[English] 日本語
Yorodumi
- PDB-3s3z: Crystal Structure an Tandem Cyanovirin-N Dimer, CVN2L10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s3z
TitleCrystal Structure an Tandem Cyanovirin-N Dimer, CVN2L10
ComponentsTandem Cyanovirin-N Dimer CVN2L10
KeywordsANTIVIRAL PROTEIN / cyanovirin-N / sugar-binding / gp120 / engineered dimer
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J. / Mayo, S.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Designed oligomers of cyanovirin-N show enhanced HIV neutralization.
Authors: Keeffe, J.R. / Gnanapragasam, P.N. / Gillespie, S.K. / Yong, J. / Bjorkman, P.J. / Mayo, S.L.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tandem Cyanovirin-N Dimer CVN2L10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0453
Polymers23,9991
Non-polymers462
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.990, 47.990, 79.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsAuthors state that the biologically relevant molecule is generated by applying the crystallographic symmetry operations Y, X, -Z to the first half of the protein.

-
Components

#1: Protein Tandem Cyanovirin-N Dimer CVN2L10 / CV-N


Mass: 23999.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81180
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20% PEG 3350, 0.2 M sodium fluoride, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.99984 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2008
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.75→41.56 Å / Num. all: 11158 / Num. obs: 11158 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.845.20.3841.7842216060.384100
1.84-1.965.40.2452.6804314810.245100
1.96-2.095.40.1783.1778914460.178100
2.09-2.265.40.1383.8718213200.138100
2.26-2.485.40.124.1661512270.12100
2.48-2.775.40.0995.1603811280.099100
2.77-3.25.30.094.4541710210.09100
3.2-3.915.30.0875.344378410.087100
3.91-5.535.20.086.435066800.08100
5.53-79.3184.50.0687.618554080.06898.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.81 Å
Translation2.5 Å36.81 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EZM

3ezm


Resolution: 1.75→36.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.1993 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.875 / SU B: 2.26 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1209 / SU Rfree: 0.1102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) Only half of the crystallized molecule is in the asymmetric unit. The entire polypeptide chain (biologically relevant molecule) is generated by the operations: Y, X, -Z. (2) Because only ...Details: (1) Only half of the crystallized molecule is in the asymmetric unit. The entire polypeptide chain (biologically relevant molecule) is generated by the operations: Y, X, -Z. (2) Because only half of the biologically relevant molecule is in the asymmetric unit, the density corresponding to residue 0 in the structure is from both an Arg in the expression tag (residue 0 of the sequence) and a Gly from the linker (residue 111 of the sequence). Since side chain density was not seen, the backbone was modeled at 100% occupancy and the side chain was not modeled. (3) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 528 4.7 %RANDOM
Rwork0.1884 ---
all0.1895 11644 --
obs0.1895 11116 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.95 Å2 / Biso mean: 20.3458 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 2 87 875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022835
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9441141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43126.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.205153
X-RAY DIFFRACTIONr_chiral_restr0.10.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02632
X-RAY DIFFRACTIONr_mcbond_it0.851.5535
X-RAY DIFFRACTIONr_mcangle_it1.5492867
X-RAY DIFFRACTIONr_scbond_it2.4643300
X-RAY DIFFRACTIONr_scangle_it4.3454.5267
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 31 -
Rwork0.217 758 -
all-789 -
obs--99.25 %

+
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