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- PDB-2ggq: complex of hypothetical glucose-1-phosphate thymidylyltransferase... -

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Basic information

Entry
Database: PDB / ID: 2ggq
Titlecomplex of hypothetical glucose-1-phosphate thymidylyltransferase from sulfolobus tokodaii
Components401aa long hypothetical glucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / BETA BARREL
Function / homology
Function and homology information


galactosamine-1-phosphate N-acetyltransferase / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / UDP-N-acetylglucosamine diphosphorylase ...galactosamine-1-phosphate N-acetyltransferase / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / nucleotide binding
Similarity search - Function
UDP-GlcNAc diphosphorylase/GlcNAc-1-P N-acetyltransferase, GlmU, archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...UDP-GlcNAc diphosphorylase/GlcNAc-1-P N-acetyltransferase, GlmU, archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / THYMIDINE-5'-TRIPHOSPHATE / : / Bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRajakannan, V. / Mizushima, T. / Suzuki, A. / Masui, R. / Kuramitsu, S. / Yamane, T.
CitationJournal: To be published
Title: complex of hypothetical glucose-1-phosphate thymidylyltransferase from sulfolobus tokodaii
Authors: Rajakannan, V. / Yamane, T.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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:
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Assembly

Deposited unit
A: 401aa long hypothetical glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4365
Polymers44,5731
Non-polymers8634
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 401aa long hypothetical glucose-1-phosphate thymidylyltransferase
hetero molecules

A: 401aa long hypothetical glucose-1-phosphate thymidylyltransferase
hetero molecules

A: 401aa long hypothetical glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,30915
Polymers133,7203
Non-polymers2,58912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10100 Å2
ΔGint-23 kcal/mol
Surface area45060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.750, 122.750, 95.518
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-687-

HOH

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Components

#1: Protein 401aa long hypothetical glucose-1-phosphate thymidylyltransferase


Mass: 44573.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Production host: Escherichia coli (E. coli)
References: GenBank: 15621447, UniProt: Q975F9*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 13% PEG 3350, 0.1M KI, 50mM dTTP, 20mM TRIS-HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36018 / Num. obs: 35513 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GG0

2gg0


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25162 1771 5 %RANDOM
Rwork0.19058 ---
all0.2485 35513 --
obs0.19354 33712 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0.67 Å20 Å2
2---1.33 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 32 197 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223226
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.994362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.2935400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54925.113133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70415601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9141514
X-RAY DIFFRACTIONr_chiral_restr0.130.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022353
X-RAY DIFFRACTIONr_nbd_refined0.2280.21552
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.221
X-RAY DIFFRACTIONr_mcbond_it0.9871.51985
X-RAY DIFFRACTIONr_mcangle_it1.75123222
X-RAY DIFFRACTIONr_scbond_it2.54831241
X-RAY DIFFRACTIONr_scangle_it4.2074.51140
LS refinement shellResolution: 2.004→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 134 -
Rwork0.188 2124 -
obs--86.65 %

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