[English] 日本語
Yorodumi
- PDB-5muq: Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5muq
TitleCrystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom
Components
  • antibody Fab heavy chain
  • antibody kappa light chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / IMIDAZOLE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
CitationJournal: To be published
Title: Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom
Authors: Skrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: antibody Fab heavy chain
L: antibody kappa light chain
A: antibody Fab heavy chain
B: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1928
Polymers95,9234
Non-polymers2694
Water48627
1
H: antibody Fab heavy chain
L: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0964
Polymers47,9612
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-48 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: antibody Fab heavy chain
B: antibody kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0964
Polymers47,9612
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-49 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.510, 113.510, 69.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Antibody antibody Fab heavy chain


Mass: 23685.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody kappa light chain


Mass: 24275.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16% PEG 3350, 0.2 M imidazol, 0.02 M ZnSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8166 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8166 Å / Relative weight: 1
ReflectionResolution: 2.616→98.3 Å / Num. obs: 29733 / % possible obs: 98.5 % / Redundancy: 5.8 % / Rrim(I) all: 0.05 / Net I/σ(I): 28.47
Reflection shellResolution: 2.616→2.67 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.16 / Num. unique all: 1802 / CC1/2: 0.794 / Rrim(I) all: 0.804 / % possible all: 80.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.62→98.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.645 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.271 / ESU R Free: 0.365
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 1503 5.1 %RANDOM
Rwork0.2122 ---
obs0.2156 28230 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 176.4 Å2 / Biso mean: 73.988 Å2 / Biso min: 34.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20.83 Å20 Å2
2--1.66 Å20 Å2
3----5.38 Å2
Refinement stepCycle: final / Resolution: 2.62→98.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 12 27 6722
Biso mean--112.21 54.22 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026865
X-RAY DIFFRACTIONr_bond_other_d0.0020.026074
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9489337
X-RAY DIFFRACTIONr_angle_other_deg1.033314187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41124.264258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.321151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9351524
X-RAY DIFFRACTIONr_chiral_restr0.0910.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021382
LS refinement shellResolution: 2.616→2.684 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 80 -
Rwork0.375 1714 -
all-1794 -
obs--80.05 %

+
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