[English] 日本語
Yorodumi
- PDB-2pys: Crystal Structure of a Five Site Mutated Cyanovirin-N with a Mann... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pys
TitleCrystal Structure of a Five Site Mutated Cyanovirin-N with a Mannose Dimer Bound at 1.8 A Resolution
ComponentsCyanovirin-N
KeywordsSUGAR BINDING PROTEIN / CYANOVIRIN-N / ANTI HIV
Function / homology
Function and homology information


oligosaccharide binding / 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
2alpha-alpha-mannobiose / Cyanovirin-N
Similarity search - Component
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFromme, R. / Katilene, Z. / Fromme, P. / Ghirlanda, G.
CitationJournal: Biochemistry / Year: 2007
Title: A Monovalent Mutant of Cyanovirin-N Provides Insight into the Role of Multiple Interactions with gp120 for Antiviral Activity.
Authors: Fromme, R. / Katiliene, Z. / Giomarelli, B. / Bogani, F. / Mahon, J.M. / Mori, T. / Fromme, P. / Ghirlanda, G.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_asym_id ..._atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyanovirin-N
B: Cyanovirin-N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5834
Polymers23,8982
Non-polymers6852
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.226, 38.281, 55.794
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cyanovirin-N / CV-N


Mass: 11949.095 Da / Num. of mol.: 2 / Mutation: K3N, T7A, E23I, P51G, N93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Gene: CYANOVIRN-N / Production host: Escherichia coli (E. coli) / Strain (production host): M51 / References: UniProt: P81180
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 8000, 100 MM MGSO4, 2 MM MAN2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→55.22 Å / Num. obs: 19361 / % possible obs: 87.7 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.13
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.92 / % possible all: 82.33

-
Processing

Software
NameVersionClassification
PHASER1.3.1 ARP/WARP 6.0phasing
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LOM

1lom


Resolution: 1.8→9.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.604 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 924 5.1 %RANDOM
Rwork0.169 ---
obs0.171 17236 94.5 %-
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: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.04 Å2
2--0.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 46 184 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211608
X-RAY DIFFRACTIONr_bond_other_d0.0290.021028
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9622183
X-RAY DIFFRACTIONr_angle_other_deg1.3893.0062507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06426.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.907156
X-RAY DIFFRACTIONr_chiral_restr0.2120.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
X-RAY DIFFRACTIONr_nbd_refined0.2180.2287
X-RAY DIFFRACTIONr_nbd_other0.2090.21120
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2803
X-RAY DIFFRACTIONr_nbtor_other0.0920.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.218
X-RAY DIFFRACTIONr_mcbond_it1.7531.51313
X-RAY DIFFRACTIONr_mcbond_other0.4491.5422
X-RAY DIFFRACTIONr_mcangle_it1.8321604
X-RAY DIFFRACTIONr_scbond_it3.533735
X-RAY DIFFRACTIONr_scangle_it4.114.5579
X-RAY DIFFRACTIONr_rigid_bond_restr2.25433318
X-RAY DIFFRACTIONr_sphericity_free6.7543190
X-RAY DIFFRACTIONr_sphericity_bonded2.36432613
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 52 -
Rwork0.231 1071 -
obs--82.33 %

+
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