[English] 日本語
Yorodumi
- PDB-3d69: Crystal Structure of the Fab Fragment of an Anti-Factor IX Antibo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d69
TitleCrystal Structure of the Fab Fragment of an Anti-Factor IX Antibody 10C12
Components(anti-factor IX antibody, 10C12) x 2
KeywordsIMMUNE SYSTEM / anticoagulant / 10C12 / Factor IX / Gla domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å
AuthorsShi, X.L. / Huang, M.D. / Zeng, T.
CitationJournal: CHIN.J.STRUCT.CHEM. / Year: 2008
Title: Crystal structure of Fab Fragment of an anti-Factor IX antibody 10C12
Authors: Shi, X.L. / Huang, M.D. / Zeng, T.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Source and taxonomy
Revision 1.3Nov 1, 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
L: anti-factor IX antibody, 10C12
H: anti-factor IX antibody, 10C12
A: anti-factor IX antibody, 10C12
B: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)93,5024
Polymers93,5024
Non-polymers00
Water0
1
A: anti-factor IX antibody, 10C12
B: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)46,7512
Polymers46,7512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-22.4 kcal/mol
Surface area19490 Å2
MethodPISA
2
L: anti-factor IX antibody, 10C12
H: anti-factor IX antibody, 10C12


Theoretical massNumber of molelcules
Total (without water)46,7512
Polymers46,7512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-20.5 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.609, 159.609, 65.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Antibody anti-factor IX antibody, 10C12


Mass: 22950.355 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)
#2: Antibody anti-factor IX antibody, 10C12


Mass: 23800.863 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)
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN CHAIN L AND A, RESIDUE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN CHAIN L AND A, RESIDUE NUMBER 10 IS SIMPLY SKIPPED. AUTHORS STATE THAT THE PROTEIN SEQUENCE IS IDENTICAL WITH 1NL0(PDB CODE). THE MISSING OF L10 IS DUE TO KABAT-WU NUMBERING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 3.0M ammonium sulfate, 0.1M HEPES, 2%MPD, pH7.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorDetector: CCD / Date: Sep 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.77→50 Å / Num. all: 17166 / Num. obs: 13950 / % possible obs: 82.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.217 / Rsym value: 0.009 / Net I/σ(I): 141.4

-
Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NL0

1nl0


Resolution: 3.77→41.26 Å / Isotropic thermal model: isotropic / Cross valid method: thoughout
RfactorNum. reflection% reflectionSelection details
Rfree0.342 --random
Rwork0.249 ---
all-17166 --
obs-13950 82.2 %-
Displacement parametersBiso mean: 87.7 Å2
Refinement stepCycle: LAST / Resolution: 3.77→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 0 6420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
LS refinement shellResolution: 3.77→3.94 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.342 13950 -
Rwork0.249 --
obs-17166 82.2 %

+
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