5MVJ | pdb_00005mvj

Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1

PDB DOI: https://doi.org/10.2210/pdb5MVJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2017-01-16 Released: 2018-05-02
Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.272 (Depositor), 0.274 (DCC)
R-Value Work:
0.219 (Depositor), 0.225 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1

Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

To be published.

Macromolecule Content

Total Structure Weight: 192.34 kDa
Atom Count: 13,492
Modeled Residue Count: 1,741
Deposited Residue Count: 1,760
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab heavy chain	A [auth H], C [auth A], E [auth C], G [auth E]	221	Mus musculus	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody kappa chain	B [auth L], D [auth B], F [auth D], H [auth F]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth F] MOL2 format, chain I [auth F] mmCIF format, chain I [auth F]	I [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth H], C [auth A], E [auth C], G [auth E]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272 (Depositor), 0.274 (DCC)
R-Value Work: 0.219 (Depositor), 0.225 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.22	α = 92.32
b = 82.26	β = 95.47
c = 89.31	γ = 89.82

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 2.0: 2020-03-11
Changes: Polymer sequence
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.