6LFX | pdb_00006lfx

Crystal structure of PCB4scFv(hN56D) in complex with PCB#77

PDB DOI: https://doi.org/10.2210/pdb6LFX/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-03 Released: 2020-12-09
Deposition Author(s): Nakamura, T., Yamagata, Y., Morioka, H.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.166 (Depositor), 0.167 (DCC)
R-Value Work:
0.136 (Depositor), 0.137 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of PCB4scFv(hN56D) in complex with PCB#77

Nakamura, T., Morioka, H.

To be published.

Macromolecule Content

Total Structure Weight: 27.52 kDa
Atom Count: 2,231
Modeled Residue Count: 239
Deposited Residue Count: 253
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCB4scFv(hN56D)	A	253	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OM4 (Subject of Investigation/LOI) Query on OM4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-bis(chloranyl)-4-(3-chloranyl-4-methoxy-phenyl)benzene C₁₃ H₉ Cl₃ O HEPYVKVRVSITAU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.166 (Depositor), 0.167 (DCC)
R-Value Work: 0.136 (Depositor), 0.137 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.842	α = 90
b = 91.842	β = 90
c = 53.969	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
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.