[English] 日本語
Yorodumi
- PDB-1shm: Convergent solutions to VHH domain stabilization from natural and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1shm
TitleConvergent solutions to VHH domain stabilization from natural and in vitro evolution
ComponentsANTIBODY RIG
KeywordsIMMUNE SYSTEM / Heavy Chain Variable Domain / VHH Domain / Immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBond, C.J. / Wiesmann, C. / Marsters, J.C. / Sidhu, S.S.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: A structure-based database of antibody variable domain diversity.
Authors: Bond, C.J. / Wiesmann, C. / Marsters, J.C. / Sidhu, S.S.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The original gene for the protein was cloned from llama (GB 4165492). One loop (residues ...SEQUENCE The original gene for the protein was cloned from llama (GB 4165492). One loop (residues 96-101, sequence: RIGRSVFNLRRESWVTW) replaces the natural sequence with an engineered sequence.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIBODY RIG
B: ANTIBODY RIG
D: ANTIBODY RIG
E: ANTIBODY RIG


Theoretical massNumber of molelcules
Total (without water)54,7214
Polymers54,7214
Non-polymers00
Water4,918273
1
A: ANTIBODY RIG


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIBODY RIG


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: ANTIBODY RIG


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: ANTIBODY RIG


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.211, 120.711, 52.246
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe relevant biological assembly is one VH domain. The asymmetric unit is composed of 4 independent VH domains.

-
Components

#1: Antibody
ANTIBODY RIG


Mass: 13680.156 Da / Num. of mol.: 4 / Fragment: RIG VHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.09 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 4K, 0.3M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 32402 / Num. obs: 32305 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HCV

1hcv


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.468 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1635 5.1 %RANDOM
Rwork0.18546 ---
obs0.18803 30610 99.62 %-
all-32305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.49 Å2
2---0.48 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 273 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213578
X-RAY DIFFRACTIONr_bond_other_d0.0020.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9164836
X-RAY DIFFRACTIONr_angle_other_deg0.90537215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385457
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_restr0.1130.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.2010.2517
X-RAY DIFFRACTIONr_nbd_other0.2550.23674
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.22282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9882.52271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.46553583
X-RAY DIFFRACTIONr_scbond_it3.6212.51307
X-RAY DIFFRACTIONr_scangle_it5.03251253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.939 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.377 87
Rwork0.272 1710
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)
11.27770.01150.08261.50970.22080.9623-0.0420.0427-0.0024-0.0578-0.0257-0.0105-0.0486-0.0360.06760.0452-0.00910.01190.06380.00640.05483.40550.51961.8157
20.914-0.01210.10251.83350.2981.7374-0.02450.1085-0.05520.0005-0.0236-0.00060.0958-0.06050.04810.0734-0.01090.00920.09910.00880.085214.08244.704125.9819
30.66830.18270.35211.84410.23890.97530.09820.0651-0.02630.001-0.0354-0.00510.0697-0.0282-0.06270.0892-0.00660.00380.1009-0.00170.1127-0.3392-26.93582.0896
40.66980.4105-0.17821.71010.18041.83690.01470.03160.0312-0.01950.0314-0.0172-0.0637-0.0995-0.04610.01050.0037-0.00040.013300.020411.648-23.047228.3643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1132 - 127
2X-RAY DIFFRACTION2BB2 - 1132 - 127
3X-RAY DIFFRACTION3DC2 - 1132 - 127
4X-RAY DIFFRACTION4ED2 - 1132 - 127

+
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