3QJG | pdb_00003qjg

Epidermin biosynthesis protein EpiD from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3QJG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-01-28 Released: 2011-02-09
Deposition Author(s): Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.263 (Depositor), 0.258 (DCC)
R-Value Work:
0.208 (Depositor), 0.205 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Epidermin biosynthesis protein EpiD from Staphylococcus aureus.

Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 244.32 kDa
Atom Count: 18,797
Modeled Residue Count: 2,041
Deposited Residue Count: 2,100
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermin biosynthesis protein EpiD	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	175	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: epiD, SACOL1875
UniProt
Find proteins for A0A0H2WWM9 (Staphylococcus aureus (strain COL)) Explore A0A0H2WWM9 Go to UniProtKB: A0A0H2WWM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2WWM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain DA [auth L] SDF format, chain CA [auth K] MOL2 format, chain X [auth H] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth L] MOL2 format, chain CA [auth K] mmCIF format, chain X [auth H] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth L] mmCIF format, chain CA [auth K]	CA [auth K] DA [auth L] M [auth A] P [auth B] Q [auth C] CA [auth K], DA [auth L], M [auth A], P [auth B], Q [auth C], R [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain CA [auth K] Focus chain DA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain CA [auth K] Focus chain DA [auth L] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain BA [auth J] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	AA [auth J] BA [auth J] N [auth A] O [auth A] S [auth D] AA [auth J], BA [auth J], N [auth A], O [auth A], S [auth D], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.263 (Depositor), 0.258 (DCC)
R-Value Work: 0.208 (Depositor), 0.205 (DCC)
R-Value Observed: 0.211 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.991	α = 90
b = 111.256	β = 97.25
c = 154.569	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description