PDB-6rg0: Structure of pdxj

ID or keywords:

Entry

Database: PDB / ID: 6rg0

Title

Structure of pdxj

Components

Pyridoxine 5'-phosphate synthase

Keywords

TRANSFERASE / Serine phosphatase SerB / serine aminotransferase SerC / histidinol phosphatase HisB / histidinol phosphatase aminotransferase HisC

Function / homology

Function and homology information

pyridoxine 5'-phosphate synthase / pyridoxine 5'-phosphate synthase activity / pyridoxine biosynthetic process / identical protein binding / cytosol
Similarity search - Function

Biological species

Escherichia coli K12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.074 Å

Authors

Rohweder, B. / Rajendran, C. / Sterner, R.

Funding support

1items

Citation

Journal: Biochemistry / Year: 2019
Title: Library Selection with a Randomized Repertoire of ( beta alpha )8-Barrel Enzymes Results in Unexpected Induction of Gene Expression.
Authors: Rohweder, B. / Lehmann, G. / Eichner, N. / Polen, T. / Rajendran, C. / Ruperti, F. / Linde, M. / Treiber, T. / Jung, O. / Dettmer, K. / Meister, G. / Bott, M. / Gronwald, W. / Sterner, R.

History

Deposition	Apr 16, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6rg0.cif.gz	366.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6rg0.ent.gz	302.8 KB	Display	PDB format
PDBx/mmJSON format	6rg0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6rg0_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	6rg0_full_validation.pdf.gz	490.3 KB	Display
Data in XML	6rg0_validation.xml.gz	35.7 KB	Display
Data in CIF	6rg0_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rg/6rg0 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/6rg0	HTTPS FTP

-
Related structure data

Related structure data	1ho1S 1m5wS S: Starting model for refinement
Similar structure data	3ayt-1 4juq-5 5zrq-d 2c8m-2 6k7z-4 3ayt-3 3iip-3 3ayv-1 1geq-2 2e09-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1ho1S

1m5wS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Pyridoxine 5'-phosphate synthase

B: Pyridoxine 5'-phosphate synthase

C: Pyridoxine 5'-phosphate synthase

D: Pyridoxine 5'-phosphate synthase

117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyridoxine 5'-phosphate synthase

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

2

B: Pyridoxine 5'-phosphate synthase

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

3

C: Pyridoxine 5'-phosphate synthase

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

4

D: Pyridoxine 5'-phosphate synthase

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

Unit cell

Length a, b, c (Å)	80.050, 188.124, 192.884
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Pyridoxine 5'-phosphate synthase / PNP synthase Mass: 29226.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: pdxJ, b2564, JW2548 / Production host: Escherichia coli (E. coli) References: UniProt: P0A794, pyridoxine 5'-phosphate synthase

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 60.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 31, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.0744→48.44 Å / Num. all: 373532 / Num. obs: 27529 / % possible obs: 99.3 % / Redundancy: 13.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.1137 / R_pim(I) all: 0.03076 / R_rim(I) all: 0.1137 / Net I/σ(I): 23.01
Reflection shell	Resolution: 3.074→3.184 Å / Redundancy: 14 % / R_merge(I) obs: 1.086 / Num. unique obs: 2544 / CC_1/2: 0.801 / R_pim(I) all: 0.2978 / R_rim(I) all: 1.127

-
Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1HO1, 1M5W

1ho1

1m5w

Resolution: 3.074→48.438 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.88

	R_factor	Num. reflection	% reflection
R_free	0.2485	1367	5.01 %
R_work	0.1821	-	-
obs	0.1854	27345	99.01 %
all	-	51807	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.074→48.438 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6975	0	0	0	6975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7081
X-RAY DIFFRACTION	f_angle_d	1.241	9584
X-RAY DIFFRACTION	f_dihedral_angle_d	13.062	4337
X-RAY DIFFRACTION	f_chiral_restr	0.06	1157
X-RAY DIFFRACTION	f_plane_restr	0.008	1257

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0744-3.1303	0.3772	127	0.3357	2212	X-RAY DIFFRACTION	86
3.1303-3.1905	0.2934	138	0.2897	2658	X-RAY DIFFRACTION	100
3.1905-3.2556	0.3845	136	0.2729	2571	X-RAY DIFFRACTION	100
3.2556-3.3264	0.3267	143	0.2633	2650	X-RAY DIFFRACTION	100
3.3264-3.4037	0.3026	141	0.2633	2597	X-RAY DIFFRACTION	100
3.4037-3.4888	0.3211	140	0.2307	2596	X-RAY DIFFRACTION	100
3.4888-3.5831	0.3274	134	0.2287	2610	X-RAY DIFFRACTION	100
3.5831-3.6885	0.2946	139	0.2082	2607	X-RAY DIFFRACTION	100
3.6885-3.8075	0.315	142	0.1874	2650	X-RAY DIFFRACTION	100
3.8075-3.9435	0.1943	131	0.1693	2589	X-RAY DIFFRACTION	100
3.9435-4.1014	0.2316	139	0.1643	2623	X-RAY DIFFRACTION	100
4.1014-4.2879	0.2227	134	0.1573	2597	X-RAY DIFFRACTION	100
4.2879-4.5138	0.1918	133	0.1393	2615	X-RAY DIFFRACTION	100
4.5138-4.7964	0.223	136	0.14	2593	X-RAY DIFFRACTION	100
4.7964-5.1663	0.1839	138	0.1454	2618	X-RAY DIFFRACTION	100
5.1663-5.6855	0.2895	144	0.174	2639	X-RAY DIFFRACTION	100
5.6855-6.5066	0.2874	135	0.2021	2586	X-RAY DIFFRACTION	100
6.5066-8.1911	0.246	138	0.1765	2588	X-RAY DIFFRACTION	99
8.1911-48.4437	0.2017	136	0.1588	2614	X-RAY DIFFRACTION	99

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	2.3746	1.8985	0.0047	1.6916	0.2436	2.2778	0.0139	0.1175	-0.2305	-0.2133	0.0723	-0.393	0.3474	0.3866	0.0002	0.5955	0.0545	0.0906	0.5126	0.0259	0.4318	24.5696	-7.3679	-23.1944
2	1.7228	-1.6821	0.8003	2.1244	0.1782	3.2057	-0.0491	0.605	0.2459	-0.4099	0.1901	0.17	0.0933	0.085	0.0004	0.6746	-0.0439	0.0518	0.6156	0.002	0.4022	26.077	-5.0823	-35.4542
3	0.2052	-0.0265	-0.2412	0.2084	-0.0837	0.3694	0.3733	0.303	0.4142	-0.8154	-0.2632	0.1963	0.4793	0.1046	-0.0006	0.6542	0.0115	-0.0507	0.9924	0.0222	0.4361	31.542	2.9956	-45.7858
4	0.3739	0.2454	-0.8988	1.8138	0.7449	1.4429	-0.2617	0.3216	0.1263	-0.2111	0.1023	-0.3073	-0.1135	0.0055	0.0006	0.4848	-0.0045	0.0233	0.5461	0.0682	0.4749	32.4028	10.5982	-34.4917
5	1.9283	0.9938	-0.6175	0.792	-0.3728	0.3005	0.1358	-0.0329	0.117	0.0192	-0.0373	0.1825	-0.1756	0.0672	0.0002	0.5212	0.0402	0.0616	0.4673	0.0959	0.3757	28.7407	12.244	-23.939
6	0.4331	-0.1765	-0.0203	0.5092	0.7361	0.7304	-0.1737	-0.031	0.606	0.5043	-0.0606	0.4012	-0.03	-0.1967	-0.0022	0.4835	0.0633	0.0544	0.4361	0.1564	0.6103	18.8642	8.6969	-15.5103
7	2.1631	-0.3803	0.0109	3.2188	0.4372	1.6197	-0.0702	0.1076	-0.2845	-0.1899	-0.495	-0.4205	0.2831	0.6101	-0.0041	0.3762	0.0986	0.09	0.6377	0.2789	0.544	39.2643	-10.1499	-4.6252
8	0.9599	0.9845	0.3463	1.2855	-0.373	1.617	0.2242	0.3741	0.2115	0.1037	-0.8146	-0.445	1.1393	0.9108	-0.0834	0.768	0.5058	0.2766	0.959	0.4687	1.0208	48.0816	-27.4767	-2.3011
9	2.0639	0.3012	1.4398	1.8285	0.1276	1.5173	0.0103	-0.0507	-0.4591	-0.1678	-0.0784	0.2561	0.789	-0.0192	-0.0051	0.6621	0.0881	0.0974	0.4144	0.17	0.5708	27.6809	-25.9682	-2.5703
10	0.3509	-0.4344	-0.3063	1.0634	0.8775	0.877	0.2047	-0.267	-0.4304	-0.9692	0.4937	0.7239	0.7881	-0.8686	-0.0002	0.5086	-0.0957	-0.0873	0.6642	0.1898	0.7031	2.7813	-16.4873	-18.7053
11	0.6816	-0.162	-0.3796	1.8461	-0.3327	1.169	0.1312	0.0761	-0.3777	-0.5059	-0.0256	-0.2398	0.1705	-0.428	-0.0001	0.8014	-0.0961	-0.0291	0.7336	0.0405	0.6718	7.3009	-22.4873	-22.5809
12	0.5538	-0.9752	-1.3182	1.6677	0.9727	2.5191	-0.3133	0.3259	-0.6463	-0.6009	0.2544	0.0416	0.7722	-0.3012	-0.0004	1.1763	-0.2051	-0.0834	0.8047	0.0509	1.017	0.5481	-39.6005	-22.9071
13	0.4862	-0.3323	0.4242	0.3143	-0.3554	0.2818	-0.2031	0.3614	-1.1306	0.1736	-0.0468	0.3162	1.0477	-0.3409	0.0056	0.9672	-0.1831	0.2363	0.7382	0.2862	1.2587	-5.4801	-36.6141	-5.8207
14	0.8659	1.0635	0.5233	1.0278	0.5704	0.5685	-0.1073	-0.2053	-0.1266	-0.1819	0.3359	0.0874	0.2296	-0.4696	-0.0001	0.771	-0.0946	0.0161	0.6374	0.2299	0.9094	0.8076	-27.0673	-6.4854
15	0.2493	-0.1647	-0.04	0.1319	0.0241	0.2376	-0.1562	-0.1353	0.0849	1.0105	0.4487	0.1175	0.1775	-0.2343	-0.0004	0.8349	-0.0334	-0.0293	0.6384	0.1918	0.5691	6.685	-21.3685	-1.5455
16	-0.0142	-0.2416	0.1301	1.5564	-1.0727	0.4804	-0.0014	-0.4103	0.0582	1.5274	0.7435	0.2945	-1.2508	-1.3158	0.048	0.6079	0.0648	0.1495	1.0615	0.2115	1.2265	-10.9709	2.2289	-10.0761
17	0.0687	0.0962	0.061	0.1339	0.0252	-0.0338	-0.1887	1.3569	-0.0391	0.4636	0.0982	0.1613	0.5338	-0.6468	-0.0016	1.1162	0.0802	-0.01	1.8965	0.1178	1.0998	-24.8816	1.8881	-19.3487
18	0.7087	0.1792	0.2431	0.6584	-0.3283	0.2818	-0.4744	0.331	-0.7902	0.0497	0.3127	0.0763	0.4297	0.2719	-0.0006	1.0055	0.2199	0.2602	1.415	-0.0435	1.5817	-19.0863	4.613	-24.1359
19	0.0272	0.0695	-0.0804	0.2405	-0.2449	0.1412	-0.4706	-0.0087	-0.2879	-0.84	1.1081	0.2293	1.5391	-1.0264	-0.0103	1.2684	0.3418	-0.2372	2.5992	-0.1017	1.3519	-24.9917	9.521	-30.6158
20	0.6483	0.1626	1.2399	0.8164	1.2909	2.402	0.302	0.3048	0.8658	-0.6443	0.031	-0.2195	-0.3973	-0.6739	0.0029	0.9568	0.2554	0.0559	1.166	0.4857	1.0297	-8.5758	12.0892	-28.4465
21	0.9548	0.2746	-0.16	0.2402	-0.4307	1.0442	-0.0611	0.7669	0.6469	0.0343	-0.5475	-1.9619	-0.3254	0.4877	0.0007	0.651	0.0035	-0.0766	0.706	0.2599	1.0222	0.3499	5.768	-15.8933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 256 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 15 through 89 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 90 through 167 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 168 through 256 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 15 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 89 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 90 through 160 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 161 through 197 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 198 through 239 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 240 through 256 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 15 through 81 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 82 through 98 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 99 through 116 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 117 through 135 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 136 through 218 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 219 through 256 )

-
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