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- PDB-7vte: uridine bound structure of Pseudouridine kinase (PUKI) from Esche... -

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Basic information

Entry
Database: PDB / ID: 7vte
Titleuridine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B
ComponentsPseudouridine kinase
KeywordsTRANSFERASE / pseudouridine kinase / pseudourdine / pfkb family
Function / homology
Function and homology information


pseudouridine kinase activity / pseudouridine kinase / phosphorylation
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
: / URIDINE / Pseudouridine kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15296568597 Å
AuthorsKim, S.H. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C2092118 Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.
Authors: Kim, S.H. / Kim, M. / Park, D. / Byun, S. / Rhee, S.
History
DepositionOct 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2May 11, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
D: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,25812
Polymers135,1244
Non-polymers1,1338
Water68538
1
A: Pseudouridine kinase
B: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1296
Polymers67,5622
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-28 kcal/mol
Surface area24420 Å2
MethodPISA
2
C: Pseudouridine kinase
D: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1296
Polymers67,5622
Non-polymers5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-29 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.689, 185.689, 50.754
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSHISHISchain 'A'AA4 - 224 - 22
12LEULEUASNASNchain 'A'AA25 - 10325 - 103
13GLUGLUASNASNchain 'A'AA106 - 308106 - 308
21LYSLYSHISHISchain 'B'BB4 - 224 - 22
22LEULEUASNASNchain 'B'BB25 - 10325 - 103
23GLUGLUASNASNchain 'B'BB106 - 308106 - 308
31LYSLYSHISHISchain 'C'CC4 - 224 - 22
32LEULEUASNASNchain 'C'CC25 - 10325 - 103
33GLUGLUASNASNchain 'C'CC106 - 308106 - 308
41LYSLYSHISHISchain 'D'DD4 - 224 - 22
42LEULEUASNASNchain 'D'DD25 - 10325 - 103
43GLUGLUASNASNchain 'D'DD106 - 308106 - 308

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Components

#1: Protein
Pseudouridine kinase / / Putative pyrimidine kinase


Mass: 33781.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, ...Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, GQE64_02140, GQM28_02110, HVV70_14180, HVX33_21995, HVZ33_08660, NCTC11022_02147, NCTC13216_04879, NCTC9706_04998, SAMEA3752557_00486, WP4S18E08_16210
Production host: Escherichia coli B (bacteria) / References: UniProt: A0A1V3W5E1, pseudouridine kinase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-URI / URIDINE / Uridine


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M magnesium formate, 20% PEG3350, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 104992 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 52.9446533634 Å2 / CC1/2: 0.98 / Net I/σ(I): 12.7
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 10537 / CC1/2: 0.45

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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: 3KZH

3kzh


Resolution: 2.15296568597→36.8926633277 Å / SU ML: 0.472919332187 / Cross valid method: FREE R-VALUE / σ(F): 1.95835313323 / Phase error: 42.0782347199
RfactorNum. reflection% reflection
Rfree0.286592009854 2002 1.92248597987 %
Rwork0.250260285481 102134 -
obs0.250970146051 104136 98.2035250516 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.3853131003 Å2
Refinement stepCycle: LAST / Resolution: 2.15296568597→36.8926633277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9113 0 4 38 9155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005462625189339277
X-RAY DIFFRACTIONf_angle_d1.028843545112637
X-RAY DIFFRACTIONf_chiral_restr0.04117956310931468
X-RAY DIFFRACTIONf_plane_restr0.004916484945491632
X-RAY DIFFRACTIONf_dihedral_angle_d13.84325745713241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.153-2.20680.4738296860811360.4232154801096734X-RAY DIFFRACTION89.8274058577
2.2068-2.26650.4164532322621450.4219798181177323X-RAY DIFFRACTION99.2821058229
2.2665-2.33310.4089353040781440.4076417352537303X-RAY DIFFRACTION98.531357502
2.3331-2.40840.4263633414751480.3883840803957449X-RAY DIFFRACTION99.5805479093
2.4084-2.49450.4709437861691380.3754188265537351X-RAY DIFFRACTION99.4819341126
2.4945-2.59430.3084074099641480.3399967428697356X-RAY DIFFRACTION99.760701941
2.5943-2.71240.4591338473061540.3208382314317444X-RAY DIFFRACTION99.476302697
2.7124-2.85530.4226465473291440.3141599721817379X-RAY DIFFRACTION99.4053911205
2.8553-3.03420.3559411677141420.3055189399847350X-RAY DIFFRACTION99.1529910005
3.0342-3.26830.3721647111011390.284946864947347X-RAY DIFFRACTION99.1129352575
3.2683-3.59690.2941231958011440.2540649577997375X-RAY DIFFRACTION99.208338831
3.5969-4.11680.3002799456711390.2333164154737297X-RAY DIFFRACTION98.1002638522
4.1168-5.18450.2317287679571430.1805148537187318X-RAY DIFFRACTION98.4560570071
5.1845-36.892660.1827794527711380.1955289134787108X-RAY DIFFRACTION95.5684515959
Refinement TLS params.Method: refined / Origin x: 60.7364118129 Å / Origin y: -1.94780530455 Å / Origin z: 13.9111275149 Å
111213212223313233
T0.556607106485 Å20.0400145826023 Å2-0.0855423311085 Å2-0.601080805268 Å20.0556895502014 Å2--0.866496267653 Å2
L0.285984863275 °2-0.228306615056 °2-0.0485723027686 °2-0.0704129355434 °20.0344397870794 °2---0.0480617493383 °2
S-0.0111373424001 Å °0.0440415839071 Å °0.0504308697387 Å °0.0354296839601 Å °0.0351814599131 Å °-0.0317282360504 Å °-0.0753066012047 Å °0.0416524609955 Å °-0.0193846861523 Å °
Refinement TLS groupSelection details: all

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