PDB-8v37: Crystal structure of HpsN D352A mutant from Cupriavidus pinatubon...

ID or keywords:

Entry

Database: PDB / ID: 8v37

Title

Crystal structure of HpsN D352A mutant from Cupriavidus pinatubonensis in complex with NAD+

Components

Sulfopropanediol 3-dehydrogenase

Keywords

OXIDOREDUCTASE / DHPS / dehydrogenase / NAD-dependent / sulfolactate

Function / homology

Function and homology information

sulfopropanediol 3-dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding / cytosol
Similarity search - Function

Biological species

Cupriavidus pinatubonensis JMP134 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.228 Å

Authors

Lee, M.

Funding support

Australia, 2items

Citation

Journal: Chem Sci / Year: 2024
Title: Structural and kinetic insights into the stereospecific oxidation of R -2,3-dihydroxypropanesulfonate by DHPS-3-dehydrogenase from Cupriavidus pinatubonensis.
Authors: Burchill, L. / Kaur, A. / Nastasovici, A. / Lee, M. / Williams, S.J.

History

Deposition	Nov 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Database references / Structure summary / Category: citation / pdbx_entry_details Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8v37.cif.gz	181.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8v37.ent.gz	136.2 KB	Display	PDB format
PDBx/mmJSON format	8v37.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/8v37 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v37	HTTPS FTP

-
Related structure data

Related structure data	8v35C 8v36C 9cp7C 9cp8C 9cp9C C: citing same article (ref.)
Similar structure data	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	#127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Sulfopropanediol 3-dehydrogenase

B: Sulfopropanediol 3-dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	76.784, 88.348, 134.110
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sulfopropanediol 3-dehydrogenase Mass: 46947.164 Da / Num. of mol.: 2 / Mutation: D352A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus pinatubonensis JMP134 (bacteria) Gene: hpsN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46N53
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, magnesium chlroide, PEG 4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.228→44.7 Å / Num. obs: 45320 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC_1/2: 1 / R_merge(I) obs: 0.086 / R_pim(I) all: 0.039 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.23→2.3 Å / R_merge(I) obs: 1.1195 / Num. unique obs: 4057 / CC_1/2: 0.621 / R_pim(I) all: 0.533

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.228→44.213 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.927 / SU B: 9.555 / SU ML: 0.218 / Cross valid method: FREE R-VALUE / ESU R: 0.3 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.258	2302	5.087 %
R_work	0.2119	42953	-
all	0.214	-	-
obs	-	45255	99.793 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.069 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.634 Å²	-0 Å²	0 Å²
2-	-	-1.191 Å²	0 Å²
3-	-	-	-2.444 Å²

Refinement step

Cycle: LAST / Resolution: 2.228→44.213 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6317	0	46	175	6538

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	6491
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6149
X-RAY DIFFRACTION	r_angle_refined_deg	0.856	1.656	8823
X-RAY DIFFRACTION	r_angle_other_deg	0.297	1.576	14125
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.012	5	828
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.287	5	46
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.667	10	1032
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.919	10	273
X-RAY DIFFRACTION	r_chiral_restr	0.041	0.2	1006
X-RAY DIFFRACTION	r_chiral_restr_other	0.011	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7715
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1462
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	1283
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	5478
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	3211
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3384
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	238
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.069	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.083	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.332	5.327	3327
X-RAY DIFFRACTION	r_mcbond_other	2.331	5.327	3327
X-RAY DIFFRACTION	r_mcangle_it	3.921	9.562	4147
X-RAY DIFFRACTION	r_mcangle_other	3.92	9.563	4148
X-RAY DIFFRACTION	r_scbond_it	2.404	5.703	3164
X-RAY DIFFRACTION	r_scbond_other	2.403	5.704	3165
X-RAY DIFFRACTION	r_scangle_it	4.122	10.36	4675
X-RAY DIFFRACTION	r_scangle_other	4.121	10.36	4676
X-RAY DIFFRACTION	r_lrange_it	6.216	49.691	7083
X-RAY DIFFRACTION	r_lrange_other	6.209	49.748	7048

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.228-2.286	0.308	178	0.33	3053	0.329	3304	0.893	0.898	97.7906	0.321
2.286-2.348	0.317	154	0.31	3060	0.31	3215	0.902	0.919	99.9689	0.295
2.348-2.416	0.341	159	0.297	2967	0.299	3126	0.915	0.93	100	0.275
2.416-2.49	0.326	164	0.284	2891	0.286	3056	0.926	0.939	99.9673	0.259
2.49-2.571	0.309	147	0.262	2798	0.265	2945	0.94	0.951	100	0.233
2.571-2.661	0.335	135	0.259	2728	0.262	2864	0.921	0.956	99.9651	0.228
2.661-2.761	0.303	122	0.251	2645	0.253	2768	0.931	0.959	99.9639	0.218
2.761-2.874	0.283	150	0.231	2513	0.234	2663	0.944	0.965	100	0.2
2.874-3.001	0.274	123	0.223	2414	0.226	2538	0.95	0.967	99.9606	0.193
3.001-3.147	0.271	118	0.239	2333	0.241	2451	0.947	0.965	100	0.213
3.147-3.316	0.294	125	0.219	2206	0.223	2331	0.941	0.969	100	0.198
3.316-3.516	0.256	102	0.211	2128	0.214	2230	0.958	0.973	100	0.198
3.516-3.757	0.254	102	0.199	1985	0.202	2088	0.962	0.976	99.9521	0.188
3.757-4.056	0.238	111	0.192	1849	0.195	1960	0.968	0.977	100	0.18
4.056-4.439	0.206	102	0.167	1710	0.169	1812	0.972	0.984	100	0.165
4.439-4.957	0.22	97	0.168	1541	0.172	1639	0.973	0.983	99.939	0.169
4.957-5.711	0.229	63	0.183	1408	0.185	1471	0.972	0.984	100	0.178
5.711-6.966	0.234	71	0.192	1189	0.194	1261	0.964	0.981	99.9207	0.188
6.966-9.732	0.179	44	0.152	959	0.153	1006	0.982	0.987	99.7018	0.16
9.732-44.213	0.302	35	0.226	576	0.23	614	0.948	0.964	99.5114	0.249

-
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