[English] 日本語
Yorodumi
- PDB-2ct9: The crystal structure of calcineurin B homologous proein 1 (CHP1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ct9
TitleThe crystal structure of calcineurin B homologous proein 1 (CHP1)
ComponentsCalcium-binding protein p22
KeywordsMETAL BINDING PROTEIN / EF-hand / calcium binding protein
Function / homology
Function and homology information


Hyaluronan uptake and degradation / : / positive regulation of sodium:proton antiporter activity / negative regulation of phosphatase activity / vesicle targeting / positive regulation of protein glycosylation / membrane docking / negative regulation of protein autophosphorylation / vesicle fusion / positive regulation of protein transport ...Hyaluronan uptake and degradation / : / positive regulation of sodium:proton antiporter activity / negative regulation of phosphatase activity / vesicle targeting / positive regulation of protein glycosylation / membrane docking / negative regulation of protein autophosphorylation / vesicle fusion / positive regulation of protein transport / cellular response to acidic pH / membrane organization / microtubule bundle formation / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein import into nucleus / negative regulation of NF-kappaB transcription factor activity / protein kinase inhibitor activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of protein targeting to membrane / cytoplasmic microtubule organization / transport vesicle / negative regulation of protein ubiquitination / protein export from nucleus / negative regulation of protein phosphorylation / regulation of intracellular pH / negative regulation of protein kinase activity / kinase binding / calcium-dependent protein binding / microtubule cytoskeleton / protein complex oligomerization / microtubule binding / membrane fusion / protein stabilization / Golgi membrane / calcium ion binding / endoplasmic reticulum / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
EF-hand / Recoverin; 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcineurin B homologous protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsNaoe, Y. / Arita, K. / Hashimoto, H. / Kanazawa, H. / Sato, M. / Shimizu, T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural characterization of calcineurin B homologous protein 1
Authors: Naoe, Y. / Arita, K. / Hashimoto, H. / Kanazawa, H. / Sato, M. / Shimizu, T.
History
DepositionMay 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 13, 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_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_conn.ptnr2_label_seq_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-binding protein p22
B: Calcium-binding protein p22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1406
Polymers47,9802
Non-polymers1604
Water2,756153
1
A: Calcium-binding protein p22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0703
Polymers23,9901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium-binding protein p22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0703
Polymers23,9901
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-71 kcal/mol
Surface area19480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.55, 38.53, 89.95
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Calcium-binding protein p22 / Calcineurin B homologous protein 1 / Calcium-binding protein CHP / Calcineurin homologous protein


Mass: 23989.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P61023
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG3350, Lithium Chloride, Calcium Chloride, CAPSO, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.34045, 1.34095, 1.32312, 1.37000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.340451
21.340951
31.323121
41.371
ReflectionResolution: 2.2→50 Å / Num. all: 19936 / Num. obs: 19708 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1920 / Rsym value: 0.221 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.275 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.376 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26753 1004 5.1 %RANDOM
Rwork0.21582 ---
all0.21855 19708 --
obs0.21855 19499 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.17 Å2
2--2.06 Å20 Å2
3----2.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.253 Å0.376 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 4 153 3263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223153
X-RAY DIFFRACTIONr_bond_other_d0.0010.022871
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9654232
X-RAY DIFFRACTIONr_angle_other_deg0.83536675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17224.205176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65115595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5921531
X-RAY DIFFRACTIONr_chiral_restr0.080.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined0.2230.2844
X-RAY DIFFRACTIONr_nbd_other0.1790.23068
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21602
X-RAY DIFFRACTIONr_nbtor_other0.0870.21839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.213
X-RAY DIFFRACTIONr_mcbond_it0.8581.51971
X-RAY DIFFRACTIONr_mcbond_other0.1581.5780
X-RAY DIFFRACTIONr_mcangle_it1.41723063
X-RAY DIFFRACTIONr_scbond_it1.96931296
X-RAY DIFFRACTIONr_scangle_it3.1584.51169
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 73 -
Rwork0.22 1371 -
obs--97.24 %
Refinement TLS params.Method: refined / Origin x: 38.7461 Å / Origin y: 25.5775 Å / Origin z: 65.5817 Å
111213212223313233
T-0.0567 Å2-0.0157 Å20.0022 Å2--0.0789 Å2-0.0247 Å2---0.0304 Å2
L0.3739 °2-0.1474 °20.0626 °2-0.2162 °2-0.069 °2--0.4572 °2
S-0.0163 Å °0.029 Å °0.0538 Å °0.0155 Å °0.0028 Å °-0.0002 Å °-0.0188 Å °0.0492 Å °0.0135 Å °

+
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://pdbjlvh1.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