[English] 日本語
Yorodumi
- PDB-3c5i: Crystal structure of Plasmodium knowlesi choline kinase, PKH_134520 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c5i
TitleCrystal structure of Plasmodium knowlesi choline kinase, PKH_134520
Components
  • Choline kinase
  • Cleaved fragment of N-terminal expression tag
KeywordsTRANSFERASE / choline / kinase / malaria / Plasmodium knowlesi / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLINE ION / Unknown ligand / Choline kinase
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWernimont, A.K. / Hills, T. / Lew, J. / Wasney, G. / Senesterra, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Schapira, M. / Bochkarev, A. ...Wernimont, A.K. / Hills, T. / Lew, J. / Wasney, G. / Senesterra, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Xiao, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Plasmodium knowlesi choline kinase, PKH_134520.
Authors: Wernimont, A.K. / Hills, T. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. ...Authors: Wernimont, A.K. / Hills, T. / Lew, J. / Wasney, G. / Senisterra, G. / Kozieradzki, I. / Cossar, D. / Vedadi, M. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Xiao, T.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choline kinase
B: Choline kinase
C: Choline kinase
D: Choline kinase
E: Cleaved fragment of N-terminal expression tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,55628
Polymers176,1695
Non-polymers1,38723
Water7,278404
1
A: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1926
Polymers43,8391
Non-polymers3535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1927
Polymers43,8391
Non-polymers3536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1807
Polymers43,8391
Non-polymers3416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1807
Polymers43,8391
Non-polymers3416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cleaved fragment of N-terminal expression tag


  • defined by software
  • 813 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8131
Polymers8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.985, 71.993, 116.393
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 280 - 310 / Label seq-ID: 280 - 310

Dom-IDAuth asym-IDLabel asym-ID
1DD
2AA
3BB
4CC

-
Components

-
Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein
Choline kinase


Mass: 43839.105 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Gene: PKH_134520 / Plasmid: p15-tev-lic / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: D0VWT1*PLUS
#2: Protein/peptide Cleaved fragment of N-terminal expression tag


Mass: 812.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cleaved fragment of N-terminal expression tag

-
Non-polymers , 6 types, 427 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 11% PEG 8000, 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.3, 4 mM CaCl2, 2 mM TCEP, 2 mM Phosphocholine, 15 % Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2007 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 107787 / Num. obs: 107787 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.0461 / Χ2: 0.955 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.4 / Num. unique all: 10742 / Rsym value: 0.702 / Χ2: 0.903 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.02 Å
Translation2.5 Å37.02 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QG7

2qg7


Resolution: 2.2→24.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.051 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.258 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4736 5 %RANDOM
Rwork0.212 ---
all0.215 94289 --
obs0.215 94289 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.797 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11551 0 85 404 12040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211995
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9516251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.651416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00224.501611
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.649152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8881548
X-RAY DIFFRACTIONr_chiral_restr0.0980.21761
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029107
X-RAY DIFFRACTIONr_nbd_refined0.2110.25431
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2586
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.223
X-RAY DIFFRACTIONr_mcbond_it0.5911.57232
X-RAY DIFFRACTIONr_mcangle_it0.961211367
X-RAY DIFFRACTIONr_scbond_it1.53935533
X-RAY DIFFRACTIONr_scangle_it2.2464.54867
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1D98TIGHT POSITIONAL0.040.05
2A98TIGHT POSITIONAL0.060.05
3B98TIGHT POSITIONAL0.050.05
4C98TIGHT POSITIONAL0.040.05
1D86LOOSE POSITIONAL0.535
2A86LOOSE POSITIONAL0.495
3B86LOOSE POSITIONAL0.475
4C86LOOSE POSITIONAL0.345
1D98TIGHT THERMAL0.090.5
2A98TIGHT THERMAL0.10.5
3B98TIGHT THERMAL0.10.5
4C98TIGHT THERMAL0.110.5
1D86LOOSE THERMAL1.1410
2A86LOOSE THERMAL1.2210
3B86LOOSE THERMAL1.7510
4C86LOOSE THERMAL1.4810
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 351 -
Rwork0.264 6548 -
all-6899 -
obs-6548 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5602-0.271-0.86613.50181.40068.5404-0.2114-0.17930.0610.01160.1198-0.4378-0.20140.43520.0916-0.0154-0.036-0.0891-0.0240.0151-0.1142114.60724.854-28.247
21.5463-0.4212-1.00482.52150.36054.31810.06360.0174-0.04620.1550.0960.17960.2546-0.0374-0.1596-0.1713-0.0093-0.0921-0.08830.0638-0.1095105.31825.316-1.557
32.82120.2978-0.10643.4477-0.56513.7390.1805-0.12270.23660.28440.17740.4464-0.2872-0.4042-0.358-0.15250.0430.0086-0.08490.0478-0.1012100.87435.3624.208
44.6205-0.347-1.73763.6970.08458.3575-0.1680.25350.1714-0.19130.00870.2682-0.5789-0.55920.15930.05650.0484-0.0994-0.00750.0133-0.105455.29557.63426.756
51.90710.17710.12843.687-0.38153.31580.11730.1740.0214-0.209-0.102-0.48610.0492-0.0284-0.0152-0.17680.0353-0.0175-0.0329-0.0166-0.037865.02656.767-0.431
63.9086-1.48360.25624.60550.14732.19150.11410.36580.4991-0.3819-0.136-0.8072-0.2280.18820.0219-0.1722-0.00030.0212-0.03430.08720.05967.48167.238-4.668
77.40691.703-3.64794.5669-0.24037.91520.1627-0.05720.3858-0.22720.0409-0.2415-0.1932-0.0646-0.2035-0.0439-0.0419-0.03660.0530.011-0.050849.81225.59868.538
82.2069-0.8271-0.05692.4701-0.85721.87420.09290.1475-0.1048-0.0783-0.09820.00180.1073-0.00860.0053-0.06920.0241-0.1052-0.02750.0037-0.207168.32727.18745.918
93.5672-1.9394-0.24476.02240.15372.31440.14390.24020.2651-0.4093-0.2467-0.6105-0.01980.25450.1028-0.0780.0143-0.03910.0370.1227-0.092277.8535.24541.106
104.00492.9483-5.27115.8977-4.30419.79340.12220.08350.2610.0110.02650.1484-0.3180.1274-0.1487-0.0172-0.0497-0.0760.06160.015-0.0611106.59229.24666.948
111.7375-1.0020.25572.7285-1.23442.06350.16540.1601-0.1271-0.3901-0.07680.07540.2864-0.1917-0.08860.03310.0247-0.1050.0124-0.0191-0.1656119.19631.22745.428
122.7663-0.47430.65914.1422-1.02482.10420.24750.3436-0.0547-0.5956-0.322-0.62380.46580.32040.07450.02260.1127-0.0270.04680.0379-0.1053132.19931.93242.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 6911 - 69
2X-RAY DIFFRACTION2AA70 - 20170 - 201
3X-RAY DIFFRACTION3AA202 - 369202 - 369
4X-RAY DIFFRACTION4BB12 - 7212 - 72
5X-RAY DIFFRACTION5BB73 - 20973 - 209
6X-RAY DIFFRACTION6BB210 - 369210 - 369
7X-RAY DIFFRACTION7CC10 - 6210 - 62
8X-RAY DIFFRACTION8CC63 - 29363 - 293
9X-RAY DIFFRACTION9CC296 - 369296 - 369
10X-RAY DIFFRACTION10DD11 - 6011 - 60
11X-RAY DIFFRACTION11DD61 - 20161 - 201
12X-RAY DIFFRACTION12DD202 - 369202 - 369

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more