[English] 日本語
Yorodumi
- PDB-3ll0: Monomeric Griffithsin with two Gly-Ser Insertions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ll0
TitleMonomeric Griffithsin with two Gly-Ser Insertions
ComponentsGriffithsin
KeywordsSUGAR BINDING PROTEIN / lectin / sugar-binding / anti-HIV / high mannose / Man9 / gp120 / gp41 / jacalin-related / Mannose-binding
Function / homology
Function and homology information


N-acetylgalactosamine binding / D-glucose binding / D-mannose binding / carbohydrate binding / identical protein binding
Similarity search - Function
Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesGriffithsia (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoulaei, T. / Wlodawer, A.
CitationJournal: Structure / Year: 2010
Title: Monomerization of viral entry inhibitor griffithsin elucidates the relationship between multivalent binding to carbohydrates and anti-HIV activity.
Authors: Moulaei, T. / Shenoy, S.R. / Giomarelli, B. / Thomas, C. / McMahon, J.B. / Dauter, Z. / O'Keefe, B.R. / Wlodawer, A.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4546
Polymers12,9891
Non-polymers4645
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.1, 55.1, 156.7
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Griffithsin / GRFT


Mass: 12989.062 Da / Num. of mol.: 1 / Mutation: Gly-Ser-Gly-Ser inserted after S16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Griffithsia (eukaryote) / Strain: Q66D336 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84801
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.1 M CdCl, 30% w/v PEG 400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2009
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 16094 / % possible obs: 97.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.003 / Net I/σ(I): 9.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1478 / Χ2: 0.987 / % possible all: 93.5

-
Phasing

Phasing MRRfactor: 40.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.75 Å
Translation2.5 Å40.75 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMAC5.4.0057refinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKY

3lky


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.563 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 936 5.8 %RANDOM
Rwork0.184 ---
obs0.185 15073 97.9 %-
all-16009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.09 Å2 / Biso mean: 20.174 Å2 / Biso min: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 29 135 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021977
X-RAY DIFFRACTIONr_bond_other_d0.0010.02663
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9661313
X-RAY DIFFRACTIONr_angle_other_deg0.95431609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12423.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48115146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.626155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02209
X-RAY DIFFRACTIONr_mcbond_it1.0061.5611
X-RAY DIFFRACTIONr_mcbond_other0.3171.5270
X-RAY DIFFRACTIONr_mcangle_it1.7042976
X-RAY DIFFRACTIONr_scbond_it2.8343366
X-RAY DIFFRACTIONr_scangle_it4.3244.5337
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 71 -
Rwork0.331 1008 -
all-1079 -
obs--92.22 %
Refinement TLS params.Method: refined / Origin x: 16.806 Å / Origin y: 6.271 Å / Origin z: 18.878 Å
111213212223313233
T-0.0222 Å2-0.0005 Å2-0.0025 Å2--0.0302 Å20.0102 Å2---0.0105 Å2
L0.2126 °2-0.1988 °20.3443 °2-1.2672 °2-0.3357 °2--0.8133 °2
S0.0028 Å °-0.0467 Å °0.0058 Å °-0.1318 Å °-0.023 Å °-0.0424 Å °0.0275 Å °-0.0315 Å °0.0203 Å °

+
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