[English] 日本語
Yorodumi
- PDB-6ugu: Crystal structure of the Fab fragment of anti-TNFa antibody infli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ugu
TitleCrystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a C-centered orthorhombic crystal form, Lot C
Components
  • PF06438179 Fab Heavy Chain
  • PF06438179 Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / infliximab / biosimilar / TNFa
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Conlan, H.D.
CitationJournal: BioDrugs / Year: 2020
Title: Crystal Structures of PF-06438179/GP1111, an Infliximab Biosimilar.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Zou, Q. / Conlon, H.D.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: PF06438179 Fab Heavy Chain
L: PF06438179 Fab Light Chain
A: PF06438179 Fab Heavy Chain
B: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)95,6344
Polymers95,6344
Non-polymers00
Water15,763875
1
H: PF06438179 Fab Heavy Chain
L: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8172
Polymers47,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-25 kcal/mol
Surface area19490 Å2
MethodPISA
2
A: PF06438179 Fab Heavy Chain
B: PF06438179 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8172
Polymers47,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-25 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.260, 138.150, 195.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Antibody PF06438179 Fab Heavy Chain


Mass: 24356.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: A8K008
#2: Antibody PF06438179 Fab Light Chain


Mass: 23460.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: Q6P5S8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/mL PF06438179 Fab lot C against Wiz 34 screen condition B4 (20% PEG3350, 0.2 M potassium citrate tribasic), supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID ...Details: 10 mg/mL PF06438179 Fab lot C against Wiz 34 screen condition B4 (20% PEG3350, 0.2 M potassium citrate tribasic), supplemented with 20% ethylene glycol as cryoprotectant, crystal tracking ID 267668b4, unique puck ID sdw5-4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59825 / % possible obs: 99.5 % / Redundancy: 6.272 % / Biso Wilson estimate: 33.543 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.101 / Χ2: 0.972 / Net I/σ(I): 17.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.266.2880.63.2943920.850.655100
2.26-2.326.2940.5133.8342870.890.56100
2.32-2.396.3010.4654.1741750.9030.507100
2.39-2.466.3060.394.9640440.9320.425100
2.46-2.546.3150.3146.1539340.9530.34299.9
2.54-2.636.3050.2467.6438140.9710.26899.8
2.63-2.736.2990.2088.9136800.980.22799.8
2.73-2.846.3250.16711.0335290.9860.18299.7
2.84-2.976.3070.13313.3933790.9910.14699.7
2.97-3.116.2960.10417.0532630.9930.11499.7
3.11-3.286.2830.0821.2430900.9960.08799.5
3.28-3.486.2990.06425.7529230.9980.0799.4
3.48-3.726.2410.05330.4827580.9980.05899.4
3.72-4.026.2480.04634.4525710.9980.05199.2
4.02-4.46.2540.03840.3723510.9990.04198.8
4.4-4.926.2080.03444.4921490.9990.03798.5
4.92-5.686.2280.03442.7718950.9990.03798.5
5.68-6.966.1920.03739.2716120.9990.04197.8
6.96-9.846.0440.02944.712610.9990.03197.8
9.84-505.5450.02648.577180.9990.02994.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX2229refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4G3Y

4g3y


Resolution: 2.2→50 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.1
RfactorNum. reflection% reflection
Rfree0.2185 2898 4.85 %
Rwork0.17 --
obs0.1724 59813 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.17 Å2 / Biso mean: 29.9191 Å2 / Biso min: 11.24 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 0 876 7382
Biso mean---35.79 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076691
X-RAY DIFFRACTIONf_angle_d0.839125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.2-2.23610.27471400.210226730100
2.2361-2.27470.30751190.202827400100
2.2747-2.3160.25771450.206326640100
2.316-2.36060.23731470.208426930100
2.3606-2.40870.33281350.216427100100
2.4087-2.46110.2691370.202926810100
2.4611-2.51840.26161310.198926960100
2.5184-2.58130.24961320.186726940100
2.5813-2.65110.25181450.192127160100
2.6511-2.72910.23311460.188126890100
2.7291-2.81720.2561320.189227450100
2.8172-2.91790.29081160.196727040100
2.9179-3.03470.26171250.199727050100
3.0347-3.17280.2481280.185227020100
3.1728-3.340.20981450.173726990100
3.34-3.54920.20491790.16542701099
3.5492-3.82310.19151510.16042687099
3.8231-4.20770.17411400.13812703099
4.2077-4.8160.14791310.11532765099
4.816-6.06570.17361290.13562731098
6.0657-500.21211450.16673817097

+
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