
hetero molecules

G: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area30120 Å2
MethodPISA
3
B: Adenosine monophosphate-protein transferase FICD
H: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area30370 Å2
MethodPISA
4
E: Adenosine monophosphate-protein transferase FICD
hetero molecules

C: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
5
C: Adenosine monophosphate-protein transferase FICD
hetero molecules

E: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3700 Å2
ΔGint-32 kcal/mol
Surface area30840 Å2
MethodPISA
6
F: Adenosine monophosphate-protein transferase FICD
hetero molecules

D: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
7
D: Adenosine monophosphate-protein transferase FICD
hetero molecules

F: Adenosine monophosphate-protein transferase FICD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1566
Polymers79,0972
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 83.754, 130.023
Angle α, β, γ (deg.)89.92, 89.57, 89.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Adenosine monophosphate-protein transferase FICD / AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin- ...AMPylator FICD / FIC domain-containing protein / Huntingtin yeast partner E / Huntingtin-interacting protein 13 / HIP-13 / Huntingtin-interacting protein E


Mass: 39548.273 Da / Num. of mol.: 8 / Fragment: UNP residues 102-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FICD, HIP13, HYPE, UNQ3041/PRO9857 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 200mM Na K Tartrate, 100mM Bis-Tris Propane 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.95→43.34 Å / Num. obs: 65073 / % possible obs: 94.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 55.82 Å2 / Net I/σ(I): 4.4
Reflection shellResolution: 2.95→3.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cuc

3cuc


Resolution: 2.95→43.34 Å / Cor.coef. Fo:Fc: 0.8842 / Cor.coef. Fo:Fc free: 0.8616 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3307 5.08 %RANDOM
Rwork0.2059 ---
obs0.2082 65073 95.02 %-
Displacement parametersBiso mean: 61.13 Å2
Baniso -1Baniso -2Baniso -3
1-10.1178 Å22.6388 Å21.8468 Å2
2---26.9335 Å2-3.9114 Å2
3---16.8157 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.95→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20256 0 1072 816 22144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120963HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1128555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7118SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes469HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3173HARMONIC5
X-RAY DIFFRACTIONt_it20963HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion21.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2843SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24240SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2793 112 4.67 %
Rwork0.2316 2285 -
all0.2338 2397 -
obs--95.02 %

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