[English] 日本語
Yorodumi
- PDB-3b9v: Crystal Structure of an Autonomous VH Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b9v
TitleCrystal Structure of an Autonomous VH Domain
Componentsheavy chain variable domain
KeywordsIMMUNE SYSTEM / antibody engineering / phage display
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsAppleton, B.A. / Barthelemy, P.A. / Wiesmann, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Comprehensive Analysis of the Factors Contributing to the Stability and Solubility of Autonomous Human VH Domains.
Authors: Barthelemy, P.A. / Raab, H. / Appleton, B.A. / Bond, C.J. / Wu, P. / Wiesmann, C. / Sidhu, S.S.
History
DepositionNov 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: heavy chain variable domain
B: heavy chain variable domain
C: heavy chain variable domain
D: heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)52,2184
Polymers52,2184
Non-polymers00
Water7,296405
1
A: heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,0541
Polymers13,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,0541
Polymers13,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,0541
Polymers13,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: heavy chain variable domain


Theoretical massNumber of molelcules
Total (without water)13,0541
Polymers13,0541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.915, 54.066, 54.242
Angle α, β, γ (deg.)109.970, 95.640, 118.650
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody
heavy chain variable domain


Mass: 13054.447 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 0.1 M Hepes, 0.5% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40233 / % possible obs: 96.2 % / Redundancy: 4 % / Rsym value: 0.039 / Χ2: 1.326 / Net I/σ(I): 43.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Mean I/σ(I) obs: 13.4 / Num. unique all: 3886 / Rsym value: 0.097 / Χ2: 0.882 / % possible all: 92.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1N8Z

1n8z


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.358 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2023 5 %RANDOM
Rwork0.155 ---
obs0.157 38187 95.98 %-
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: 19.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0.1 Å20.38 Å2
2---0.5 Å20.1 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 0 405 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223756
X-RAY DIFFRACTIONr_bond_other_d0.0010.022509
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.935115
X-RAY DIFFRACTIONr_angle_other_deg0.8773.0036036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36422.917168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41528
X-RAY DIFFRACTIONr_chiral_restr0.1040.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_nbd_refined0.1990.2508
X-RAY DIFFRACTIONr_nbd_other0.2110.22449
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21794
X-RAY DIFFRACTIONr_nbtor_other0.0860.22161
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.223
X-RAY DIFFRACTIONr_mcbond_it3.752.52949
X-RAY DIFFRACTIONr_mcbond_other0.7212.5998
X-RAY DIFFRACTIONr_mcangle_it4.47253705
X-RAY DIFFRACTIONr_scbond_it4.0062.51811
X-RAY DIFFRACTIONr_scangle_it5.09351400
LS refinement shellResolution: 1.8→1.837 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.233 113 -
Rwork0.143 2010 -
all-2123 -
obs--85.99 %
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)
10.76190.4246-0.16351.2193-0.1411.72010.0860.01860.00650.06410.04540.002-0.00790.1126-0.1313-0.03930.00830.0011-0.0251-0.0054-0.0377-13.75995.064114.8588
21.08930.11080.31851.8731-0.09861.88570.06580.008-0.0248-0.0594-0.0074-0.01070.0270.1169-0.0584-0.0540.00480.0012-0.0419-0.0027-0.04951.3647-7.4094-9.0496
30.70110.3236-0.07642.57240.06851.1335-0.01230.1326-0.00510.1153-0.01780.1581-0.0421-0.0620.0301-0.0522-0.00710.0042-0.02680.0017-0.0482-26.5016-19.769318.7838
42.0524-0.4521-0.09271.9494-0.08671.1689-0.00280.16290.00370.0077-0.10.0239-0.0105-0.02970.1028-0.0575-0.00480.0029-0.02890.0057-0.0527-11.206-31.611-5.348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1121 - 119
2X-RAY DIFFRACTION2BB1 - 1121 - 119
3X-RAY DIFFRACTION3CC1 - 1121 - 119
4X-RAY DIFFRACTION4DD1 - 1121 - 119

+
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