[English] 日本語
Yorodumi
- PDB-3oz6: Crystal structure of MapK from Cryptosporidium Parvum, cgd2_1960 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oz6
TitleCrystal structure of MapK from Cryptosporidium Parvum, cgd2_1960
ComponentsMitogen-activated protein kinase 1, serine/threonine protein kinase
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / kinase
Function / homology
Function and homology information


MAP kinase activity / mitogen-activated protein kinase / ATP binding
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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
Mitogen-activated protein kinase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa II (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å
AuthorsWernimont, A.K. / Lew, J. / Lin, Y.H. / Sullivan, H. / Hassanali, A. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bochkarev, A. / Bountra, C. ...Wernimont, A.K. / Lew, J. / Lin, Y.H. / Sullivan, H. / Hassanali, A. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bochkarev, A. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Hui, R. / Neculai, A.M. / Hutchinson, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of MapK from Cryptosporidium Parvum, cgd2_1960
Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Sullivan, H. / Hassanali, A. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bochkarev, A. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Hui, R. / ...Authors: Wernimont, A.K. / Lew, J. / Lin, Y.H. / Sullivan, H. / Hassanali, A. / Kozieradzki, I. / Cossar, D. / Arrowsmith, C.H. / Bochkarev, A. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Hui, R. / Neculai, A.M. / Hutchinson, A.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Mitogen-activated protein kinase 1, serine/threonine protein kinase
B: Mitogen-activated protein kinase 1, serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7253
Polymers89,6332
Non-polymers921
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.298, 91.746, 119.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mitogen-activated protein kinase 1, serine/threonine protein kinase


Mass: 44816.305 Da / Num. of mol.: 2 / Fragment: UNP residues 4-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote)
Gene: cgd2_1960 / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A3FQ79
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350 0.1 M MgAcetate 4 mM AMPPNP 4 mM MGCl2 4 mM TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 33513 / Num. obs: 33480 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.115 / Χ2: 0.993 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.35-2.396.60.8891.616390.66699.2
2.39-2.436.80.8321.816510.65499.9
2.43-2.486.90.7352.116380.65199.9
2.48-2.5370.64916390.672100
2.53-2.597.10.55816300.65499.9
2.59-2.657.10.45216660.691100
2.65-2.717.20.3816590.683100
2.71-2.797.20.31416450.717100
2.79-2.877.20.29116530.706100
2.87-2.967.20.24316700.73299.9
2.96-3.077.20.20816640.77100
3.07-3.197.20.15616590.818100
3.19-3.337.20.13316720.905100
3.33-3.517.20.1116711.054100
3.51-3.737.10.09216741.258100
3.73-4.027.10.08416931.526100
4.02-4.4270.07716832.023100
4.42-5.066.80.06817081.914100
5.06-6.376.70.06117351.405100
6.37-506.50.03718311.33699.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 60.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.61 Å
Translation2.5 Å41.61 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→46.68 Å / Cor.coef. Fo:Fc: 0.8953 / Cor.coef. Fo:Fc free: 0.8715 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1697 5.08 %RANDOM
Rwork0.2306 ---
all0.2321 33973 --
obs0.2321 33427 98.39 %-
Displacement parametersBiso max: 124.6 Å2 / Biso mean: 51.1002 Å2 / Biso min: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1--20.8965 Å20 Å20 Å2
2--15.8151 Å20 Å2
3---5.0814 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.37→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 6 96 5355
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d18242
X-RAY DIFFRACTIONt_trig_c_planes1272
X-RAY DIFFRACTIONt_gen_planes7875
X-RAY DIFFRACTIONt_it539820
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion7445
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact62074
X-RAY DIFFRACTIONt_bond_d539820.01
X-RAY DIFFRACTIONt_angle_deg733521.1
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.72
LS refinement shellResolution: 2.37→2.44 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2983 128 5.48 %
Rwork0.2596 2206 -
all0.2617 2334 -

+
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