5DMH | pdb_00005dmh

Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.

PDB DOI: https://doi.org/10.2210/pdb5DMH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Cupriavidus necator H16
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-08 Released: 2015-10-28
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.185 (Depositor), 0.187 (DCC)
R-Value Work:
0.153 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a domain of unknown function (DUF1537) from Ralstonia eutropha H16 (H16_A1561), Target EFI-511666, complex with ADP.

Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Chamala, S., Chowdhury, S., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 95.26 kDa
Atom Count: 6,927
Modeled Residue Count: 836
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein conserved in bacteria	A, B	454	Cupriavidus necator H16	Mutation(s): 0 Gene Names: H16_A1561 EC: 2.7.1.217
UniProt
Find proteins for Q0KBC8 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0KBC8 Go to UniProtKB: Q0KBC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0KBC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185 (Depositor), 0.187 (DCC)
R-Value Work: 0.153 (Depositor), 0.156 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.13	α = 90
b = 87.666	β = 90
c = 178.988	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary