[English] 日本語
Yorodumi
- PDB-6dn0: Retrofitted antibodies with stabilizing mutations: Herceptin scFv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dn0
TitleRetrofitted antibodies with stabilizing mutations: Herceptin scFv mutant with VH K30D and VL S52D.
Components
  • Human Variable Heavy Chain of Herceptin containing VH mutation K30D
  • Human Variable Light Chain of Herceptin containing VL mutation S52D
KeywordsIMMUNE SYSTEM / Herceptin / retrofit / stabilizing mutation
Function / homologyFORMIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLangley, D.B. / Roome, B. / Christ, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1113904 Australia
Australian Research Council (ARC)160104915 Australia
CitationJournal: To Be Published
Title: Retrofitting antibodies with stabilizing mutations
Authors: Roome, B. / Langley, D.B. / Rouet, R. / Christ, D.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2019ID: 4X4Y
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Human Variable Heavy Chain of Herceptin containing VH mutation K30D
B: Human Variable Light Chain of Herceptin containing VL mutation S52D
C: Human Variable Heavy Chain of Herceptin containing VH mutation K30D
D: Human Variable Light Chain of Herceptin containing VL mutation S52D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6858
Polymers51,5014
Non-polymers1844
Water1,13563
1
A: Human Variable Heavy Chain of Herceptin containing VH mutation K30D
B: Human Variable Light Chain of Herceptin containing VL mutation S52D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8885
Polymers25,7502
Non-polymers1383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area10070 Å2
MethodPISA
2
C: Human Variable Heavy Chain of Herceptin containing VH mutation K30D
D: Human Variable Light Chain of Herceptin containing VL mutation S52D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7963
Polymers25,7502
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.981, 91.981, 114.677
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERAA1 - 1191 - 119
21GLUGLUSERSERCC1 - 1191 - 119
12ASPASPILEILEBB1 - 1061 - 106
22ASPASPILEILEDD1 - 1061 - 106

NCS ensembles :
ID
1
2

-
Components

#1: Antibody Human Variable Heavy Chain of Herceptin containing VH mutation K30D


Mass: 14145.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
#2: Antibody Human Variable Light Chain of Herceptin containing VL mutation S52D


Mass: 11604.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.84 Å3/Da / Density % sol: 56.76 % / Description: hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Equal volumes of protein (8.0 mg/mL in 25 mM Tris (pH 8.0)) were combined with an equal volume of well solution (3.5 M sodium formate, 100 mM sodium acetate (pH 4.6)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→39.83 Å / Num. obs: 38572 / % possible obs: 99.9 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Net I/σ(I): 14.6 / Num. measured all: 458269 / Scaling rejects: 95
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.018 / Num. unique obs: 2773 / CC1/2: 0.855 / Rpim(I) all: 0.304 / Rrim(I) all: 1.064 / % possible all: 98.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.16 Å39.83 Å
Translation6.16 Å39.83 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.17data scaling
PHASER2.5.7phasing
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x4x

4x4x


Resolution: 2→39.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.929 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1637 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1925 5 %RANDOM
Rwork0.2048 ---
obs0.2063 36495 99.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 98.12 Å2 / Biso mean: 45.853 Å2 / Biso min: 23.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----3.2 Å2
Refinement stepCycle: final / Resolution: 2→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 12 63 3464
Biso mean--56.22 42.51 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0143500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172968
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.6614762
X-RAY DIFFRACTIONr_angle_other_deg0.8861.6426939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21521.726168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9761521
X-RAY DIFFRACTIONr_chiral_restr0.0630.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A33610.14
12C33610.14
21B28690.12
22D28690.12
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 148 -
Rwork0.265 2646 -
all-2794 -
obs--99.75 %
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)
12.72110.7819-0.45761.38530.41243.7769-0.17540.06780.0759-0.12430.1869-0.0915-0.27680.2138-0.01160.0399-0.0304-0.00210.0389-0.01620.030330.3333-16.984115.8307
23.6573-0.27880.6042.95451.3134.77310.14890.1211-0.2316-0.1552-0.0150.03060.03840.113-0.13390.0986-0.08060.04630.0979-0.07070.114727.1226-30.2321-1.0752
34.09721.8435-1.34394.0123-1.31254.7596-0.0307-0.4592-0.1856-0.083-0.2273-0.19650.09320.49640.2580.01370.02180.02220.09470.05270.042162.4098-15.09831.545
44.008-0.5035-0.31823.313-0.70175.2446-0.1222-0.35860.00650.5335-0.1403-0.32550.03240.69960.26240.19130.0858-0.00440.37280.18560.202566.9853-24.564420.9771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2B1 - 106
3X-RAY DIFFRACTION3C1 - 119
4X-RAY DIFFRACTION4D1 - 106

+
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