9HI6 | pdb_00009hi6

Structure of scaffold FI6-focused design_04 in complex with FI6-Fab

PDB DOI: https://doi.org/10.2210/pdb9HI6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Homo sapiens, Bacteroides uniformis ATCC 8492
Expression System: Drosophila melanogaster, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-24 Released: 2025-12-03
Deposition Author(s): Cramer, J.T., Krey, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.204 (Depositor), 0.203 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Structure of scaffold FI6-focused design_04 in complex with FI6-Fab

Cramer, J.T., Krey, T.

To be published.

Macromolecule Content

Total Structure Weight: 74.6 kDa
Atom Count: 5,764
Modeled Residue Count: 651
Deposited Residue Count: 672
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FI6 Fab Heavy Chain	A [auth H]	235	Homo sapiens	Mutation(s): 0

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FI6-Fab Light Chain	B [auth L]	217	Homo sapiens	Mutation(s): 0

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FI6-focused design_04	C [auth A]	220	Bacteroides uniformis ATCC 8492	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.204 (Depositor), 0.203 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.213	α = 90
b = 47.869	β = 106.13
c = 107.093	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-12-03
Type: Initial release

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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.