PDB-3b8b: Crystal structure of CysQ from Bacteroides thetaiotaomicron, a ba...

ID or keywords:

Entry

Database: PDB / ID: 3b8b

Title

Crystal structure of CysQ from Bacteroides thetaiotaomicron, a bacterial member of the inositol monophosphatase family

Components

CysQ, sulfite synthesis pathway protein

Keywords

HYDROLASE / 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase / CysQ / sulfite synthesis pathway / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / : / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfate assimilation / magnesium ion binding / plasma membrane
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Cuff, M.E. / Mulligan, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of CysQ from Bacteroides thetaiotaomicron, a bacterial member of the inositol monophosphatase family.
Authors: Cuff, M.E. / Mulligan, R. / Abdullah, J. / Joachimiak, A.

History

Deposition	Oct 31, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3b8b.cif.gz	78 KB	Display	PDBx/mmCIF format
PDB format	pdb3b8b.ent.gz	60.1 KB	Display	PDB format
PDBx/mmJSON format	3b8b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3b8b_validation.pdf.gz	448.3 KB	Display	wwPDB validaton report
Full document	3b8b_full_validation.pdf.gz	450.6 KB	Display
Data in XML	3b8b_validation.xml.gz	15.7 KB	Display
Data in CIF	3b8b_validation.cif.gz	23.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/3b8b ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b8b	HTTPS FTP

-
Related structure data

Similar structure data	6vp4-2 6isp-3 3mmu-3 2ftn-d 4ad4-d 6a7b-1 7kl6-d 6dno-d 1krm-d 3htw-d 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: APC81317

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CysQ, sulfite synthesis pathway protein

hetero molecules

33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	93.927, 93.927, 140.783
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-291- HOH

Details

Authors state that the biological unit of this protein is unknown.

#1: Protein	CysQ, sulfite synthesis pathway protein Mass: 32967.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Species: Bacteroides thetaiotaomicron / Strain: VPI-5482, DSM 2079, NCTC 10582, E50 / Gene: cysQ, BT_0411 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8AAQ3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.72 Å³/Da / Density % sol: 54.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.26M Ammonium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97923, 0.97860

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2007

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97923	1
2	0.9786	1

Reflection

Redundancy: 21 % / Av σ(I) over netI: 9.2 / Number: 864081 / R_merge(I) obs: 0.082 / Χ²: 1.72 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 41147 / % possible obs: 99.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.19	50	99.3	1	0.058	5.549	19.3
3.33	4.19	100	1	0.064	4.399	20.1
2.91	3.33	100	1	0.081	3.781	20.8
2.64	2.91	99.8	1	0.086	2.435	21.3
2.45	2.64	99.8	1	0.092	1.965	21.4
2.31	2.45	99.7	1	0.099	1.547	21.5
2.19	2.31	99.6	1	0.111	1.231	21.6
2.1	2.19	99.6	1	0.121	0.98	21.6
2.02	2.1	99.6	1	0.139	0.812	21.5
1.95	2.02	99.3	1	0.168	0.669	21.4
1.89	1.95	99.4	1	0.214	0.544	21.4
1.83	1.89	99.3	1	0.275	0.466	21.2
1.78	1.83	99.1	1	0.354	0.424	21
1.74	1.78	99	1	0.429	0.398	20.8
1.7	1.74	99	1	0.57	0.378	20.3

Reflection

Resolution: 1.7→50 Å / Num. all: 41147 / Num. obs: 41147 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 21 % / B_iso Wilson estimate: 23.4 Å² / R_merge(I) obs: 0.082 / Χ²: 1.717 / Net I/σ(I): 9.2

Reflection shell

Resolution: 1.7→1.74 Å / Redundancy: 20.3 % / R_merge(I) obs: 0.57 / Num. unique all: 2663 / R_sym value: 0.378 / Χ²: 3.9 / % possible all: 99

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.69 Å / D res low: 50 Å / FOM : 0.451 / FOM acentric: 0.479 / FOM centric: 0.265 / Reflection: 41101 / Reflection acentric: 35688 / Reflection centric: 5413

Phasing MAD set

Highest resolution: 1.69 Å / Lowest resolution: 50 Å / Reflection centric: 5413

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric
1	2.2	1	0.2	0.2	0	0	35688
2	0.93	0.84	6.3	8.9	0.56	0.54	35687

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.93-50	1.51	1	0.8	0.4	0	0	86	110
1	6.14-10.93	1.7	1	0.8	0.4	0	0	525	282
1	4.27-6.14	1.53	1	0.7	0.4	0	0	1375	443
1	3.27-4.27	1.33	1	0.5	0.3	0	0	2653	620
1	2.65-3.27	2.01	1	0.4	0.2	0	0	4326	783
1	2.23-2.65	2.6	1	0.3	0.1	0	0	6397	936
1	1.92-2.23	3.35	1	0.1	0	0	0	8911	1074
1	1.69-1.92	9.14	1	0.1	0	0	0	11415	1165
2	10.93-50	0.59	0.44	7.6	8.3	2.23	1.75	86	110
2	6.14-10.93	0.64	0.56	6.9	9	1.9	1.48	525	282
2	4.27-6.14	0.75	0.71	8	10.6	1.37	0.98	1375	443
2	3.27-4.27	0.91	0.84	9.7	13.3	0.82	0.59	2653	620
2	2.65-3.27	0.91	0.86	7.3	9.9	0.75	0.55	4326	783
2	2.23-2.65	0.92	0.9	5.8	7.6	0.61	0.46	6397	936
2	1.92-2.23	0.98	0.98	5.6	7.6	0.4	0.28	8911	1074
2	1.69-1.92	1	1	5.6	7.4	0.23	0.17	11414	1165

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	25.11107	0.508	0.227	-0.001	0
2	Se	24.36447	0.448	0.061	-0.149	0
3	Se	38.00618	0.226	-0.046	-0.25	0
4	Se	40.78844	0.506	0.114	-0.148	0
5	Se	29.28839	0.366	0.047	-0.095	0
6	Se	29.26484	0.527	0.208	-0.068	0
7	Se	27.20475	0.386	0.086	-0.101	0
8	Se	48.27295	0.07	-0.109	-0.286	0
9	Se	24.82116	0.508	0.227	-0.001	0.082
10	Se	25.67648	0.448	0.061	-0.149	0.062
11	Se	41.21453	0.226	-0.046	-0.25	0.071
12	Se	51.60811	0.505	0.113	-0.148	0.061
13	Se	28.57502	0.366	0.047	-0.095	0.037
14	Se	33.37499	0.529	0.211	-0.067	0.071
15	Se	26.57562	0.386	0.086	-0.101	0.002
16	Se	49.13473	0.069	-0.109	-0.287	0.043

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.93-50	0.774	0.89	0.684	196	86	110
6.14-10.93	0.788	0.873	0.631	807	525	282
4.27-6.14	0.731	0.804	0.505	1818	1375	443
3.27-4.27	0.642	0.702	0.389	3273	2653	620
2.65-3.27	0.643	0.696	0.35	5109	4326	783
2.23-2.65	0.584	0.631	0.264	7333	6397	936
1.92-2.23	0.424	0.459	0.136	9985	8911	1074
1.69-1.92	0.199	0.216	0.041	12580	11415	1165

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 41101

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.71-100	44.9	0.82	517
5.9-7.71	37.8	0.894	600
4.96-5.9	35.7	0.914	724
4.36-4.96	36.4	0.919	814
3.94-4.36	41.4	0.936	906
3.62-3.94	44.5	0.919	981
3.36-3.62	42.9	0.916	1065
3.16-3.36	44.6	0.909	1127
2.99-3.16	45.1	0.911	1197
2.84-2.99	44.1	0.906	1249
2.71-2.84	42.5	0.913	1300
2.6-2.71	42.9	0.92	1358
2.5-2.6	41.9	0.919	1403
2.41-2.5	43.7	0.923	1462
2.33-2.41	44.9	0.924	1514
2.26-2.33	43.2	0.922	1548
2.2-2.26	46.1	0.919	1593
2.13-2.2	46.9	0.921	1634
2.08-2.13	49.5	0.912	1702
2.03-2.08	51.7	0.923	1726
1.98-2.03	53.8	0.917	1769
1.94-1.98	54.9	0.907	1791
1.89-1.94	58.3	0.903	1827
1.85-1.89	59	0.907	1876
1.82-1.85	63.1	0.904	1900
1.78-1.82	64.9	0.895	1954
1.75-1.78	68.1	0.891	1967
1.72-1.75	71.7	0.873	2050
1.69-1.72	76.3	0.815	1547

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.7→40.66 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.955 / SU B: 2.907 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.188	2061	5.1 %	RANDOM
R_work	0.166	-	-	-
all	0.167	40803	-	-
obs	0.167	40803	99.55 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.597 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.41 Å²	-0.21 Å²	0 Å²
2-	-	-0.41 Å²	0 Å²
3-	-	-	0.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→40.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2114	0	31	282	2427

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2396
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1640
X-RAY DIFFRACTION	r_angle_refined_deg	1.47	1.979	3287
X-RAY DIFFRACTION	r_angle_other_deg	0.903	3	4046
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.361	5.062	324
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.448	24.737	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.424	15	436
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.351	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	360
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2697
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	470
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	485
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	1793
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1150
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	1257
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	229
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.138	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.258	0.2	33
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.288	0.2	61
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	1.363	1.5	1797
X-RAY DIFFRACTION	r_mcbond_other	0.232	1.5	579
X-RAY DIFFRACTION	r_mcangle_it	1.597	2	2366
X-RAY DIFFRACTION	r_scbond_it	2.761	3	1063
X-RAY DIFFRACTION	r_scangle_it	3.61	4.5	895

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.253	160	-
R_work	0.211	2777	-
all	-	2937	-
obs	-	-	99.06 %

Refinement TLS params.

Method: refined / Origin x: -0.5843 Å / Origin y: 33.6228 Å / Origin z: 10.4721 Å

	11	12	13	21	22	23	31	32	33
T	-0.0674 Å²	-0.0039 Å²	0.0218 Å²	-	-0.0777 Å²	-0.0042 Å²	-	-	-0.0493 Å²
L	1.2299 °²	-0.437 °²	-0.5301 °²	-	1.0006 °²	0.1521 °²	-	-	1.0561 °²
S	-0.0196 Å °	-0.0044 Å °	-0.1389 Å °	-0.019 Å °	-0.017 Å °	0.0036 Å °	-0.0079 Å °	0.0479 Å °	0.0366 Å °

-
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