[English] 日本語
Yorodumi
- PDB-3nir: Crystal structure of small protein crambin at 0.48 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nir
TitleCrystal structure of small protein crambin at 0.48 A resolution
ComponentsCrambin
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica (Abyssinian kale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS TO PDB ENTRY 1EJG / Resolution: 0.48 Å
AuthorsSchmidt, A. / Teeter, M. / Weckert, E. / Lamzin, V.S.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystal structure of small protein crambin at 0.48 A resolution
Authors: Schmidt, A. / Teeter, M. / Weckert, E. / Lamzin, V.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Authors: Jelsch, C. / Teeter, M.M. / Lamzin, V.S. / Pichon-Pesme, V. / Blessing, R.H. / Lecomte, C.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.6Sep 6, 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_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 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Crambin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9235
Polymers4,7381
Non-polymers1844
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.329, 18.471, 40.769
Angle α, β, γ (deg.)90.00, 90.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide Crambin


Mass: 4738.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Crambe hispanica (Abyssinian kale) / Strain: SUBSP. ABYSSINICA / References: UniProt: P01542
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.7730.67
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% ethanol in water, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA II, DESYPETRA110.5498
SYNCHROTRONPETRA II, DESYPETRA120.5636
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 5, 2001
MAR CCD 165 mm2CCDFeb 25, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond (111) - germanium (220)SINGLE WAVELENGTHMx-ray1
2diamond (111) - germanium (220)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.54981
20.56361
ReflectionResolution: 0.48→20 Å / Num. all: 156860 / Num. obs: 156860 / % possible obs: 97 % / Redundancy: 3.7 % / Biso Wilson estimate: 2.14 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 0.48→0.49 Å / Mean I/σ(I) obs: 1.5

-
Processing

Software
NameClassification
MAR345data collection
MOPROrefinement
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: ISOMORPHOUS TO PDB ENTRY 1EJG
Starting model: PDB entry 1EJG

1ejg


Resolution: 0.48→20 Å / Isotropic thermal model: overall / Cross valid method: RFREE INITIALLY, FINAL STAGES NONE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: INITIAL REFINEMENT WITH REFMAC THEN SHELX, THEN MOPRO FOR MULTIPOLE REFINEMENT. ONLY DURING REFMAC CROSS VALIDATION WITH RFREE. IN THE LAST STAGES OF REFINEMENT THE SUM OF OCCUPANCIES FOR ...Details: INITIAL REFINEMENT WITH REFMAC THEN SHELX, THEN MOPRO FOR MULTIPOLE REFINEMENT. ONLY DURING REFMAC CROSS VALIDATION WITH RFREE. IN THE LAST STAGES OF REFINEMENT THE SUM OF OCCUPANCIES FOR THE MULTIPLE CONFORMERS WAS NOT CONSTRAINED TO 1.00 AND ONLY WEAK STEREOCHEMICAL RESTRAINTS WERE APPLIED. ALTHOUGH OVERALL SUCH REFINEMENT OF THE MULTIPLE CONFORMERS WENT FINE, THERE WAS SOME INSTABILITY - FOR EXAMPLE THE REFINEMENT OF THE TEMPERATURE FACTORS FOR CA AND C ATOMS OF THE THIRD CONFORMER OF TYR A 29 DID NOT CONVERGE AND WERE TRUNCATED TO THE VALUE OF 50. BULK SOLVENT MODELING METHOD USED:BULK SOLVENT ENVELOPE METHOD FC(MOL)+FC(BULK)
RfactorNum. reflection% reflectionSelection details
Rwork0.127 ---
obs0.127 156860 97 %-
all-156860 --
Rfree---random
Displacement parametersBiso mean: 4.12 Å2
Refinement stepCycle: LAST / Resolution: 0.48→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms341 0 12 98 451

+
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