5X5X | pdb_00005x5x

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

PDB DOI: https://doi.org/10.2210/pdb5X5X/pdb

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

Deposited: 2017-02-18 Released: 2018-02-21
Deposition Author(s): Komatsu, M., Dong, J., Ueda, H., Arai, R.
Funding Organization(s): Cooperative Research Program of Network Joint Research Center for Materials and Devices, Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.224 (Depositor), 0.232 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

Arai, R., Komatsu, M., Dong, J., Ueda, H.

To be published.

Macromolecule Content

Total Structure Weight: 52.71 kDa
Atom Count: 3,623
Modeled Residue Count: 433
Deposited Residue Count: 481
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fd chain of anti-osteocalcin antibody KTM219	A [auth H]	249	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L chain of anti-osteocalcin antibody KTM219	B [auth L]	232	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth H] SDF format, chain H MOL2 format, chain G [auth H] MOL2 format, chain H mmCIF format, chain G [auth H] mmCIF format, chain H	G [auth H], H	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Interactions & Density Focus chain G [auth H] Focus chain H
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth L] SDF format, chain L MOL2 format, chain K [auth L] MOL2 format, chain L mmCIF format, chain K [auth L] mmCIF format, chain L	K [auth L], L	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth L] Focus chain L Interactions & Density Focus chain K [auth L] Focus chain L
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H]	C [auth H], D [auth H], E [auth H], F [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain M [auth L] MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain M [auth L] mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain M [auth L]	I [auth H], J [auth H], M [auth L]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth H] Focus chain M [auth L] Interactions & Density Focus chain I [auth H] Focus chain J [auth H] Focus chain M [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.224 (Depositor), 0.232 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.8	α = 90
b = 71.472	β = 90
c = 96.882	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Cooperative Research Program of Network Joint Research Center for Materials and Devices	Japan	20161175
Japan Society for the Promotion of Science	Japan	JP15H04191
Japan Society for the Promotion of Science	Japan	JP24780097
Japan Society for the Promotion of Science	Japan	JP16H00761
Japan Society for the Promotion of Science	Japan	JP16K05841
Japan Society for the Promotion of Science	Japan	JP26420793
Japan Society for the Promotion of Science	Japan	JP24360336

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary