PDB-3u4g: The Structure of CobT from Pyrococcus horikoshii

ID or keywords:

Entry

Database: PDB / ID: 3u4g

Title

The Structure of CobT from Pyrococcus horikoshii

Components

NaMN:DMB phosphoribosyltransferase

Keywords

TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / putative Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / DMB-PRT / CobT / Coenzyme metabolism

Function / homology

Function and homology information

nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Cuff, M.E. / Evdokimova, E. / Mursleen, A. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of CobT from Pyrococcus horikoshii
Authors: Cuff, M.E. / Evdokimova, E. / Mursleen, A. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Oct 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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	3u4g.cif.gz	146.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3u4g.ent.gz	113.8 KB	Display	PDB format
PDBx/mmJSON format	3u4g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3u4g_validation.pdf.gz	447.9 KB	Display	wwPDB validaton report
Full document	3u4g_full_validation.pdf.gz	449.5 KB	Display
Data in XML	3u4g_validation.xml.gz	17.5 KB	Display
Data in CIF	3u4g_validation.cif.gz	23.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u4/3u4g ftp://data.pdbj.org/pub/pdb/validation_reports/u4/3u4g	HTTPS FTP

-
Related structure data

Similar structure data	7cny-d 2azk-d 3d5t-2 3hhp-2 6g3b-d 5a1t-1 5fkr-d 2z4z-d 6xu3-2 6mgj-8 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: apc102145

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: NaMN:DMB phosphoribosyltransferase

hetero molecules

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

1

A: NaMN:DMB phosphoribosyltransferase

hetero molecules

A: NaMN:DMB phosphoribosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.751, 82.751, 84.814
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	172
Space group name H-M	P6₄

#1: Protein	NaMN:DMB phosphoribosyltransferase / UPF0284 protein PH0034 Mass: 36650.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0034 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: O57746
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.22 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M Amonium Sulfate, 0.1M Sodium Acetate, pH 4.6, 25% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97918, 0.97953

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 6, 2009

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	0.97918	1
2	0.97953	1

Reflection

Redundancy: 12.2 % / Av σ(I) over netI: 40.41 / Number: 311223 / R_merge(I) obs: 0.071 / Χ²: 1.35 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 25516 / % possible obs: 98.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.16	50	92.9	1	0.057	3.065	11.9
4.09	5.16	96.3	1	0.047	2.174	12.4
3.58	4.09	96.8	1	0.054	2.216	12.4
3.25	3.58	97.6	1	0.059	2.017	12.4
3.02	3.25	97.5	1	0.065	1.813	12.3
2.84	3.02	97.8	1	0.075	1.619	12.4
2.7	2.84	97.8	1	0.09	1.442	12.3
2.58	2.7	98.5	1	0.102	1.303	12.2
2.48	2.58	98.3	1	0.118	1.225	12.3
2.39	2.48	98.2	1	0.132	1.127	12.2
2.32	2.39	98.6	1	0.152	1.062	12.2
2.25	2.32	98.9	1	0.181	1.011	12.1
2.19	2.25	98.9	1	0.179	1.013	12.2
2.14	2.19	98.9	1	0.225	0.919	12.1
2.09	2.14	98.9	1	0.302	0.875	12.2
2.05	2.09	99	1	0.341	0.873	12.1
2.01	2.05	99.2	1	0.432	0.833	12.1
1.97	2.01	99.6	1	0.5	0.802	11.9
1.93	1.97	99.3	1	0.683	0.787	12
1.9	1.93	99.2	1	0.664	0.789	12

Reflection

Resolution: 1.9→50 Å / Num. all: 25516 / Num. obs: 25516 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / B_iso Wilson estimate: 31.7 Å² / R_merge(I) obs: 0.071 / Χ²: 1.346 / Net I/σ(I): 11.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.93	12	0.664	1316	0.789	1	99.2
1.93-1.97	12	0.683	1285	0.787	1	99.3
1.97-2.01	11.9	0.5	1289	0.802	1	99.6
2.01-2.05	12.1	0.432	1272	0.833	1	99.2
2.05-2.09	12.1	0.341	1265	0.873	1	99
2.09-2.14	12.2	0.302	1281	0.875	1	98.9
2.14-2.19	12.1	0.225	1297	0.919	1	98.9
2.19-2.25	12.2	0.179	1252	1.013	1	98.9
2.25-2.32	12.1	0.181	1296	1.011	1	98.9
2.32-2.39	12.2	0.152	1263	1.062	1	98.6
2.39-2.48	12.2	0.132	1291	1.127	1	98.2
2.48-2.58	12.3	0.118	1290	1.225	1	98.3
2.58-2.7	12.2	0.102	1265	1.303	1	98.5
2.7-2.84	12.3	0.09	1265	1.442	1	97.8
2.84-3.02	12.4	0.075	1263	1.619	1	97.8
3.02-3.25	12.3	0.065	1271	1.813	1	97.5
3.25-3.58	12.4	0.059	1274	2.017	1	97.6
3.58-4.09	12.4	0.054	1270	2.216	1	96.8
4.09-5.16	12.4	0.047	1264	2.174	1	96.3
5.16-50	11.9	0.057	1247	3.065	1	92.9

-
Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.9 Å / D res low: 50 Å / FOM : 0.366 / FOM acentric: 0.369 / FOM centric: 0.278 / Reflection: 25460 / Reflection acentric: 24607 / Reflection centric: 853

Phasing MAD set

Highest resolution: 1.9 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.79	1	0.1	0.1	0	0	24607	853
2	0.92	0.89	8.9	13.6	0.67	0.56	21269	773

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	12.01-50	1.54	1	0.5	0.2	0	0	68	15
1	6.82-12.01	0.97	1	0.3	0.3	0	0	405	44
1	4.77-6.82	1.42	1	0.3	0.2	0	0	988	71
1	3.66-4.77	1.15	1	0.2	0.2	0	0	1854	95
1	2.97-3.66	1.39	1	0.1	0.1	0	0	2950	119
1	2.5-2.97	2.6	1	0.1	0	0	0	4381	147
1	2.16-2.5	4.26	1	0.1	0	0	0	6019	172
1	1.9-2.16	13.91	1	0	0	0	0	7942	190
2	12.01-50	0.85	1.1	16.4	27.8	1.55	1.46	68	15
2	6.82-12.01	0.88	0.72	17.2	20.5	1.25	1.43	404	43
2	4.77-6.82	0.82	0.8	14.1	17.8	1.25	1.04	987	71
2	3.66-4.77	0.88	0.86	14.8	19.5	0.91	0.49	1852	95
2	2.97-3.66	0.91	0.91	11.8	15.6	0.73	0.33	2944	119
2	2.5-2.97	0.92	0.91	8	10.4	0.65	0.36	4361	147
2	2.16-2.5	0.97	0.96	6.7	9.7	0.45	0.26	5994	172
2	1.9-2.16	0.99	0.99	6.6	9.3	0.26	0.19	4659	111

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	41.6131	-0.27	-0.828	-0.298	5.139	0
2	42.698	-0.249	-0.812	-0.239	5.274	0
3	58.0783	-0.263	-0.796	-0.096	5.594	0
4	41.2035	-0.27	-0.828	-0.298	3.483	-0.27
5	39.5862	-0.249	-0.813	-0.238	3.601	-0.164
6	48.7269	-0.264	-0.797	-0.097	3.342	-0.216

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.01-50	0.644	0.627	0.719	83	68	15
6.82-12.01	0.675	0.683	0.599	449	405	44
4.77-6.82	0.726	0.738	0.565	1059	988	71
3.66-4.77	0.659	0.673	0.391	1949	1854	95
2.97-3.66	0.592	0.604	0.286	3069	2950	119
2.5-2.97	0.497	0.504	0.285	4528	4381	147
2.16-2.5	0.308	0.311	0.2	6191	6019	172
1.9-2.16	0.116	0.117	0.064	8132	7942	190

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 25460

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.89-100	47.7	0.915	509
5.53-6.89	39.3	0.933	502
4.84-5.53	39.5	0.947	508
4.38-4.84	43.1	0.946	532
4.03-4.38	41.9	0.948	598
3.75-4.03	45.5	0.945	630
3.53-3.75	45.5	0.942	688
3.34-3.53	46.7	0.932	705
3.17-3.34	46.1	0.919	756
3.03-3.17	49.1	0.923	793
2.91-3.03	50.1	0.914	838
2.8-2.91	49.5	0.913	884
2.7-2.8	50.2	0.899	877
2.61-2.7	53.9	0.9	935
2.53-2.61	55.2	0.895	973
2.46-2.53	53.2	0.91	979
2.39-2.46	57.9	0.9	1020
2.33-2.39	59.8	0.904	1037
2.27-2.33	61.1	0.896	1086
2.22-2.27	66.4	0.935	1105
2.17-2.22	67	0.909	1124
2.12-2.17	73.7	0.915	1162
2.08-2.12	70	0.924	1167
2.04-2.08	74.4	0.923	1232
2-2.04	73.7	0.926	1236
1.96-2	82.2	0.929	1234
1.9-1.96	82.6	0.891	2350

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.1	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: 1.9→50 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.295 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2156	1296	5.1 %	RANDOM
R_work	0.1685	-	-	-
all	0.1708	25516	-	-
obs	0.1708	25516	98.15 %	-

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 max: 124.37 Å² / B_iso mean: 43.1976 Å² / B_iso min: 20.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.71 Å²	-0.35 Å²	0 Å²
2-	-	-0.71 Å²	0 Å²
3-	-	-	1.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2481	0	18	150	2649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.02	2619
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1797
X-RAY DIFFRACTION	r_angle_refined_deg	1.71	2.005	3558
X-RAY DIFFRACTION	r_angle_other_deg	0.985	3	4427
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.771	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.109	24.375	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.98	15	467
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.115	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	412
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2902
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	492

LS refinement shell

Resolution: 1.902→1.951 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	106	-
R_work	0.232	1780	-
all	-	1886	-
obs	-	-	99.26 %

Refinement TLS params.

Method: refined / Origin x: -4.2519 Å / Origin y: 27.0182 Å / Origin z: 4.6661 Å

	11	12	13	21	22	23	31	32	33
T	0.0569 Å²	0.0536 Å²	-0.0552 Å²	-	0.1147 Å²	-0.0005 Å²	-	-	0.1128 Å²
L	1.5617 °²	0.0918 °²	0.0623 °²	-	0.9437 °²	0.0371 °²	-	-	2.0765 °²
S	0.1343 Å °	-0.0324 Å °	-0.2951 Å °	0.0758 Å °	-0.0367 Å °	-0.1737 Å °	0.2815 Å °	0.3777 Å °	-0.0976 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://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