9HI5 | pdb_00009hi5

Structure of scaffold FI6-focused design_02

PDB DOI: https://doi.org/10.2210/pdb9HI5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Bacteroides uniformis ATCC 8492
Expression System: Escherichia coli
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: 1.90 Å
R-Value Free:
0.202 (Depositor), 0.202 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of scaffold FI6-focused design_02

Cramer, J.T., Krey, T.

To be published.

Macromolecule Content

Total Structure Weight: 98.66 kDa
Atom Count: 6,861
Modeled Residue Count: 819
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-like protein	A, B, C, D	223	Bacteroides uniformis ATCC 8492	Mutation(s): 0 Gene Names: BACUNI_03406
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.202 (Depositor), 0.202 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.05	α = 96.36
b = 63.31	β = 99.53
c = 98.18	γ = 114.57

Software Package:

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

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

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.