PDB-5dvz: Holo TrpB from Pyrococcus furiosus

ID or keywords:

Entry

Database: PDB / ID: 5dvz

Title

Holo TrpB from Pyrococcus furiosus

Components

Tryptophan synthase beta chain 1

Keywords

LYASE / Type II PLP enzyme / Tryptophan Biosynthesis / EC 4.2.1.20

Function / homology

Function and homology information

tryptophan synthase / tryptophan synthase activity
Similarity search - Function

Biological species

Pyrococcus furiosus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.69 Å

Authors

Buller, A.R. / Arnold, F.H.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Directed evolution of the tryptophan synthase beta-subunit for stand-alone function recapitulates allosteric activation.
Authors: Buller, A.R. / Brinkmann-Chen, S. / Romney, D.K. / Herger, M. / Murciano-Calles, J. / Arnold, F.H.

History

Deposition	Sep 21, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2017	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5dvz.cif.gz	592.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5dvz.ent.gz	503.9 KB	Display	PDB format
PDBx/mmJSON format	5dvz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5dvz_validation.pdf.gz	474.1 KB	Display	wwPDB validaton report
Full document	5dvz_full_validation.pdf.gz	482.4 KB	Display
Data in XML	5dvz_validation.xml.gz	58.8 KB	Display
Data in CIF	5dvz_validation.cif.gz	83.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dv/5dvz ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dvz	HTTPS FTP

-
Related structure data

Related structure data	5dw0C 5dw3C 5e0kC C: citing same article (ref.)
Similar structure data	6cuv-2 5dw0-1 6ami-1 6amc-2 6amh-2 5t6m-2 6am7-1 5vm5-1 5dw0-2 5vm5-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (9)

Deposited unit

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

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

1

A: Tryptophan synthase beta chain 1

B: Tryptophan synthase beta chain 1

hetero molecules

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

2

C: Tryptophan synthase beta chain 1

D: Tryptophan synthase beta chain 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.051, 111.882, 160.832
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tryptophan synthase beta chain 1 Mass: 43885.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.15 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 20% PEG3350, 0.1 M HEPES / Temp details: 293

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.69→40 Å / Num. obs: 161910 / % possible obs: 99.6 % / Redundancy: 4.9 % / Net I/σ(I): 7.3
Reflection shell	Resolution: 1.69→1.72 Å / Mean I/σ(I) obs: 0.6 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0124	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Resolution: 1.69→39.33 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.951 / SU B: 7.927 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22772	8573	5 %	RANDOM
R_work	0.20192	-	-	-
obs	0.20322	161910	97.05 %	-

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: 31.231 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	-0 Å²	0 Å²
2-	-	0.18 Å²	-0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→39.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11711	0	24	654	12389

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.019	12040
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11562
X-RAY DIFFRACTION	r_angle_refined_deg	1.15	1.973	16318
X-RAY DIFFRACTION	r_angle_other_deg	0.782	3	26550
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.071	5	1549
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.519	24.076	498
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.18	15	1977
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.319	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1795
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	13724
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2699
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	0.418	1.518	6157
X-RAY DIFFRACTION	r_mcbond_other	0.418	1.518	6156
X-RAY DIFFRACTION	r_mcangle_it	0.729	2.273	7692
X-RAY DIFFRACTION	r_mcangle_other	0.729	2.274	7693
X-RAY DIFFRACTION	r_scbond_it	0.472	1.59	5883
X-RAY DIFFRACTION	r_scbond_other	0.464	1.581	5868
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.793	2.345	8593
X-RAY DIFFRACTION	r_long_range_B_refined	4.765	12.937	13857
X-RAY DIFFRACTION	r_long_range_B_other	4.696	12.522	13594
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.69→1.734 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.39	623	-
R_work	0.391	10356	-
obs	-	-	85.51 %

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	0.8883	-0.0003	0.0787	1.2037	0.3044	1.5423	-0.0583	0.127	0.0469	-0.1244	0.0214	-0.0209	-0.2133	0.0518	0.0368	0.0799	-0.0105	0.0062	0.1762	-0.0088	0.0439	-34.452	-65.254	-63.688
2	4.0266	0.6043	2.1109	1.5763	0.4157	4.445	-0.0668	0.1664	-0.1987	-0.1165	0.0401	0.1526	0.0374	-0.3238	0.0267	0.1626	0.0557	-0.0028	0.2017	-0.0207	0.1429	-52.702	-59.919	-63.177
3	0.9027	0.0453	0.1201	1.457	-0.1811	1.597	-0.0198	0.165	-0.0511	-0.1993	0.0162	0.1092	0.0297	-0.0674	0.0036	0.1331	-0.0046	0.0181	0.199	-0.0119	0.0216	-37.371	-72.435	-71.184
4	1.6445	0.4344	-0.7507	0.8932	-0.5798	3.6186	-0.0165	0.1206	-0.1187	-0.1718	0.037	0.1629	0.2711	-0.2336	-0.0204	0.1327	-0.0156	-0.0138	0.1443	-0.0329	0.0957	-43.04	-81.799	-65.96
5	3.5929	-0.8725	-0.6949	2.6363	-0.2901	1.6463	-0.042	0.0055	-0.3412	-0.031	0.003	0.1904	0.2339	-0.081	0.039	0.1685	-0.0461	-0.0101	0.17	-0.0037	0.0456	-40.358	-84.416	-57.12
6	0.7475	0.0371	-0.1328	1.2812	-0.0357	1.769	-0.0231	-0.0885	-0.0621	0.0788	-0.0066	-0.0189	0.2275	0.0477	0.0297	0.0689	0.0205	0.0056	0.1734	-0.0048	0.0468	-36.026	-74.992	-33.24
7	2.53	-0.3637	1.1211	1.9359	-0.0001	4.3909	-0.0349	-0.2336	0.05	0.1764	-0.0685	0.1967	0.1649	-0.6271	0.1034	0.1945	-0.0714	0.0287	0.2869	-0.0231	0.1816	-52.997	-83.489	-32.412
8	0.7494	-0.3461	-0.0718	1.4778	-0.1748	1.7025	-0.0252	-0.1655	0.0798	0.1697	0.0396	0.0422	-0.0759	-0.0027	-0.0143	0.0963	0.0195	-0.0069	0.1773	-0.0137	0.0183	-38.308	-64.673	-26.707
9	2.52	-1.0697	1.7854	1.6548	-1.0637	3.9521	0.0424	-0.3075	-0.0773	0.197	0.019	0.3425	0.0151	-0.4052	-0.0614	0.1382	0.0339	0.0488	0.2147	-0.0321	0.0936	-47.923	-61.292	-25.643
10	2.8583	0.5138	0.4207	2.2043	-0.1231	2.7386	-0.0304	0.0279	0.3107	-0.0777	-0.0077	0.1752	-0.2738	-0.1891	0.0381	0.1093	0.0667	0.0123	0.1733	0.0025	0.0497	-43.826	-55.778	-40.645
11	0.9886	-0.3441	0.1868	0.9216	-0.0025	1.2312	0.0017	0.1458	0.1012	-0.1812	0.0148	0.0192	-0.1724	-0.0259	-0.0165	0.1483	-0.0057	0.0121	0.1987	0.0114	0.043	1.856	-31.956	-63.401
12	2.9327	1.1691	1.0352	4.7803	1.1976	4.4849	-0.0437	0.1761	-0.2111	-0.4894	0.0907	0.3368	0.5201	-0.4166	-0.047	0.2888	-0.0388	-0.0337	0.315	0.0246	0.1896	-17.959	-35.868	-61.661
13	0.9908	-0.324	0.1783	1.5935	-0.112	1.1995	0.0391	0.1819	-0.0504	-0.2291	0.0051	0.0634	-0.0076	-0.0268	-0.0442	0.1703	-0.0104	0.0124	0.239	-0.0009	0.0083	3.438	-39.358	-70.248
14	0.7448	0.4756	-0.5111	1.9702	-1.8433	3.6644	0.0337	0.2736	-0.1227	-0.3436	0.1561	0.2939	0.2078	-0.4252	-0.1898	0.2383	-0.001	-0.0528	0.2821	-0.0527	0.116	-1.266	-49.369	-71.933
15	1.9747	0.1434	-0.1894	1.8707	-0.4868	2.1192	-0.0579	0.1318	-0.291	-0.06	0.0432	0.0565	0.2051	-0.0135	0.0147	0.1322	-0.0118	-0.0163	0.1546	-0.033	0.0528	4.574	-52.605	-56.679
16	0.8008	-0.1913	0.0976	1.2127	0.1208	1.4272	0.0275	-0.0753	-0.0578	0.0503	-0.0012	-0.0363	0.1317	0.0785	-0.0263	0.0426	-0.008	-0.0008	0.142	-0.0012	0.0316	7.543	-42.301	-33.608
17	3.4414	-0.2286	-0.4218	2.215	0.1336	2.6538	0.0874	-0.254	0.0404	0.1863	-0.0369	0.3522	0.142	-0.5435	-0.0505	0.1877	-0.0803	-0.0032	0.2734	0.0024	0.141	-7.695	-54.426	-32.905
18	1.1698	-0.2546	0.2129	1.6963	-0.1544	1.6675	-0.0135	-0.0938	0.0427	0.118	0.0512	-0.0079	-0.0449	-0.0813	-0.0377	0.0417	0.0092	-0.0068	0.1414	-0.011	0.005	3.449	-34.604	-27.338
19	2.2892	-1.2516	2.5475	0.6867	-1.3732	3.2555	0.0118	-0.3588	-0.3247	-0.0009	0.1827	0.1981	0.3296	-0.6781	-0.1945	0.3339	-0.1184	0.0796	0.421	-0.0064	0.2307	-9.664	-41.542	-20.223
20	1.2755	-0.2943	0.5693	1.3429	-0.6659	2.5803	-0.0255	-0.0651	0.1442	0.0201	0.0225	0.2033	-0.1861	-0.3008	0.0031	0.0543	0.0395	0.0188	0.1811	-0.003	0.0731	-6.75	-27.9	-34.327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 114
2	X-RAY DIFFRACTION	2	A	115 - 166
3	X-RAY DIFFRACTION	3	A	167 - 288
4	X-RAY DIFFRACTION	4	A	289 - 355
5	X-RAY DIFFRACTION	5	A	356 - 384
6	X-RAY DIFFRACTION	6	B	1 - 121
7	X-RAY DIFFRACTION	7	B	122 - 179
8	X-RAY DIFFRACTION	8	B	180 - 282
9	X-RAY DIFFRACTION	9	B	283 - 332
10	X-RAY DIFFRACTION	10	B	333 - 384
11	X-RAY DIFFRACTION	11	C	1 - 122
12	X-RAY DIFFRACTION	12	C	123 - 166
13	X-RAY DIFFRACTION	13	C	167 - 279
14	X-RAY DIFFRACTION	14	C	280 - 332
15	X-RAY DIFFRACTION	15	C	333 - 384
16	X-RAY DIFFRACTION	16	D	1 - 132
17	X-RAY DIFFRACTION	17	D	133 - 169
18	X-RAY DIFFRACTION	18	D	170 - 274
19	X-RAY DIFFRACTION	19	D	275 - 301
20	X-RAY DIFFRACTION	20	D	302 - 385

-
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