[English] 日本語
Yorodumi
- PDB-3szs: Crystal structure analysis of hellethionin D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3szs
TitleCrystal structure analysis of hellethionin D
ComponentsHellethionin-D
KeywordsTOXIN / MR-SAD / gamma thionin / plant defense / secreted
Function / homology
Function and homology information


defense response / toxin activity / 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 speciesHelleborus purpurascens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement SAD / Resolution: 1.95 Å
AuthorsThorn, A. / Uson, I. / Eduardo, C. / Sheldrick, G.M.
CitationJournal: To be Published
Title: Crystal Structure Analysis of Hellethionin D
Authors: Thorn, A. / Uson, I. / Eduardo, C. / Sheldrick, G.M.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Hellethionin-D
B: Hellethionin-D
C: Hellethionin-D
D: Hellethionin-D
E: Hellethionin-D
F: Hellethionin-D
G: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01659
Polymers34,4097
Non-polymers1,60752
Water6,810378
1
A: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0917
Polymers4,9161
Non-polymers1756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9743
Polymers4,9161
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9873
Polymers4,9161
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0455
Polymers4,9161
Non-polymers1294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,45618
Polymers4,9161
Non-polymers54017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1629
Polymers4,9161
Non-polymers2468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hellethionin-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,30214
Polymers4,9161
Non-polymers38613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.829, 129.829, 103.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-42-

SER

21D-52-

NA

31D-53-

CL

-
Components

#1: Protein/peptide
Hellethionin-D


Mass: 4915.618 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Helleborus purpurascens (plant) / Tissue: root and root stock / References: UniProt: P60057
#2: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M sodium iodide, 0.1 M Tris, pH 7.0, 0.2 M magnesium chloride hexahydrate, 1.9 M sodium chloride, protein solution was 45 mg/mL in HEPES diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9540,1.900
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2009
RadiationMonochromator: DOUBLE LAYER MIRROR SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.91
ReflectionResolution: 1.95→91.8 Å / Num. all: 32601 / Num. obs: 32570 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 45.9 % / Biso Wilson estimate: 22.26 Å2 / Rmerge(I) obs: 0.1224 / Rsym value: 0.1224 / Net I/σ(I): 38.36
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 16.75 % / Rmerge(I) obs: 0.4054 / Mean I/σ(I) obs: 38.36 / Num. unique all: 4446 / Rsym value: 0.4054 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASER/ SHELXC/D/E / ARCIMBOLDOphasing
REFMAC5.5.0102refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: molecular replacement SAD
Starting model: PDB ENTRY 1NBL

1nbl


Resolution: 1.95→91.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.213 / SU ML: 0.096 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: Engh & Huber
Details: TLS-REFINEMENT WITH EACH POLYPEPTIDE AS ONE DOMAIN (7 TOTAL) AND ADDITIONAL ISOTROPIC REFINEMENT OF EACH ATOM. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1622 5.1 %SHELLS
Rwork0.19 ---
obs0.192 31827 97.6 %-
all-32601 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2---2.11 Å20 Å2
3---4.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→91.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 52 378 2752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212402
X-RAY DIFFRACTIONr_bond_other_d0.0010.021588
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9413284
X-RAY DIFFRACTIONr_angle_other_deg0.86633876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.75821.66784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7891521
X-RAY DIFFRACTIONr_chiral_restr0.0660.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_mcbond_it0.4311.51594
X-RAY DIFFRACTIONr_mcbond_other0.1281.5632
X-RAY DIFFRACTIONr_mcangle_it0.75622599
X-RAY DIFFRACTIONr_scbond_it1.3013808
X-RAY DIFFRACTIONr_scangle_it2.0264.5685
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 187 -
Rwork0.231 2193 -
obs-2394 99.92 %
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)
123.11194.31311.11962.82640.54690.7696-0.82072.06732.8262-0.45090.55290.6679-0.29380.09410.26780.2853-0.0795-0.13270.36110.26730.398572.67844.50212.095
21.0416-0.34950.37420.78090.60732.11460.09290.0279-0.10020.1054-0.0497-0.09160.18710.0308-0.04320.1664-0.0123-0.01640.1387-0.00540.110676.58818.2268.579
33.54720.24052.06231.965-0.22015.8462-0.13160.22540.08430.05790.07280.0196-0.3250.35180.05880.181-0.07370.03430.1593-0.00310.049182.13233.5650.454
42.311-0.15131.2397.075-0.43171.35380.04690.1021-0.1331-0.1770.0443-0.51280.22660.136-0.09120.16170.0110.01910.1245-0.03180.099575.6019.508-7.679
51.3596-1.01950.02951.58-0.70221.0687-0.0147-0.1327-0.01090.2987-0.0670.09690.00640.04820.08170.3416-0.0510.0220.27210.00530.147283.02129.94125.996
62.99770.8096-0.04455.4396-2.09072.69030.0205-0.28090.24310.22810.0566-0.070.0327-0.088-0.07710.159-0.0204-0.00180.1301-0.00110.078892.64246.19518.928
72.68060.27570.24961.80620.31070.62840.0746-0.3428-0.06720.2176-0.03170.04910.049-0.0403-0.04280.16140.01560.01170.20230.01380.063361.08828.0918.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 42
2X-RAY DIFFRACTION2B1 - 46
3X-RAY DIFFRACTION3C1 - 46
4X-RAY DIFFRACTION4D1 - 46
5X-RAY DIFFRACTION5E1 - 46
6X-RAY DIFFRACTION6F1 - 46
7X-RAY DIFFRACTION7G1 - 46

+
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