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- PDB-5xu6: Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinas... -

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Basic information

Entry
Database: PDB / ID: 5xu6
TitleCrystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) from Cryptococcus neoformans
ComponentsInositol-pentakisphosphate 2-kinase
KeywordsTRANSFERASE / Inositol 1 / 3 / 4 / 5 / 6-pentakisphosphate 2-kinase / IPK1 / Inositol phosphate kinase
Function / homology
Function and homology information


inositol-pentakisphosphate 2-kinase / inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity / ATP binding
Similarity search - Function
Inositol-pentakisphosphate 2-kinase, N-lobe / Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase, N-terminal lobe / Inositol-pentakisphosphate 2-kinase / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inositol-pentakisphosphate 2-kinase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsOh, J. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01101901 Korea, Republic Of
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from Cryptococcus neoformans.
Authors: Oh, J. / Lee, D.G. / Bahn, Y.S. / Rhee, S.
History
DepositionJun 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Inositol-pentakisphosphate 2-kinase
B: Inositol-pentakisphosphate 2-kinase
C: Inositol-pentakisphosphate 2-kinase
D: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,07613
Polymers187,2114
Non-polymers8659
Water6,431357
1
A: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9953
Polymers46,8031
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9953
Polymers46,8031
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0914
Polymers46,8031
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Inositol-pentakisphosphate 2-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9953
Polymers46,8031
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.810, 59.740, 379.674
Angle α, β, γ (deg.)90.000, 96.360, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11C-669-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRARGARGchain AAA19 - 41521 - 417
2THRTHRTHRTHRchain BBB19 - 41421 - 416
3PROPROARGARGchain CCC13 - 41515 - 417
4PROPROARGARGchain DDD13 - 41515 - 417

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Components

#1: Protein
Inositol-pentakisphosphate 2-kinase / Inositol-pentakisphosphate 2-kinase / variant


Mass: 46802.840 Da / Num. of mol.: 4 / Mutation: Q64A, E66A, E67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_01294 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VKS8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6.0, 2.2 M ammonium sulfate, 50 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.35→50.61 Å / Num. obs: 88651 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.082 / Rrim(I) all: 0.159 / Net I/σ(I): 5.7 / Num. measured all: 322811 / Scaling rejects: 207
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.393.70.6241687645920.5010.3770.7331.699
12.66-50.612.50.08411504640.9750.060.1049.873.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.31data scaling
SOLVEphasing
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.35→37.37 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 4401 4.97 %
Rwork0.2342 84212 -
obs0.2358 88613 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.71 Å2 / Biso mean: 52.2376 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 2.35→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 45 357 11782
Biso mean--69.45 45.01 -
Num. residues----1477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511674
X-RAY DIFFRACTIONf_angle_d1.05915880
X-RAY DIFFRACTIONf_chiral_restr0.0451786
X-RAY DIFFRACTIONf_plane_restr0.0062026
X-RAY DIFFRACTIONf_dihedral_angle_d13.8864198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6456X-RAY DIFFRACTION13.576TORSIONAL
12B6456X-RAY DIFFRACTION13.576TORSIONAL
13C6456X-RAY DIFFRACTION13.576TORSIONAL
14D6456X-RAY DIFFRACTION13.576TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.32281240.30892800292499
2.3767-2.40470.34391460.30832798294499
2.4047-2.4340.35891390.29452781292099
2.434-2.46480.31451410.292728292970100
2.4648-2.49720.3191330.292828462979100
2.4972-2.53140.36021320.2812760289299
2.5314-2.56760.27761470.2842830297799
2.5676-2.60590.31341470.27542822296999
2.6059-2.64660.32941620.291627602922100
2.6466-2.690.33551580.28122826298499
2.69-2.73630.31171620.2682795295799
2.7363-2.78610.29981700.26022734290499
2.7861-2.83960.30031620.265528332995100
2.8396-2.89760.31051420.25722796293899
2.8976-2.96060.29041200.2612807292798
2.9606-3.02940.31411220.26982804292699
3.0294-3.10510.33781550.25562827298299
3.1051-3.1890.30581660.26522783294999
3.189-3.28280.28261220.25562800292298
3.2828-3.38870.29491460.24532791293799
3.3887-3.50980.25311440.22692825296998
3.5098-3.65020.28851630.22022768293198
3.6502-3.81610.2011460.20982777292399
3.8161-4.01710.25071370.21012854299198
4.0171-4.26850.22311450.19162839298499
4.2685-4.59750.19141460.19142847299399
4.5975-5.05920.22421550.19152827298299
5.0592-5.78890.26011520.20722842299499
5.7889-7.28450.26111570.23352908306599
7.2845-37.3750.2251600.20952703286391

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