[English] 日本語
Yorodumi
- PDB-2b0r: Crystal Structure of Cyclase-Associated Protein from Cryptosporid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b0r
TitleCrystal Structure of Cyclase-Associated Protein from Cryptosporidium parvum
Componentspossible adenyl cyclase-associated protein
KeywordsUNKNOWN FUNCTION / structural genomics consortium / Cryptosporidium parvum / cyclase-associated protein / SGC
Function / homology
Function and homology information


cytoskeleton organization / cell morphogenesis / actin binding
Similarity search - Function
Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal ...Adenylate cyclase-associated CAP / Adenylate cyclase-associated CAP, C-terminal / Adenylate cyclase associated (CAP) C terminal / Pectate Lyase C-like - #70 / Adenylate cyclase-associated CAP, C-terminal superfamily / CARP motif / Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / Pectate Lyase C-like / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
: / Protein with 2 CAP (CARP) domains, possible adenyl cyclase-associated protein
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsTempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Kozieradzki, I. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Arrowsmith, C. ...Tempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Kozieradzki, I. / Alam, Z. / Melone, M. / Wasney, G. / Vedadi, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Hui, R. / Bochkarev, A. / Artz, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure and function of a G-actin sequestering protein with a vital role in malaria oocyst development inside the mosquito vector
Authors: Hliscs, M. / Sattler, J. / Tempel, W. / Artz, J.D. / Dong, A. / Hui, R. / Matuschewski, K. / Schuler, H.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Remark 350GENERATING THE BIOMOLECULE THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS UNKNOWN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: possible adenyl cyclase-associated protein
B: possible adenyl cyclase-associated protein


Theoretical massNumber of molelcules
Total (without water)44,9733
Polymers44,9732
Non-polymers01
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.258, 58.863, 65.810
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU5AA35 - 10535 - 105
21ARGARGLEULEU5BB35 - 10535 - 105
32LYSLYSASNASN5AA174 - 187174 - 187
42LYSLYSASNASN5BB174 - 187174 - 187
53GLUGLULYSLYS3AA188 - 190188 - 190
63GLUGLULYSLYS3BB188 - 190188 - 190
74GLYGLYSERSER5AA191 - 198191 - 198
84GLYGLYSERSER5BB191 - 198191 - 198
95VALVALGLYGLY3AA106 - 108106 - 108
105VALVALGLYGLY3BB106 - 108106 - 108
116VALVALLEULEU5AA109 - 164109 - 164
126VALVALLEULEU5BB109 - 164109 - 164

-
Components

#1: Protein possible adenyl cyclase-associated protein


Mass: 22486.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Plasmid: p28-LIC-Thrombin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-CodonPlus-RIL / References: GenBank: 46227316, UniProt: Q5CS32*PLUS
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 17% PEG 3350, 0.2M diammonium tartrate, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 15686 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.046 / Χ2: 1.114
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2
2.52-2.5699.13.30.5387940.896
2.56-2.611003.30.4847720.948
2.61-2.6699.53.30.4267850.968
2.66-2.7199.73.30.3387950.96
2.71-2.7799.93.30.2817810.942
2.77-2.8499.53.30.2437840.979
2.84-2.9199.93.30.1867820.973
2.91-2.9999.93.30.1517961.057
2.99-3.081003.30.1248081.086
3.08-3.171003.30.0987691.132
3.17-3.2999.93.30.0758001.167
3.29-3.421003.30.0627891.195
3.42-3.5899.63.30.0527901.257
3.58-3.7678.630.0546221.502
3.76-41003.30.0427881.241
4-4.311003.30.0397891.303
4.31-4.7499.83.30.0338171.317
4.74-5.4399.63.30.0317981.267
5.43-6.8399.53.30.0288031.08
6.83-50983.10.0218241.101

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1K8F

1k8f


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.208 / SU B: 10.301 / SU ML: 0.22 / ESU R: 0.462 / ESU R Free: 0.301
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 742 5.214 %Thin shells
Rwork0.216 ---
all0.219 ---
obs-14232 98.594 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 56.842 Å2
Baniso -1Baniso -2Baniso -3
1-1.433 Å20 Å20.943 Å2
2--0.866 Å20 Å2
3----1.489 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 1 0 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222461
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9623336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.90726.90797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85715445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.874155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021781
X-RAY DIFFRACTIONr_nbd_refined0.2230.2899
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.22
X-RAY DIFFRACTIONr_mcbond_it2.39121648
X-RAY DIFFRACTIONr_mcangle_it3.77732617
X-RAY DIFFRACTIONr_scbond_it2.732912
X-RAY DIFFRACTIONr_scangle_it3.9553719
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberRmsTypeWeight
240.055TIGHT POSITIONAL0.05
5960.224MEDIUM POSITIONAL0.5
5190.464LOOSE POSITIONAL5
240.693TIGHT THERMAL0.5
5961.698MEDIUM THERMAL2
5194.044LOOSE THERMAL10
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6660.369530.33986104399.616
2.666-2.7380.368530.293948100399.801
2.738-2.8160.331530.262956101399.605
2.816-2.9010.374530.274897950100
2.901-2.9940.31530.25489494999.789
2.994-3.0960.301530.253845898100
3.096-3.210.334530.25881586999.885
3.21-3.3380.322530.262785838100
3.338-3.48200.23381381599.755
3.482-3.6460.247530.22355277578.065
3.646-3.8360.218530.21469675299.601
3.836-4.0600.192689689100
4.06-4.3270.269530.184610663100
4.327-4.6560.193530.16858363799.843
4.656-5.07300.15857257599.478
5.073-5.6270.22530.17947252699.81
5.627-6.41300.20746847199.363
6.413-7.6600.21240440599.753
7.66-10.1160.286530.19628033499.701
10.116-2000.2422523097.826

+
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