PDB-3qjg: Epidermin biosynthesis protein EpiD from Staphylococcus aureus

ID or keywords:

Entry

Database: PDB / ID: 3qjg

Title

Epidermin biosynthesis protein EpiD from Staphylococcus aureus

Components

Epidermin biosynthesis protein EpiD

Keywords

OXIDOREDUCTASE /

structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

catalytic activity /

nucleotide binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Osipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Epidermin biosynthesis protein EpiD from Staphylococcus aureus.
Authors: Osipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Jan 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3qjg.cif.gz	911.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3qjg.ent.gz	761.7 KB	Display	PDB format
PDBx/mmJSON format	3qjg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjg ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjg	HTTPS FTP

-
Related structure data

Related structure data	1g5qS S: Starting model for refinement
Similar structure data	889 1g5q-1 6dfk-1 1g63-d 6dfk-2 4o0k-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP00629

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Epidermin biosynthesis protein EpiD

B: Epidermin biosynthesis protein EpiD

C: Epidermin biosynthesis protein EpiD

D: Epidermin biosynthesis protein EpiD

E: Epidermin biosynthesis protein EpiD

F: Epidermin biosynthesis protein EpiD

G: Epidermin biosynthesis protein EpiD

H: Epidermin biosynthesis protein EpiD

I: Epidermin biosynthesis protein EpiD

J: Epidermin biosynthesis protein EpiD

K: Epidermin biosynthesis protein EpiD

L: Epidermin biosynthesis protein EpiD

hetero molecules

244 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	160.991, 111.256, 154.569
Angle α, β, γ (deg.)	90.000, 97.250, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Epidermin biosynthesis protein EpiD Mass: 19885.779 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: subsp. aureus COL / Gene: epiD, SACOL1875 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HEV4, UniProt: A0A0H2WWM9*PLUS
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1504 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.25 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, 20% PEG-MME-5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 12, 2010

Radiation

Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.04→45.8 Å / Num. all: 162302 / Num. obs: 162302 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / B_iso Wilson estimate: 33.7 Å² / R_merge(I) obs: 0.116 / Χ²: 1.712 / Net I/σ(I): 8.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.04-2.09	2.5	0.481	2.08	6320	0.947	74.4
2.09-2.12	2.7	0.441		6566	0.973	78.1
2.12-2.16	3	0.4		7040	0.962	83.2
2.16-2.21	3.3	0.383		7435	1.033	87.5
2.21-2.26	3.6	0.368		7820	1.083	92
2.26-2.31	3.7	0.326		8009	1.197	94.6
2.31-2.37	3.8	0.314		8298	1.177	97.8
2.37-2.43	3.9	0.292		8443	1.208	99.3
2.43-2.5	4	0.256		8483	1.338	99.9
2.5-2.58	4.1	0.222		8531	1.438	100
2.58-2.68	4.1	0.198		8433	1.54	100
2.68-2.78	4.2	0.177		8526	1.631	100
2.78-2.91	4.2	0.15		8507	1.807	100
2.91-3.06	4.2	0.135		8521	1.934	100
3.06-3.25	4.3	0.115		8495	2.049	100
3.25-3.51	4.3	0.101		8560	2.276	100
3.51-3.86	4.3	0.092		8486	2.341	100
3.86-4.42	4.3	0.082		8561	2.526	100
4.42-5.56	4.4	0.077		8577	2.341	100
5.56-50	4.2	0.067		8691	2.331	99.7

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1G5Q

1g5q

Resolution: 2.04→45.8 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.919 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 12.445 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2626	8177	5 %	RANDOM
R_work	0.2082	-	-	-
all	0.211	162164	-	-
obs	0.211	162164	94.99 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 73.5 Å² / B_iso mean: 32.7319 Å² / B_iso min: 8.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.66 Å²	0 Å²	0.65 Å²
2-	-	-1.83 Å²	0 Å²
3-	-	-	-3.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→45.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16396	0	378	1504	18278

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	17744
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11672
X-RAY DIFFRACTION	r_angle_refined_deg	1.629	1.985	24285
X-RAY DIFFRACTION	r_angle_other_deg	0.962	3	28924
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.221	5	2200
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.908	25.896	848
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.314	15	3159
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.385	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	2767
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	19490
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3279
X-RAY DIFFRACTION	r_mcbond_it	0.755	1.5	10504
X-RAY DIFFRACTION	r_mcbond_other	0.214	1.5	4139
X-RAY DIFFRACTION	r_mcangle_it	1.289	2	17309
X-RAY DIFFRACTION	r_scbond_it	2.169	3	7240
X-RAY DIFFRACTION	r_scangle_it	3.326	4.5	6886

LS refinement shell

Resolution: 2.044→2.097 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	470	-
R_work	0.258	8555	-
all	-	9025	-
obs	-	9025	71.84 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.7803	-0.0172	0.2689	0.9919	0.003	1.0552	-0.0058	-0.0225	0.0562	0.0925	0.0056	0.016	-0.2096	-0.0265	0.0002	0.0564	-0.0046	0.0185	0.0849	-0.0046	0.1033	26.6656	119.5105	70.2432
2	0.4903	0.0647	0.0131	0.6321	0.1442	1.2537	-0.0018	-0.0009	-0.0477	0.1262	0.0085	0.0518	0.2984	-0.0135	-0.0067	0.089	-0.0159	0.0104	0.0587	0.0168	0.1129	21.1391	90.9091	62.4703
3	0.3132	0.3253	-0.1443	1	-0.1786	1.3662	-0.0036	0.0175	-0.0115	-0.0767	-0.0141	0.1728	-0.1153	-0.2469	0.0177	0.0192	0.0282	-0.0191	0.1903	-0.0109	0.1752	5.3647	113.4082	49.8266
4	0.7179	-0.1748	-0.0561	0.972	0.0166	0.835	-0.008	-0.0646	-0.0395	0.0262	0.0588	-0.0186	-0.2912	0.0826	-0.0508	0.1264	-0.0626	0.0255	0.0767	-0.0243	0.0772	43.5356	140.6064	54.4147
5	0.2728	0.0286	-0.2733	1.5948	-0.3846	1.8518	0.0201	-0.0518	-0.0418	-0.1136	0.0204	-0.3372	0.0271	0.463	-0.0406	0.0345	-0.0575	0.0105	0.2852	-0.0788	0.243	67.9699	124.4198	48.1569
6	0.7969	0.0396	-0.036	1.0383	0.2602	1.1944	-0.0079	0.0782	0.0294	-0.3033	0.0513	-0.0813	-0.3437	0.1523	-0.0434	0.2154	-0.1169	0.0567	0.1077	-0.0189	0.055	53.1348	138.5507	25.8918
7	0.9143	-0.0879	-0.1812	0.6921	0.0188	0.6962	-0.0125	0.0231	-0.0853	-0.1741	-0.0147	-0.0446	0.1064	-0.0155	0.0272	0.2501	-0.008	0.0001	0.0492	-0.0049	0.0355	34.7244	100.3714	5.2951
8	0.5836	-0.0048	-0.1276	0.6336	0.2398	0.9871	0.0679	0.0433	0.0801	-0.1831	-0.0032	-0.0318	-0.283	-0.0356	-0.0647	0.2563	0.0098	-0.0157	0.0472	0.0232	0.0565	27.5013	129.0184	11.3526
9	0.2466	-0.1307	-0.2824	1.727	-0.3771	2.1781	0.0156	0.0202	-0.028	-0.0952	-0.017	0.2555	-0.0543	-0.313	0.0015	0.0483	-0.0264	-0.0634	0.1813	-0.0162	0.1231	9.032	106.6044	19.704
10	0.9646	0.3029	-0.0007	0.8704	-0.0888	0.6493	-0.0981	0.0436	0.0162	-0.1518	0.0677	-0.0537	0.2763	0.0706	0.0304	0.2169	0.0515	0.0269	0.0573	-0.0144	0.0565	47.2068	79.3242	24.771
11	0.8319	-0.0553	0.033	0.9935	0.3872	1.1734	-0.0603	-0.1314	-0.0013	0.1304	0.0126	-0.0573	0.3859	0.1178	0.0477	0.1917	0.1108	0.007	0.1038	0.0149	0.0501	49.6766	81.4068	54.7751
12	0.6926	-0.0143	-0.0735	1.7177	-0.706	1.4554	-0.0701	-0.1144	0.0423	0.0844	0.0723	-0.2804	0.0069	0.3821	-0.0022	0.0338	0.0685	0.0002	0.2602	-0.066	0.2054	69.4253	95.4899	36.8025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999
5	X-RAY DIFFRACTION	5	E	-10 - 9999
6	X-RAY DIFFRACTION	6	F	-10 - 9999
7	X-RAY DIFFRACTION	7	G	-10 - 9999
8	X-RAY DIFFRACTION	8	H	-10 - 9999
9	X-RAY DIFFRACTION	9	I	-10 - 9999
10	X-RAY DIFFRACTION	10	J	-10 - 9999
11	X-RAY DIFFRACTION	11	K	-10 - 9999
12	X-RAY DIFFRACTION	12	L	-10 - 9999

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi