[English] 日本語
Yorodumi
- PDB-3igo: Crystal structure of Cryptosporidium parvum CDPK1, cgd3_920 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3igo
TitleCrystal structure of Cryptosporidium parvum CDPK1, cgd3_920
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / parasite / kinase / cdpk / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / S,R MESO-TARTARIC ACID / Calmodulin-domain protein kinase 1, putative
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWernimont, A.K. / Artz, J.D. / Finnerty, P. / Amani, M. / Allali-Hassanali, A. / Vedadi, M. / Tempel, W. / MacKenzie, F. / Edwards, A.M. / Arrowsmith, C.H. ...Wernimont, A.K. / Artz, J.D. / Finnerty, P. / Amani, M. / Allali-Hassanali, A. / Vedadi, M. / Tempel, W. / MacKenzie, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.
Authors: Wernimont, A.K. / Artz, J.D. / Finerty, P. / Lin, Y.H. / Amani, M. / Allali-Hassani, A. / Senisterra, G. / Vedadi, M. / Tempel, W. / Mackenzie, F. / Chau, I. / Lourido, S. / Sibley, L.D. / Hui, R.
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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 / _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.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: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,61714
Polymers56,1531
Non-polymers1,46413
Water2,288127
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.388, 55.550, 81.697
Angle α, β, γ (deg.)90.000, 105.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Calmodulin-domain protein kinase 1


Mass: 56152.793 Da / Num. of mol.: 1 / Fragment: UNP residues 70-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd3_920 / Plasmid: pET15MHL / Production host: Escherichia coli (E. coli) / References: UniProt: A3FQ16

-
Non-polymers , 6 types, 140 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M Diammonium tartrate, 2 mM ANP, CaCl2, TCEP, 4 mM MgCl2, 30% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 25110 / Num. obs: 25110 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.053 / Χ2: 1.262 / Net I/σ(I): 7.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.65 / Num. unique all: 2502 / Rsym value: 0.741 / Χ2: 1.29 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
JBluIce-EPICSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DXN

3dxn


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.802 / SU B: 15.855 / SU ML: 0.186 / SU R Cruickshank DPI: 0.303 / SU Rfree: 0.234 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1280 5.1 %RANDOM
Rwork0.203 ---
all0.205 25095 --
obs0.205 25095 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.62 Å2 / Biso mean: 29.329 Å2 / Biso min: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.5 Å2
2---0.97 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 86 127 3709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223692
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9884991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42224.882170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28115656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0581519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022731
X-RAY DIFFRACTIONr_mcbond_it0.671.52243
X-RAY DIFFRACTIONr_mcangle_it1.26223606
X-RAY DIFFRACTIONr_scbond_it1.9631449
X-RAY DIFFRACTIONr_scangle_it3.1754.51375
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 96 -
Rwork0.261 1737 -
all-1833 -
obs-2502 98.92 %
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)
12.01770.39240.17930.4854-0.74861.7164-0.02410.0410.17540.05480.0360.0341-0.1790.2007-0.01190.1941-0.03410.01550.1439-0.01450.224731.256916.1178.1636
21.81680.7998-0.12120.52760.24960.5714-0.00760.0463-0.00510.0253-0.0176-0.01390.0325-0.02040.02520.19770.0061-0.00140.1710.01310.181718.76647.86179.1946
32.0945-0.3783-0.05892.16710.07961.6605-0.01260.09540.0385-0.0529-0.02540.16310.0537-0.19850.0380.1354-0.0235-0.00480.188500.16790.66774.97079.4106
40.96090.5338-0.61230.7677-0.56860.7693-0.0133-0.1051-0.06510.0867-0.1072-0.10390.02660.1380.12050.19660.0126-0.00080.19640.00930.18229.0023.587632.8685
54.3201-8.2874-8.318827.74755.57162.84830.4747-0.3045-0.1021-0.0943-0.14090.0944-2.3991-0.0809-0.33380.3944-0.03020.15640.2863-0.12120.302648.871123.35427.3523
613.99761.6522-9.55816.4442-3.44513.80950.2091-1.3003-0.09860.5699-0.3275-0.5068-0.52720.57570.11840.04310.0059-0.08120.3651-0.0750.124550.531214.779929.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 140
2X-RAY DIFFRACTION2A141 - 238
3X-RAY DIFFRACTION3A239 - 338
4X-RAY DIFFRACTION4A339 - 475
5X-RAY DIFFRACTION5A476 - 518
6X-RAY DIFFRACTION6A519 - 537

+
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