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- PDB-7vtd: Unliganded structure of Pseudouridine kinase (PUKI) from Escheric... -

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Basic information

Entry
Database: PDB / ID: 7vtd
TitleUnliganded 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
: / Pseudouridine kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15054869646 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

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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)135,2818
Polymers135,1244
Non-polymers1564
Water3,675204
1
A: Pseudouridine kinase
B: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6404
Polymers67,5622
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-27 kcal/mol
Surface area24920 Å2
MethodPISA
2
C: Pseudouridine kinase
D: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6404
Polymers67,5622
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.805, 186.805, 49.648
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 3 - 308 / Label seq-ID: 3 - 308

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AA
2chain 'B'BB
3chain 'C'CC
4chain 'D'DD

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M magnesium formate, 20% PEG 3350, 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: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 104841 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 49.5724471261 Å2 / CC1/2: 0.99 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 10500 / CC1/2: 0.5

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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: 2.15054869646→33.2888937491 Å / SU ML: 0.507065525363 / Cross valid method: FREE R-VALUE / σ(F): 1.95834498789 / Phase error: 41.2002494246
RfactorNum. reflection% reflection
Rfree0.267634467536 1990 1.90485306787 %
Rwork0.232103541092 102480 -
obs0.232811756303 104470 99.2211985944 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.9681233502 Å2
Refinement stepCycle: LAST / Resolution: 2.15054869646→33.2888937491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9236 0 4 204 9444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004222101781239404
X-RAY DIFFRACTIONf_angle_d0.90470669729512802
X-RAY DIFFRACTIONf_chiral_restr0.0342824800491472
X-RAY DIFFRACTIONf_plane_restr0.003969641698661670
X-RAY DIFFRACTIONf_dihedral_angle_d14.161152943314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15054869646-2.20430.4637666401041380.3982052113817173X-RAY DIFFRACTION97.9501607717
2.2043-2.26390.475635719971380.3944408606097395X-RAY DIFFRACTION99.8541887593
2.2639-2.33050.4817027106511440.3932568202987391X-RAY DIFFRACTION99.8674618953
2.3305-2.40570.4161901192011400.3719262325897352X-RAY DIFFRACTION99.8800159979
2.4057-2.49170.4479975713681420.3532669848637400X-RAY DIFFRACTION99.8808104887
2.4917-2.59140.4409794282211460.3540751654337319X-RAY DIFFRACTION99.8662207358
2.5914-2.70930.4063884022181500.3144750650427389X-RAY DIFFRACTION99.8014297061
2.7093-2.8520.4457588894081420.3088861161647350X-RAY DIFFRACTION99.7868939798
2.852-3.03060.3478739714531340.2978005715487375X-RAY DIFFRACTION99.6946362188
3.0306-3.26440.304644234741460.2563935525877307X-RAY DIFFRACTION99.2542282594
3.2644-3.59260.2735712920871380.2306778949297337X-RAY DIFFRACTION99.0197377136
3.5926-4.11160.2349170265461460.2027538443267311X-RAY DIFFRACTION99.3207245605
4.1116-5.17710.1806719030831390.1579752257727299X-RAY DIFFRACTION99.080857866
5.1771-33.28889370.1728178208871470.1664122611477082X-RAY DIFFRACTION95.8880488128
Refinement TLS params.Method: refined / Origin x: 61.0291501445 Å / Origin y: -1.80495814318 Å / Origin z: 14.4077919991 Å
111213212223313233
T0.484509761296 Å20.0572490752128 Å2-0.0471974415529 Å2-0.5471109693 Å20.0273007284827 Å2--1.25405984789 Å2
L0.142120169053 °2-0.148219988834 °20.0213623770022 °2-0.00589765033873 °2-0.00847991108152 °2---0.0887582310041 °2
S-0.00564706535936 Å °0.0370333924997 Å °0.0586966705952 Å °0.0301446480891 Å °0.02307211557 Å °-0.0303259819005 Å °-0.105687178038 Å °0.0619318101932 Å °-0.015922391733 Å °
Refinement TLS groupSelection details: all

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