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- PDB-5z09: ST0452(Y97N)-UTP binding form -

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Basic information

Entry
Database: PDB / ID: 5z09
TitleST0452(Y97N)-UTP binding form
ComponentsDual sugar-1-phosphate nucleotidylyltransferase
KeywordsSUGAR BINDING PROTEIN / UTP binding
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
URIDINE 5'-TRIPHOSPHATE / Bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsHonda, Y. / Nakano, S. / Ito, S. / Dadashipour, M. / Zhang, Z. / Kawarabayasi, Y.
CitationJournal: Appl. Environ. Microbiol. / Year: 2018
Title: Improvement of ST0452N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering
Authors: Honda, Y. / Nakano, S. / Ito, S. / Dadashipour, M. / Zhang, Z. / Kawarabayasi, Y.
History
DepositionDec 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual sugar-1-phosphate nucleotidylyltransferase
B: Dual sugar-1-phosphate nucleotidylyltransferase
C: Dual sugar-1-phosphate nucleotidylyltransferase
D: Dual sugar-1-phosphate nucleotidylyltransferase
E: Dual sugar-1-phosphate nucleotidylyltransferase
F: Dual sugar-1-phosphate nucleotidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,50910
Polymers273,5736
Non-polymers1,9374
Water0
1
A: Dual sugar-1-phosphate nucleotidylyltransferase
hetero molecules

F: Dual sugar-1-phosphate nucleotidylyltransferase

B: Dual sugar-1-phosphate nucleotidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7555
Polymers136,7863
Non-polymers9682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area5710 Å2
ΔGint-19 kcal/mol
Surface area45530 Å2
MethodPISA
2
C: Dual sugar-1-phosphate nucleotidylyltransferase
hetero molecules

E: Dual sugar-1-phosphate nucleotidylyltransferase

D: Dual sugar-1-phosphate nucleotidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7555
Polymers136,7863
Non-polymers9682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area5810 Å2
ΔGint-21 kcal/mol
Surface area45810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.662, 88.417, 179.339
Angle α, β, γ (deg.)90.00, 121.59, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 1 - 401 / Label seq-ID: 1 - 401

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Dual sugar-1-phosphate nucleotidylyltransferase


Mass: 45595.430 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST0452, STK_04520 / Production host: Escherichia coli (E. coli)
References: UniProt: Q975F9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) PEG3350, 0.2M potassium citrate tribasic monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→153 Å / Num. obs: 61139 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.6
Reflection shellResolution: 2.9→2.98 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 3018

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GGO

2ggo


Resolution: 2.91→152.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 19.996 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26662 3064 5 %RANDOM
Rwork0.20884 ---
obs0.21176 58075 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.04 Å2
2---0.17 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.91→152.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18198 0 116 0 18314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01918632
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218503
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.98125173
X-RAY DIFFRACTIONr_angle_other_deg0.841342693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.352326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77125.229765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.473153439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1271577
X-RAY DIFFRACTIONr_chiral_restr0.0730.22876
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0220621
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023878
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.6427.9269337
X-RAY DIFFRACTIONr_mcbond_other9.6387.9259336
X-RAY DIFFRACTIONr_mcangle_it13.7311.87611652
X-RAY DIFFRACTIONr_mcangle_other13.73111.87711653
X-RAY DIFFRACTIONr_scbond_it10.0048.6169293
X-RAY DIFFRACTIONr_scbond_other9.9778.6129281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.80112.64313500
X-RAY DIFFRACTIONr_long_range_B_refined18.03962.41720236
X-RAY DIFFRACTIONr_long_range_B_other18.01962.420230
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A538580.05
12B538580.05
21A543220.04
22C543220.04
31A541620.05
32D541620.05
41A476020.08
42E476020.08
51A466940.08
52F466940.08
61B542060.04
62C542060.04
71B538480.05
72D538480.05
81B477540.07
82E477540.07
91B466240.08
92F466240.08
101C543120.05
102D543120.05
111C478440.07
112E478440.07
121C468060.08
122F468060.08
131D479520.07
132E479520.07
141D469940.08
142F469940.08
151E461080.09
152F461080.09
LS refinement shellResolution: 2.908→2.984 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 199 -
Rwork0.32 3960 -
obs--91.27 %

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