[English] 日本語
Yorodumi
- PDB-9bcf: Chimeric protein of crocodile allergen Cro p 1.0101 and GFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bcf
TitleChimeric protein of crocodile allergen Cro p 1.0101 and GFP
ComponentsParvalbumin, Green fluorescent protein chimera
KeywordsALLERGEN / allergy
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / calcium ion binding / cytoplasm
Similarity search - Function
Parvalbumin / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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. ...Parvalbumin / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Similarity search - Domain/homology
Green fluorescent protein / Parvalbumin
Similarity search - Component
Biological speciesCrocodylus porosus (Australian saltwater crocodile)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsO'Malley, A. / Ruethers, T. / Lopata, A.L. / Chruszcz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Protein Sci. / Year: 2024
Title: Comparative studies of seafood and reptile alpha- and beta-parvalbumins.
Authors: O'Malley, A. / Ray, J.M. / Kitlas, P. / Ruethers, T. / Kapingidza, A.B. / Cierpicki, T. / Lopata, A. / Kowal, K. / Chruszcz, M.
#1: Journal: Protein Sci. / Year: 2024
Title: Crystal structure of cod allergen Gad m 1.0201 coordinating lanthanum
Authors: O'Malley, A. / Chruszcz, M.
History
DepositionApr 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parvalbumin, Green fluorescent protein chimera
B: Parvalbumin, Green fluorescent protein chimera
C: Parvalbumin, Green fluorescent protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1995
Polymers119,1193
Non-polymers802
Water48627
1
A: Parvalbumin, Green fluorescent protein chimera


Theoretical massNumber of molelcules
Total (without water)39,7061
Polymers39,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Parvalbumin, Green fluorescent protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7863
Polymers39,7061
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Parvalbumin, Green fluorescent protein chimera


Theoretical massNumber of molelcules
Total (without water)39,7061
Polymers39,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.778, 158.778, 123.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Parvalbumin, Green fluorescent protein chimera


Mass: 39706.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crocodylus porosus (Australian saltwater crocodile), (gene. exp.) Aequorea victoria (jellyfish)
Gene: LOC109314825, gfp / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7M4EAX1, UniProt: A0A059PIQ0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 40% v/v PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 26890 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.131 / Rsym value: 0.071 / Net I/σ(I): 17.8
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 1.213 / Num. unique obs: 1321 / CC1/2: 0.78 / Rpim(I) all: 0.367 / Rrim(I) all: 1.46 / Rsym value: 1.213

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→39.88 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 41.194 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 2.112 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1280 4.8 %RANDOM
Rwork0.19881 ---
obs0.20078 25312 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 3.2→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6154 0 2 27 6183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0126288
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165747
X-RAY DIFFRACTIONr_angle_refined_deg1.261.8268532
X-RAY DIFFRACTIONr_angle_other_deg0.7341.76713266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.414542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.954101019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027380
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0056.6213154
X-RAY DIFFRACTIONr_mcbond_other3.0056.6213154
X-RAY DIFFRACTIONr_mcangle_it4.85611.8883932
X-RAY DIFFRACTIONr_mcangle_other4.85511.8893933
X-RAY DIFFRACTIONr_scbond_it3.996.9233134
X-RAY DIFFRACTIONr_scbond_other3.996.9243135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.49312.574601
X-RAY DIFFRACTIONr_long_range_B_refined9.96180.5326475
X-RAY DIFFRACTIONr_long_range_B_other9.95980.5226473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 97 -
Rwork0.294 1807 -
obs--100 %
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)
15.377-0.3985-0.23253.56950.22492.95930.42160.43291.3-0.2478-0.54170.4713-1.0563-0.32080.12020.84880.2795-0.01220.3560.00690.414455.68228.531-34.998
21.4211.5093-0.21013.1266-0.08941.337-0.0068-0.0318-0.0514-0.0335-0.06920.0965-0.0212-0.22080.0760.3725-0.0561-0.0250.4178-0.03050.021865.146-5.277-28.869
32.09930.9678-0.21132.56510.0893.42250.0086-0.4765-0.63210.1662-0.1107-0.68210.35560.91440.10210.4495-0.2642-0.03160.84010.33620.44959.909-55.092-16.287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 340
2X-RAY DIFFRACTION2B1 - 343
3X-RAY DIFFRACTION3C113 - 340

+
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