[English] 日本語
Yorodumi
- PDB-3f45: Structure of the R75A mutant of rat alpha-Parvalbumin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f45
TitleStructure of the R75A mutant of rat alpha-Parvalbumin
ComponentsParvalbumin alpha
KeywordsCALCIUM BINDING PROTEIN / EF-hand / Acetylation / Calcium / Muscle protein / Phosphoprotein
Function / homology
Function and homology information


inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding ...inhibitory chemical synaptic transmission / cuticular plate / excitatory chemical synaptic transmission / stereocilium / cochlea development / terminal bouton / gene expression / axon / neuronal cell body / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Parvalbumin / 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 ...Parvalbumin / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsHoh, F. / Padilla, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure
Authors: Hoh, F. / Cave, A. / Strub, M.P. / Baneres, J.L. / Padilla, A.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parvalbumin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0005
Polymers11,7271
Non-polymers2724
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.315, 55.050, 28.768
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Parvalbumin alpha


Mass: 11727.225 Da / Num. of mol.: 1 / Mutation: R75A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pvalb, Pva / Plasmid: pgemex / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02625
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.776738 Å3/Da / Density % sol: 30.772001 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.2 Ammonium sulfate, 2% PEG 600, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2005 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→27.71 Å / Num. obs: 5621 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Num. measured all: 20256

-
Processing

Software
NameVersionClassification
EPMRphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1RTP

1rtp


Resolution: 2→27.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.497 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20485 251 4.6 %RANDOM
Rwork0.14436 ---
all0.158 5621 --
obs0.14726 5480 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.078 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 12 155 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022839
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9891119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9095108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87826.9733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56815166
X-RAY DIFFRACTIONr_chiral_restr0.0960.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02596
X-RAY DIFFRACTIONr_nbd_refined0.2250.2520
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2136
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.235
X-RAY DIFFRACTIONr_mcbond_it0.9081.5553
X-RAY DIFFRACTIONr_mcangle_it1.4262848
X-RAY DIFFRACTIONr_scbond_it2.4923314
X-RAY DIFFRACTIONr_scangle_it3.5514.5271
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 18 -
Rwork0.2 327 -
obs-327 87.79 %

+
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