[English] 日本語
Yorodumi
- PDB-1uyw: Crystal Structure of the antiflavivirus Fab4g2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uyw
TitleCrystal Structure of the antiflavivirus Fab4g2
Components
  • FAB ANTIBODY HEAVY CHAIN
  • FAB ANTIBODY LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez-Fleites, C. / Ortiz-Lombardia, M. / Taylor, E.J. / Gil-Valdes, J. / Chinea, G. / Davies, G.
CitationJournal: To be Published
Title: Crystal Structure of the Antiflavivirus Fab4G2
Authors: Martinez-Fleites, C. / Ortiz-Lombardia, M. / Taylor, E.J. / Gil-Valdes, J. / Chinea, G. / Davies, G.
History
DepositionMar 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: FAB ANTIBODY HEAVY CHAIN
L: FAB ANTIBODY LIGHT CHAIN
M: FAB ANTIBODY HEAVY CHAIN
N: FAB ANTIBODY LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)93,0614
Polymers93,0614
Non-polymers00
Water8,521473
1
H: FAB ANTIBODY HEAVY CHAIN
L: FAB ANTIBODY LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,5312
Polymers46,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: FAB ANTIBODY HEAVY CHAIN
N: FAB ANTIBODY LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,5312
Polymers46,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.564, 89.611, 138.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99988, -0.01251, 0.0096), (-0.01266, -0.99981, 0.015), (0.00941, -0.01511, -0.99984)37.17276, 90.5022, 35.38548
2given(0.99994, -0.00495, 0.01009), (-0.00499, -0.99998, 0.00394), (0.01007, -0.00399, -0.99994)36.97194, 90.2744, 34.60938

-
Components

#1: Antibody FAB ANTIBODY HEAVY CHAIN


Mass: 23100.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB ANTIBODY LIGHT CHAIN


Mass: 23429.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5 / Details: 13% PEG8K, 100MM HEPES PH=7.5, 5MM B-OG, pH 7.50

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.08
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→74.536 Å / Num. obs: 60545 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 1.7 / % possible all: 83.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEC

1yec


Resolution: 2→74.54 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.701 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.21953 4293 7.1 %RANDOM
Rwork0.19943 ---
obs0.20087 56177 96.91 %-
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: 13.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.72 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 0 473 7003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216749
X-RAY DIFFRACTIONr_bond_other_d0.0030.025795
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9439208
X-RAY DIFFRACTIONr_angle_other_deg0.783313630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9085855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021311
X-RAY DIFFRACTIONr_nbd_refined0.1750.21029
X-RAY DIFFRACTIONr_nbd_other0.2510.26636
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.54285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15626987
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63632464
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8794.52221
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 257
Rwork0.248 3381
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)
10.3433-0.439-0.07130.65950.14120.47170.05560.00010.0208-0.0298-0.02990.00320.0420.0198-0.02580.0290.00010.00150.0516-0.00130.04122.71342.51-7.743
20.4915-0.7190.22460.8591-0.41480.68590.01350.03270.07190.0935-0.0241-0.0306-0.01590.08010.01070.02890.0171-0.01310.0605-0.01270.046429.69451.02925.101
30.27660.5874-0.09760.5836-0.26530.99770.08420.007-0.0580.0847-0.07120.0156-0.21980.0617-0.0130.06-0.00510.00280.04230.00610.037259.32847.51542.312
40.88981.15570.1331.7788-0.01810.65130.0402-0.119-0.099-0.142-0.0695-0.12830.01020.05330.02940.01570.00580.02410.05870.01060.037266.48239.3949.837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 120
2X-RAY DIFFRACTION1L1 - 108
3X-RAY DIFFRACTION2H121 - 213
4X-RAY DIFFRACTION2L109 - 211
5X-RAY DIFFRACTION3N1 - 108
6X-RAY DIFFRACTION3M2 - 120
7X-RAY DIFFRACTION4N109 - 211
8X-RAY DIFFRACTION4M121 - 213

+
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