PDB-3tr3: Structure of a bolA protein homologue from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 3tr3

Title

Structure of a bolA protein homologue from Coxiella burnetii

Components

BolA

Keywords

UNKNOWN FUNCTION / Cellular processes / stress-induced

Function / homology

BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / : / BolA

Function and homology information

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.456 Å

Authors

Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 20, 2016	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tr3.cif.gz	76.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3tr3.ent.gz	61.2 KB	Display	PDB format
PDBx/mmJSON format	3tr3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3tr3_validation.pdf.gz	423.3 KB	Display	wwPDB validaton report
Full document	3tr3_full_validation.pdf.gz	423.3 KB	Display
Data in XML	3tr3_validation.xml.gz	8.8 KB	Display
Data in CIF	3tr3_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/3tr3 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3tr3	HTTPS FTP

-
Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	2y4v-d 6fq1-1 1v9h-d 6pwg-1 6xh0-d 6ie7-1 1cku-d 6ie4-2 6gx6-d 4pnr-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: BolA

B: BolA

hetero molecules

18.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: BolA

hetero molecules

B: BolA

hetero molecules

defined by software
18.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.245, 66.245, 118.009
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	B-104- HOH

#1: Protein	BolA Mass: 9261.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: bolA, CBU_0582 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83DW0
#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 77 / 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: 4.04 Å³/Da / Density % sol: 69.52 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES pH 6.5 1.8M ammonium sulphate 0.010M cobalt chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X4C		1	0.979
ROTATING ANODE			RIGAKU MICROMAX-007 HF	2	1.5418

Detector

Type	ID	Detector	Date
MAR CCD 165 mm	1	CCD	Jul 29, 2011
RIGAKU SATURN 944	2	CCD	Jul 14, 2011

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	VARIMAX HF	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	1.5418	1

Reflection

Redundancy: 4.3 % / Av σ(I) over netI: 19.03 / Number: 35908 / R_merge(I) obs: 0.063 / Χ²: 1.27 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 8436 / % possible obs: 98.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.3	30	99.8	1	0.036	1.838	4.2
5.8	7.3	99.8	1	0.059	1.764	4.5
5.07	5.8	99.8	1	0.054	1.436	4.7
4.61	5.07	99.8	1	0.046	1.448	4.7
4.28	4.61	100	1	0.046	1.638	4.7
4.03	4.28	100	1	0.047	1.357	4.8
3.83	4.03	100	1	0.052	1.213	4.8
3.66	3.83	100	1	0.054	1.196	4.7
3.52	3.66	100	1	0.057	1.162	4.7
3.4	3.52	100	1	0.071	1.142	4.8
3.29	3.4	100	1	0.083	1.11	4.7
3.2	3.29	100	1	0.115	1.204	4.8
3.12	3.2	100	1	0.109	1.047	4.8
3.04	3.12	100	1	0.139	1.01	4.8
2.97	3.04	100	1	0.154	1.025	4.4
2.91	2.97	99	1	0.148	1.079	3.6
2.85	2.91	98	1	0.173	0.998	3
2.8	2.85	95.5	1	0.194	0.996	2.7
2.75	2.8	88.7	1	0.235	1.204	2.6
2.7	2.75	84.1	1	0.256	0.985	2.3

Reflection

Resolution: 2.45→50 Å / Num. all: 11441 / Num. obs: 11190 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / R_merge(I) obs: 0.088 / Χ²: 1.208 / Net I/σ(I): 9.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.45-2.49	2.5	0.402	473	0.781	1,2	88.2
2.49-2.54	3	0.41	533	0.807	1,2	94.5
2.54-2.59	3.4	0.343	513	0.971	1,2	95.5
2.59-2.64	3.9	0.361	572	0.822	1,2	97.1
2.64-2.7	4.3	0.364	540	1.148	1,2	99.1
2.7-2.76	5	0.325	572	0.815	1,2	99.5
2.76-2.83	5.5	0.282	538	0.892	1,2	99.4
2.83-2.9	5.8	0.267	564	0.908	1,2	99.5
2.9-2.99	6	0.22	578	0.871	1,2	99.5
2.99-3.09	6.1	0.208	546	0.923	1,2	99.5
3.09-3.2	6	0.165	564	0.948	1,2	98.9
3.2-3.32	6.3	0.138	567	0.962	1,2	99.5
3.32-3.48	6.1	0.1	569	1.111	1,2	99
3.48-3.66	6.1	0.081	576	1.153	1,2	99.5
3.66-3.89	6.2	0.066	560	1.327	1,2	98.6
3.89-4.19	6	0.059	566	1.385	1,2	98.6
4.19-4.61	6.1	0.049	568	1.505	1,2	98.3
4.61-5.28	6	0.05	581	1.427	1,2	98.5
5.28-6.65	6	0.058	595	1.72	1,2	97.5
6.65-50	5.5	0.046	615	2.66	1,2	94.8

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
SOLOMON		phasing
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.456→41.132 Å / Occupancy max: 1 / Occupancy min: 0.68 / FOM work R set: 0.8563 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2198	537	4.8 %	RANDOM
R_work	0.1864	-	-	-
all	0.1881	11973	-	-
obs	0.1881	11183	97.88 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.442 Å² / k_sol: 0.348 e/Å³

Displacement parameters

B_iso max: 271.57 Å² / B_iso mean: 45.1491 Å² / B_iso min: 22.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.8379 Å²	-0 Å²	-0 Å²
2-	-	7.8379 Å²	-0 Å²
3-	-	-	-15.6759 Å²

Refinement step

Cycle: LAST / Resolution: 2.456→41.132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1258	0	2	77	1337

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	1286
X-RAY DIFFRACTION	f_angle_d	1.364	1745
X-RAY DIFFRACTION	f_chiral_restr	0.081	196
X-RAY DIFFRACTION	f_plane_restr	0.005	225
X-RAY DIFFRACTION	f_dihedral_angle_d	13.847	458

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4559-2.703	0.3176	115	0.2616	2508	2623	95
2.703-3.094	0.2533	157	0.2003	2650	2807	99
3.094-3.8976	0.2164	131	0.1768	2697	2828	99
3.8976-41.1381	0.1885	134	0.1701	2791	2925	98

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	1.5121	-0.8706	0.3294	0.7628	-0.3601	1.0443	-0.0933	-0.1366	0.9775	-0.2025	-0.2664	-0.0615	-0.7934	-0.0843	0.0967	0.5394	0.0329	-0.0449	0.2895	-0.0607	0.3373	37.8174	-11.322	-1.004
2	0.28	0.2274	-0.0943	0.3122	-0.245	0.2831	0.0659	-0.024	0.0802	0.1409	-0.1495	0.3615	0.0077	-0.506	-0.0657	0.3565	0.2413	-0.1164	0.5776	-0.0917	0.393	29.4153	-14.2615	2.5516
3	0.0788	0.2542	0.045	0.7525	0.1263	0.6625	-0.132	-0.0803	0.0749	0.0258	0.0312	-0.0588	-0.1429	-0.3029	0.0392	0.3134	0.0876	-0.0109	0.499	-0.0356	0.3045	28.4593	-18.4447	-5.2919
4	0.3986	0.0306	-0.3261	0.1777	-0.0708	0.3193	-0.1389	0.1766	-0.3167	0.0423	-0.0311	-0.186	-0.1693	0.1612	0.0754	-0.0202	-0.0689	0.0747	0.6558	-0.0602	0.2355	34.6114	-19.9054	-5.4097
5	0.0859	-0.0534	0.0485	0.0786	0.0425	0.1568	0.0688	-0.374	0.1352	0.165	-0.0811	0.0726	0.0127	-0.218	0.0197	0.5912	-0.0847	0.2026	1.0709	-0.227	0.4551	19.3006	-20.1794	8.22
6	0.1618	0.1127	0.1688	0.1712	0.1357	0.1822	-0.1251	-0.0703	-0.0862	-0.0347	-0.1648	0.0011	0.019	0.153	0.1005	0.3464	0.1706	0.001	0.4736	0.0494	0.194	45.4944	-33.9598	6.6137
7	0.749	-0.0219	-0.2843	0.3839	0.4866	0.7772	-0.0646	-0.0968	-0.1299	0.0222	0.1045	0.1213	0.1033	0.0408	-0.0062	0.3576	0.0576	0.0074	0.2693	-0.0039	0.2431	40.922	-20.6385	16.7283

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:14)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 15:25)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 26:59)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 60:71)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 72:78)	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq -1:3)	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 4:79)	B

-
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://pdbjlvh1.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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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