[English] 日本語
Yorodumi
- PDB-3o2w: Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o2w
TitleCrystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog
Components(Chimeric antibody Fab 1E9, ...) x 2
KeywordsIMMUNE SYSTEM / IgG antibody Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION / Chem-O2W
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.55 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog
Authors: Verdino, P. / Aldag, C. / Jonsson, S. / Hilvert, D. / Wilson, I.A.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Chimeric antibody Fab 1E9, light chain
H: Chimeric antibody Fab 1E9, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54025
Polymers48,5112
Non-polymers3,02923
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-110 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.203, 128.203, 92.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Antibody , 2 types, 2 molecules LH

#1: Antibody Chimeric antibody Fab 1E9, light chain


Mass: 24082.904 Da / Num. of mol.: 1 / Mutation: F89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody Chimeric antibody Fab 1E9, heavy chain


Mass: 24428.510 Da / Num. of mol.: 1 / Mutation: L47T,M100bF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2

-
Non-polymers , 5 types, 88 molecules

#3: Chemical ChemComp-O2W / methyl ({[(3aR,4R,7R,7aR)-2-(4-aminophenyl)-1,3-dioxooctahydro-4H-4,7-ethanoisoindol-4-yl]carbamoyl}oxy)acetate


Mass: 401.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O6
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.51 Å3/Da / Density % sol: 72.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.25M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.059658 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.059658 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 28353 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.071 / Net I/σ(I): 14.6
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.55 / % possible all: 99.9

-
Processing

Software
NameClassification
BOSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab apo structure

Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.48 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24825 1365 4.9 %RANDOM
Rwork0.20713 ---
obs0.20907 26768 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.982 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å22.03 Å20 Å2
2--4.05 Å20 Å2
3----6.08 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 190 65 3567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223618
X-RAY DIFFRACTIONr_angle_refined_deg1.7424934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27224.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0215559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5011510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022672
X-RAY DIFFRACTIONr_nbd_refined0.2180.21457
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.211
X-RAY DIFFRACTIONr_mcbond_it0.6561.52249
X-RAY DIFFRACTIONr_mcangle_it1.14523599
X-RAY DIFFRACTIONr_scbond_it1.83931534
X-RAY DIFFRACTIONr_scangle_it2.8394.51332
LS refinement shellResolution: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 114 -
Rwork0.331 1936 -
obs--98.75 %
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)
11.07311.96370.63379.3505-0.84884.3577-0.17690.00160.00860.545-0.0516-0.8539-0.2979-0.070.2286-0.06320.0768-0.1447-0.5004-0.0338-0.191266.5305-21.6048-17.4366
22.61310.45023.38762.763-0.773515.2567-0.17740.4735-0.1072-0.72210.11470.08371.0956-0.9080.0628-0.0339-0.31960.0345-0.103-0.0859-0.350548.8881-44.6502-42.8371
31.35440.7063-0.18814.07662.9469.61270.22420.11370.1325-0.1896-0.0737-0.3079-0.4793-0.1698-0.15050.01330.2018-0.0316-0.58520.0048-0.266260.3421-6.5521-32.7762
44.22572.5254-3.50344.3733-2.08638.30280.07760.31900.0997-0.05120.7087-0.3316-2.0953-0.0264-0.26650.1917-0.11270.3114-0.0287-0.25342.3136-29.4709-42.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 213
3X-RAY DIFFRACTION3H1 - 113
4X-RAY DIFFRACTION4H114 - 227

+
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