[English] 日本語
Yorodumi
- PDB-4iml: CrossFab binding to human Angiopoietin 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iml
TitleCrossFab binding to human Angiopoietin 2
Components
  • Crossed heavy chain (VH-Ckappa)
  • Crossed light chain (VL-CH1)
KeywordsIMMUNE SYSTEM / CrossFab / antigen binding / human Angiopoietin 2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.931 Å
AuthorsFenn, S. / Schiller, C. / Griese, J. / Hopfner, K.-P. / Kettenberger, H.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of an Anti-Ang2 CrossFab Demonstrates Complete Structural and Functional Integrity of the Variable Domain.
Authors: Fenn, S. / Schiller, C.B. / Griese, J.J. / Duerr, H. / Imhof-Jung, S. / Gassner, C. / Moelleken, J. / Regula, J.T. / Schaefer, W. / Thomas, M. / Klein, C. / Hopfner, K.P. / Kettenberger, H.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Crossed heavy chain (VH-Ckappa)
L: Crossed light chain (VL-CH1)
A: Crossed heavy chain (VH-Ckappa)
B: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7796
Polymers98,5954
Non-polymers1842
Water1267
1
H: Crossed heavy chain (VH-Ckappa)
L: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3903
Polymers49,2972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-24 kcal/mol
Surface area20250 Å2
MethodPISA
2
A: Crossed heavy chain (VH-Ckappa)
B: Crossed light chain (VL-CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3903
Polymers49,2972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.755, 80.552, 158.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain H and (resseq 1:232 ) and (not element H) and (not element D)
211chain A and (resseq 1:232 ) and (not element H) and (not element D)
112chain L and (resseq 2:210 ) and (not element H) and (not element D)
212chain B and (resseq 2:210 ) and (not element H) and (not element D)

NCS ensembles :
ID
1
2

-
Components

#1: Antibody Crossed heavy chain (VH-Ckappa)


Mass: 27083.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Crossed light chain (VL-CH1)


Mass: 22213.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17.5-20 %(w/v) PEG6000, 0.1 M citric acid, 0.2 M NDSB-221, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.795→44.133 Å / Num. obs: 24225

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.931→44.133 Å / SU ML: 0.42 / σ(F): 2.03 / Phase error: 32.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 1060 5.01 %
Rwork0.237 --
obs0.2387 21156 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8085 Å20 Å20 Å2
2---9.0101 Å20 Å2
3---2.2016 Å2
Refinement stepCycle: LAST / Resolution: 2.931→44.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 12 7 6743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036914
X-RAY DIFFRACTIONf_angle_d0.8639412
X-RAY DIFFRACTIONf_dihedral_angle_d13.9162453
X-RAY DIFFRACTIONf_chiral_restr0.0581038
X-RAY DIFFRACTIONf_plane_restr0.0041214
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H1792X-RAY DIFFRACTIONPOSITIONAL
12A1792X-RAY DIFFRACTIONPOSITIONAL0.085
21L1531X-RAY DIFFRACTIONPOSITIONAL
22B1531X-RAY DIFFRACTIONPOSITIONAL0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9309-3.06420.34371190.34122247X-RAY DIFFRACTION90
3.0642-3.22570.37621310.29872497X-RAY DIFFRACTION100
3.2257-3.42780.31731330.26822515X-RAY DIFFRACTION100
3.4278-3.69230.25841330.24212507X-RAY DIFFRACTION100
3.6923-4.06360.28561330.23742524X-RAY DIFFRACTION100
4.0636-4.65110.21711340.19442545X-RAY DIFFRACTION100
4.6511-5.85770.2631350.20442579X-RAY DIFFRACTION100
5.8577-44.13780.24311420.23882682X-RAY DIFFRACTION99

+
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