PDB-8v35: Crystal structure of HpsN from Cupriavidus pinatubonensis

ID or keywords:

Entry

Database: PDB / ID: 8v35

Title

Crystal structure of HpsN from Cupriavidus pinatubonensis

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: 1.94 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

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PDBx/mmCIF format	8v35.cif.gz	180.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8v35.ent.gz	135.4 KB	Display	PDB format
PDBx/mmJSON format	8v35.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8v35_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8v35_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8v35_validation.xml.gz	36.1 KB	Display
Data in CIF	8v35_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v3/8v35 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v35	HTTPS FTP

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Related structure data

Related structure data	8v36C 8v37C 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

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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

94.2 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)	77.032, 87.767, 134.800
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: 46991.172 Da / Num. of mol.: 2 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#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.: 227 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, magnesium chloride, PEG 4000

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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: Jul 11, 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: 1.94→44.93 Å / Num. obs: 68501 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 1 / R_merge(I) obs: 0.036 / R_pim(I) all: 0.016 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.94→1.98 Å / R_merge(I) obs: 1.073 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4501 / CC_1/2: 0.789 / R_pim(I) all: 0.476

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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: 1.94→43.956 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.943 / SU B: 5.961 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.262	3480	5.093 %
R_work	0.2188	64854	-
all	0.221	-	-
obs	-	68334	99.947 %

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: 57.116 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.294 Å²	-0 Å²	0 Å²
2-	-	0.689 Å²	-0 Å²
3-	-	-	-3.982 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→43.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6273	0	6	227	6506

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	6409
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	6087
X-RAY DIFFRACTION	r_angle_refined_deg	0.988	1.655	8705
X-RAY DIFFRACTION	r_angle_other_deg	0.335	1.576	13988
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.086	5	823
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.818	5	43
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.486	10	1020
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.664	10	268
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	995
X-RAY DIFFRACTION	r_chiral_restr_other	0.013	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7616
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1424
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1274
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	5428
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	3171
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	3278
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	294
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.052	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.016	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.026	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.118	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	2.953	5.815	3313
X-RAY DIFFRACTION	r_mcbond_other	2.952	5.815	3313
X-RAY DIFFRACTION	r_mcangle_it	4.446	10.429	4126
X-RAY DIFFRACTION	r_mcangle_other	4.445	10.43	4127
X-RAY DIFFRACTION	r_scbond_it	3.007	6.147	3096
X-RAY DIFFRACTION	r_scbond_other	3.007	6.147	3097
X-RAY DIFFRACTION	r_scangle_it	4.807	11.18	4578
X-RAY DIFFRACTION	r_scangle_other	4.807	11.18	4579
X-RAY DIFFRACTION	r_lrange_it	6.714	53.845	7036
X-RAY DIFFRACTION	r_lrange_other	6.712	53.677	6995

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
1.94-1.99	0.36	249	0.349	4731	0.349	4983	0.88	0.885	99.9398	0.337
1.99-2.045	0.327	248	0.315	4618	0.316	4866	0.898	0.908	100	0.296
2.045-2.104	0.312	220	0.289	4490	0.29	4711	0.922	0.931	99.9788	0.267
2.104-2.168	0.3	234	0.274	4356	0.275	4591	0.933	0.941	99.9782	0.251
2.168-2.239	0.28	264	0.253	4188	0.255	4452	0.944	0.955	100	0.226
2.239-2.318	0.292	238	0.249	4093	0.251	4332	0.939	0.957	99.9769	0.219
2.318-2.405	0.348	183	0.242	3989	0.246	4172	0.929	0.962	100	0.21
2.405-2.503	0.306	207	0.236	3816	0.24	4024	0.945	0.966	99.9752	0.205
2.503-2.614	0.282	189	0.235	3662	0.238	3851	0.948	0.966	100	0.206
2.614-2.741	0.296	195	0.242	3507	0.246	3703	0.945	0.965	99.973	0.213
2.741-2.889	0.3	168	0.231	3340	0.235	3508	0.95	0.968	100	0.208
2.889-3.063	0.28	165	0.242	3185	0.244	3351	0.951	0.964	99.9702	0.225
3.063-3.273	0.274	171	0.243	2974	0.245	3146	0.956	0.964	99.9682	0.232
3.273-3.534	0.269	148	0.229	2808	0.231	2958	0.951	0.969	99.9324	0.229
3.534-3.869	0.241	169	0.212	2556	0.214	2725	0.965	0.973	100	0.221
3.869-4.321	0.258	110	0.192	2363	0.195	2474	0.955	0.977	99.9596	0.207
4.321-4.982	0.212	105	0.173	2084	0.175	2189	0.974	0.983	100	0.2
4.982-6.082	0.277	93	0.207	1783	0.21	1882	0.962	0.978	99.6812	0.234
6.082-8.52	0.217	78	0.182	1433	0.184	1514	0.975	0.982	99.8018	0.219
8.52-43.956	0.196	44	0.185	856	0.185	907	0.979	0.979	99.2282	0.228

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