3UE7 | pdb_00003ue7

X-ray crystal structure of a novel topological analogue of crambin

PDB DOI: https://doi.org/10.2210/pdb3UE7/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Crambe hispanica subsp. abyssinica
Mutation(s): No

Deposited: 2011-10-28 Released: 2012-02-08
Deposition Author(s): Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.176 (Depositor), 0.180 (DCC)
R-Value Work:
0.144 (Depositor)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Design, total chemical synthesis, and x-ray structure of a protein having a novel linear-loop polypeptide chain topology.

Mandal, K., Pentelute, B.L., Bang, D., Gates, Z.P., Torbeev, V.Y., Kent, S.B.

(2012) Angew Chem Int Ed Engl 51: 1481-1486

PubMed: 22213444 Search on PubMed
DOI: https://doi.org/10.1002/anie.201107846
Primary Citation Related Structures:
3UE7

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.

Macromolecule Content

Total Structure Weight: 9.39 kDa
Atom Count: 746
Modeled Residue Count: 92
Deposited Residue Count: 92
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Crambin	A	46	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Crambin	B	46	Crambe hispanica subsp. abyssinica	Mutation(s): 0
UniProt
Find proteins for P01542 (Crambe hispanica subsp. abyssinica) Explore P01542 Go to UniProtKB: P01542
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01542
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 14 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL Query on DAL	A	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
DAR Query on DAR	A	D-PEPTIDE LINKING	C₆ H₁₅ N₄ O₂		--
DAS Query on DAS	A	D-PEPTIDE LINKING	C₄ H₇ N O₄		--
DCY Query on DCY	A	D-PEPTIDE LINKING	C₃ H₇ N O₂ S		--
DGL Query on DGL	A	D-PEPTIDE LINKING	C₅ H₉ N O₄		--
DIL Query on DIL	A	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DLE Query on DLE	A	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		--
DPN Query on DPN	A	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		--
DPR Query on DPR	A	D-PEPTIDE LINKING	C₅ H₉ N O₂		--
DSG Query on DSG	A	D-PEPTIDE LINKING	C₄ H₈ N₂ O₃		--
DSN Query on DSN	A	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
DTH Query on DTH	A	D-PEPTIDE LINKING	C₄ H₉ N O₃		--
DTY Query on DTY	A	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		--
DVA Query on DVA	A	D-PEPTIDE LINKING	C₅ H₁₁ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.176 (Depositor), 0.180 (DCC)
R-Value Work: 0.144 (Depositor)
R-Value Observed: 0.146 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.447	α = 90
b = 43.901	β = 108.68
c = 28.716	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2012-02-15
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary