PDB-3h9p: Crystal structure of putative triphosphoribosyl-dephospho-coA syn...

ID or keywords:

Entry

Database: PDB / ID: 3h9p

Title

Crystal structure of putative triphosphoribosyl-dephospho-coA synthase from Archaeoglobus fulgidus

Components

putative triphosphoribosyl-dephospho-coA synthase

Keywords

structural genomics / unknown function / Archaeoglobus fulgidus / putative triphosphoribosyl-dephospho-coA synthase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

triphosphoribosyl-dephospho-CoA synthase activity / phosphorylation / ATP binding
Similarity search - Function

Biological species

Archaeoglobus fulgidus DSM 4304 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Chang, C. / Wu, R. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of putative triphosphoribosyl-dephospho-coA synthase from Archaeoglobus fulgidus
Authors: Chang, C. / Wu, R. / Gu, M. / Joachimiak, A.

History

Deposition	Apr 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3h9p.cif.gz	138.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3h9p.ent.gz	115.6 KB	Display	PDB format
PDBx/mmJSON format	3h9p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3h9p_validation.pdf.gz	466.9 KB	Display	wwPDB validaton report
Full document	3h9p_full_validation.pdf.gz	477.6 KB	Display
Data in XML	3h9p_validation.xml.gz	26.4 KB	Display
Data in CIF	3h9p_validation.cif.gz	36.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/3h9p ftp://data.pdbj.org/pub/pdb/validation_reports/h9/3h9p	HTTPS FTP

-
Related structure data

Similar structure data	2gfb-2 4odu-1 4ma3-2 2o5z-d 2ajx-d 6wju-2 5tpl-d 6rlm-3 6kx0-d 4wcw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: APC86791.1

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: putative triphosphoribosyl-dephospho-coA synthase

B: putative triphosphoribosyl-dephospho-coA synthase

C: putative triphosphoribosyl-dephospho-coA synthase

hetero molecules

85.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: putative triphosphoribosyl-dephospho-coA synthase

B: putative triphosphoribosyl-dephospho-coA synthase

hetero molecules

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

2

C: putative triphosphoribosyl-dephospho-coA synthase

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

Unit cell

Length a, b, c (Å)	135.806, 77.725, 66.654
Angle α, β, γ (deg.)	90.00, 97.99, 90.00
Int Tables number	5
Space group name H-M	C121

Details

A and B makes dimer as is. C makes dimer with symmetric counter part of C using vector (1-x, y, 1-z)

#1: Protein	putative triphosphoribosyl-dephospho-coA synthase Mass: 28431.672 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: AF_1835 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: O28441
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.04 Å³/Da / Density % sol: 39.77 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES pH 9.5, 25% PEG8000 , VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2009
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. all: 30676 / Num. obs: 30320 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.072 / Net I/σ(I): 27.2
Reflection shell	Resolution: 2.3→2.32 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.433 / Mean I/σ(I) obs: 3.71 / % possible all: 98.9

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
MLPHARE		phasing
DM		model building
SHELXD		phasing
RESOLVE		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.93 / SU B: 15.817 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23876	1527	5.1 %	RANDOM
R_work	0.19488	-	-	-
obs	0.19713	28681	98.35 %	-
all	-	30208	-	-

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: 35.612 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.74 Å²	0 Å²	1.01 Å²
2-	-	0.69 Å²	0 Å²
3-	-	-	-4.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5094	0	20	142	5256

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	5198
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.428	1.97	7001
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.308	5	655
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.62	23.818	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.765	15	894
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.599	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	784
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3858
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.761	1.5	3294
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.423	2	5177
X-RAY DIFFRACTION	r_scbond_it	2.407	3	1904
X-RAY DIFFRACTION	r_scangle_it	3.937	4.5	1824
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.298→2.358 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.257	112	-
R_work	0.215	2045	-
obs	-	-	95.95 %

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	1.1398	0.8436	-0.3628	1.7544	1.3542	5.9285	0.0378	-0.0639	0.0688	-0.0978	-0.0123	-0.2005	-0.6666	0.4733	-0.0255	0.1283	-0.0591	0.0111	0.0595	0.026	0.1167	35.8594	54.834	24.4217
2	3.1376	-0.7502	-0.3518	3.0685	0.5721	3.4491	0.1498	0.3246	-0.1153	-0.235	-0.2037	0.0736	0.2771	-0.3983	0.0539	0.0548	-0.0082	-0.0119	0.0748	-0.0219	0.0312	27.1575	45.5709	22.7812
3	3.9409	-0.7316	-2.1555	2.8264	0.8943	4.3925	-0.2423	0.0133	-0.3398	0.2527	-0.0952	-0.0198	0.4511	0.0201	0.3375	0.1134	-0.0212	0.0242	0.0105	-0.0021	0.0814	34.3218	33.0263	28.8417
4	5.9533	0.0726	-0.5951	9.6089	-2.3709	8.296	-0.3124	0.318	-0.4019	0.0456	0.019	-0.8305	0.3283	0.8387	0.2934	0.0393	0.0319	0.0039	0.1407	-0.0589	0.1963	47.9625	26.8689	21.0011
5	2.3355	-1.0183	-1.6032	2.0849	1.638	8.4002	-0.1916	0.0057	-0.4265	0.1379	-0.0181	0.1769	0.8099	-0.296	0.2097	0.1395	-0.0842	0.0254	0.0652	0.0103	0.13	29.4539	43.8121	-9.679
6	2.4168	-1.6655	0.144	2.3083	0.26	4.3606	-0.0184	-0.2585	0.0011	0.143	0.063	-0.004	-0.4698	0.2847	-0.0446	0.1254	-0.0906	0.0008	0.0996	0.0017	0.1114	37.9362	53.5139	-7.9243
7	1.3015	-0.3281	-1.1279	3.4655	-2.4326	7.5179	-0.0827	-0.1786	-0.1262	-0.0104	-0.2608	-0.2909	0.0329	0.8593	0.3435	0.0385	-0.049	0.0116	0.1998	0.0392	0.0696	51.7235	47.1628	-11.0019
8	11.3051	1.3861	-4.3963	6.8169	3.7734	6.0318	-0.1013	-0.335	-0.4499	0.5019	0.0931	-0.4741	0.8319	0.9029	0.0083	0.1995	0.1872	-0.0344	0.3722	0.1124	0.1215	58.109	35.2632	-0.834
9	1.7433	-0.2953	-1.7393	2.2651	1.723	10.4452	0.0409	0.0631	0.1856	0.0444	-0.1729	0.1227	0.0821	-0.6966	0.132	0.0066	-0.019	0.007	0.0834	-0.0087	0.04	53.3834	64.9702	47.8608
10	2.6428	-0.2621	-0.5315	4.6427	-0.0125	6.142	0.0314	0.0101	0.1253	-0.0903	-0.0373	-0.1179	0.3401	0.527	0.0059	0.0319	0.0068	0.0004	0.1102	-0.0031	0.0692	65.8756	65.43	49.2037
11	1.402	-0.9292	-0.6779	6.2107	-4.3956	9.8155	0.0513	-0.3463	0.6098	0.5792	-0.2847	-0.6941	-0.5499	0.5473	0.2334	0.1067	-0.1368	-0.0466	0.2559	-0.061	0.3307	69.9961	79.3892	54.5139
12	4.5132	2.2244	4.9012	4.8147	0.1121	11.6734	-0.0882	0.3378	0.7453	-0.0964	-0.2271	-0.1331	-0.9694	-0.0735	0.3153	0.1998	0.1182	0.1078	0.1775	0.2037	0.3982	69.0223	92.826	45.1413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	39 - 77
2	X-RAY DIFFRACTION	1	A	118 - 133
3	X-RAY DIFFRACTION	1	A	147 - 158
4	X-RAY DIFFRACTION	2	A	83 - 117
5	X-RAY DIFFRACTION	2	A	159 - 180
6	X-RAY DIFFRACTION	3	A	181 - 219
7	X-RAY DIFFRACTION	3	A	254 - 275
8	X-RAY DIFFRACTION	4	A	220 - 253
9	X-RAY DIFFRACTION	5	B	41 - 77
10	X-RAY DIFFRACTION	5	B	118 - 133
11	X-RAY DIFFRACTION	5	B	147 - 158
12	X-RAY DIFFRACTION	6	B	83 - 117
13	X-RAY DIFFRACTION	6	B	159 - 180
14	X-RAY DIFFRACTION	7	B	181 - 219
15	X-RAY DIFFRACTION	7	B	254 - 275
16	X-RAY DIFFRACTION	8	B	220 - 253
17	X-RAY DIFFRACTION	9	C	43 - 76
18	X-RAY DIFFRACTION	9	C	118 - 133
19	X-RAY DIFFRACTION	9	C	147 - 158
20	X-RAY DIFFRACTION	10	C	83 - 117
21	X-RAY DIFFRACTION	10	C	159 - 180
22	X-RAY DIFFRACTION	11	C	181 - 219
23	X-RAY DIFFRACTION	11	C	254 - 275
24	X-RAY DIFFRACTION	12	C	220 - 253

-
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

-
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