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- PDB-1tt9: Structure of the bifunctional and Golgi associated formiminotrans... -

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Basic information

Entry
Database: PDB / ID: 1tt9
TitleStructure of the bifunctional and Golgi associated formiminotransferase cyclodeaminase octamer
ComponentsFormimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
KeywordsTRANSFERASE / LYASE / hepatitis autoantigen / intermediate channeling / protein assembly / vimentin
Function / homology
Function and homology information


Histidine catabolism / glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / intermediate filament binding / smooth endoplasmic reticulum membrane / histidine catabolic process to glutamate and formamide / histidine catabolic process to glutamate and formate / folic acid binding ...Histidine catabolism / glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / intermediate filament binding / smooth endoplasmic reticulum membrane / histidine catabolic process to glutamate and formamide / histidine catabolic process to glutamate and formate / folic acid binding / endoplasmic reticulum-Golgi intermediate compartment / cytoskeleton organization / centriole / microtubule binding / Golgi membrane / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain ...Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase
Similarity search - Domain/homology
Formimidoyltransferase-cyclodeaminase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.42 Å
AuthorsMao, Y. / Vyas, N.K. / Vyas, M.N. / Chen, D.H. / Ludtke, S.J. / Chiu, W. / Quiocho, F.A.
CitationJournal: Embo J. / Year: 2004
Title: Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer
Authors: Mao, Y. / Vyas, N.K. / Vyas, M.N. / Chen, D.H. / Ludtke, S.J. / Chiu, W. / Quiocho, F.A.
History
DepositionJun 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
B: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
C: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
D: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)


Theoretical massNumber of molelcules
Total (without water)237,4184
Polymers237,4184
Non-polymers00
Water0
1
A: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
B: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

A: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
B: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

A: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
B: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

A: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
B: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)


Theoretical massNumber of molelcules
Total (without water)474,8378
Polymers474,8378
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
2
C: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
D: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

C: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
D: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

C: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
D: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)

C: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)
D: Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein)


Theoretical massNumber of molelcules
Total (without water)474,8378
Polymers474,8378
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)134.848, 134.848, 156.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Formimidoyltransferase-cyclodeaminase (Formiminotransferase- cyclodeaminase) (FTCD) (58 kDa microtubule-binding protein) / Coordinate model: Cα atoms only


Mass: 59354.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ftcd / Plasmid: PET-21(b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O88618, glutamate formimidoyltransferase, formimidoyltetrahydrofolate cyclodeaminase

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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 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 600, sodium sulphate, HEPES, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791, 0.9793, 0.9716
DetectorType: SBC-2 / Detector: CCD / Date: Nov 4, 2003 / Details: Si 111 monochromator
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97161
ReflectionResolution: 3.4→50 Å / Num. all: 36461 / Num. obs: 31393 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 99 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.113 / Net I/σ(I): 6
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 8 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3775 / Rsym value: 0.249 / % possible all: 64.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 3.42→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 5784186.16 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: this structure contains only alpha carbons
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1525 4.9 %RANDOM
Rwork0.251 ---
all0.262 33845 --
obs0.251 31393 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--14.69 Å20 Å20 Å2
2---14.69 Å20 Å2
3---29.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 3.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 0 2160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d1.15
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.6 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 185 4.7 %
Rwork0.337 3775 -
obs-3775 64.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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