[English] 日本語
Yorodumi
- PDB-4qox: Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qox
TitleCrystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500
ComponentsCalcium-dependent protein kinase 4
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / cdpk / plasmodium / malaria
Function / homology
Function and homology information


MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine phosphatase activity / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / catalytic activity / cell differentiation / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...MAPK6/MAPK4 signaling / calcium-dependent protein serine/threonine phosphatase activity / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / catalytic activity / cell differentiation / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / calcium ion binding / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DXR / Calcium-dependent protein kinase 4
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.748 Å
AuthorsWernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. ...Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of CDPK4 from Plasmodium Falciparum, PF3D7_0717500
Authors: Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Authors: Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Seitova, A. / He, H. / Loppnau, P. / Neculai, M. / Amani, M. / Lin, Y.H. / Ravichandran, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Lovato, D.V.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: Calcium-dependent protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5243
Polymers62,1391
Non-polymers3852
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.289, 75.967, 92.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Calcium-dependent protein kinase 4


Mass: 62139.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: CDPK4, CPK4, PF07_0072 / Plasmid: DH5-alpha / Cell line (production host): SF9SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8IBS5, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DXR / 3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 360.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18BrN5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5% glycerol 1mM 3MBPP1 5 mM TCEP 28% PEG2000 MME 0.1 M BisTris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Number: 100901 / Rmerge(I) obs: 0.143 / Χ2: 0.97 / D res high: 2.75 Å / D res low: 45 Å / Num. obs: 13454 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
7.454510.0822.4316.5
5.927.4510.0791.0367.1
5.175.9210.11.2017.2
4.75.1710.0971.4887.4
4.364.710.0951.5037.4
4.114.3610.0971.3057.5
3.94.1110.1141.1347.6
3.733.910.1361.1117.6
3.593.7310.1721.0357.6
3.463.5910.180.8287.6
3.363.4610.2390.8687.6
3.263.3610.2810.7447.6
3.173.2610.3110.7457.7
3.13.1710.3840.6637.7
3.033.110.4660.6097.6
2.963.0310.5180.6117.7
2.92.9610.5920.6217.7
2.852.910.6330.5547.7
2.82.8510.7420.5537.7
2.752.810.9020.5197.7
ReflectionResolution: 2.75→45 Å / Num. all: 13464 / Num. obs: 13454 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 55.87 Å2 / Rmerge(I) obs: 0.143 / Χ2: 0.973 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.75-2.87.70.9022.866740.519100
2.8-2.857.70.7426410.553100
2.85-2.97.70.6336720.554100
2.9-2.967.70.5926520.621100
2.96-3.037.70.5186670.611100
3.03-3.17.60.4666410.609100
3.1-3.177.70.3846660.663100
3.17-3.267.70.3116490.745100
3.26-3.367.60.2816840.744100
3.36-3.467.60.2396550.868100
3.46-3.597.60.186560.828100
3.59-3.737.60.1726831.035100
3.73-3.97.60.1366661.111100
3.9-4.117.60.1146701.134100
4.11-4.367.50.0976641.305100
4.36-4.77.40.0956921.503100
4.7-5.177.40.0976751.488100
5.17-5.927.20.16881.201100
5.92-7.457.10.0797011.036100
7.45-456.50.0827582.43199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.55 Å39.56 Å
Translation5.55 Å39.56 Å

-
Processing

Software
NameVersionClassificationNB
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.748→39.563 Å / SU ML: 0.33 / σ(F): 1.37 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 675 5.03 %random
Rwork0.2025 ---
obs0.2058 13411 99.75 %-
all-13444 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.8 Å2 / Biso mean: 58.3087 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: LAST / Resolution: 2.748→39.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 23 18 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033745
X-RAY DIFFRACTIONf_angle_d0.5965054
X-RAY DIFFRACTIONf_chiral_restr0.02569
X-RAY DIFFRACTIONf_plane_restr0.003635
X-RAY DIFFRACTIONf_dihedral_angle_d13.8341362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7484-2.96060.30471550.24222451260699
2.9606-3.25840.3244990.240925312630100
3.2584-3.72960.28481230.212625552678100
3.7296-4.69770.26011510.170825382689100
4.6977-39.56720.23841470.201526612808100
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)
11.1787-0.04111.36963.4732-2.25562.97240.0315-0.2453-0.06810.3459-0.0263-0.0649-0.1447-0.0441-0.02550.249-0.00880.02150.3216-0.01560.276527.3025-10.8107-0.8831
21.4064-0.20251.01810.5122-0.48651.2761-0.0474-0.0430.20110.0373-0.0181-0.0483-0.0318-0.03380.07220.3535-0.00640.04780.2722-0.03380.352343.3163-1.07764.5655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 248 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 528 )A0

+
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://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