3DMN | pdb_00003dmn

The crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1

PDB DOI: https://doi.org/10.2210/pdb3DMN/pdb

Classification: structural genomics, unknown function
Organism(s): Lactiplantibacillus plantarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-01 Released: 2008-08-26
Deposition Author(s): Tan, K., Zhou, M., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.191 (Depositor), 0.189 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the C-terminal domain of a possilbe DNA helicase from Lactobacillus plantarun WCFS1

Tan, K., Zhou, M., Gu, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.13 kDa
Atom Count: 1,506
Modeled Residue Count: 161
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA helicase	A	174	Lactiplantibacillus plantarum	Mutation(s): 0 Gene Names: lp_0910 EC: 3.6.1
UniProt
Find proteins for F9UMB1 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9UMB1 Go to UniProtKB: F9UMB1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F9UMB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	O [auth A], P [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.191 (Depositor), 0.189 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.292	α = 90
b = 99.292	β = 90
c = 72.365	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary