PDB-8h4z: Crystal structure of carboxyspermidine dehydrogenase from Helicob...

ID or keywords:

Entry

Database: PDB / ID: 8h4z

Title

Crystal structure of carboxyspermidine dehydrogenase from Helicobacter pylori in space group P21212

Components

Saccharopine dehydrogenase

Keywords

BIOSYNTHETIC PROTEIN / carboxyspermidine dehydrogenase

Function / homology

Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily / Saccharopine dehydrogenase

Function and homology information

Biological species

Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Ko, K.Y. / Park, S.C. / Cho, S.Y. / Yoon, S.I.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural analysis of carboxyspermidine dehydrogenase from Helicobacter pylori.
Authors: Ko, K.Y. / Park, S.C. / Cho, S.Y. / Yoon, S.I.

History

Deposition	Oct 11, 2022	Deposition site: PDBJ / Processing site: RCSB
Revision 1.0	Nov 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8h4z.cif.gz	738.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8h4z_validation.pdf.gz	451 KB	Display	wwPDB validaton report
Full document	8h4z_full_validation.pdf.gz	460.3 KB	Display
Data in XML	8h4z_validation.xml.gz	55.2 KB	Display
Data in CIF	8h4z_validation.cif.gz	78.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/8h4z ftp://data.pdbj.org/pub/pdb/validation_reports/h4/8h4z	HTTPS FTP

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Related structure data

Related structure data	8h50C 8h52C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Saccharopine dehydrogenase

B: Saccharopine dehydrogenase

C: Saccharopine dehydrogenase

D: Saccharopine dehydrogenase

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

1

A: Saccharopine dehydrogenase

B: Saccharopine dehydrogenase

defined by author&software
Evidence: gel filtration
91.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Saccharopine dehydrogenase

D: Saccharopine dehydrogenase

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

Unit cell

Length a, b, c (Å)	128.875, 153.154, 97.739
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	C-402- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	PHE	PHE	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	2 - 27	8 - 33
1	2	ASN	ASN	ASP	ASP	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	29 - 105	35 - 111
1	3	TRP	TRP	ASP	ASP	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	123 - 126	129 - 132
1	4	ALA	ALA	LEU	LEU	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	128 - 189	134 - 195
1	5	GLU	GLU	ILE	ILE	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	191 - 212	197 - 218
1	6	GLN	GLN	SER	SER	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	214 - 364	220 - 370
1	7	ALA	ALA	GLU	GLU	(chain 'A' and (resid 2 through 27 or resid 29...	A	A	370 - 398	376 - 404
2	1	HIS	HIS	PHE	PHE	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	2 - 27	8 - 33
2	2	ASN	ASN	ASP	ASP	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	29 - 105	35 - 111
2	3	TRP	TRP	ASP	ASP	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	123 - 126	129 - 132
2	4	ALA	ALA	LEU	LEU	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	128 - 189	134 - 195
2	5	GLU	GLU	ILE	ILE	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	191 - 212	197 - 218
2	6	GLN	GLN	SER	SER	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	214 - 364	220 - 370
2	7	ALA	ALA	GLU	GLU	(chain 'B' and (resid 2 through 27 or resid 29...	B	B	370 - 398	376 - 404
3	1	HIS	HIS	PHE	PHE	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	2 - 27	8 - 33
3	2	ASN	ASN	ASP	ASP	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	29 - 105	35 - 111
3	3	TRP	TRP	ASP	ASP	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	123 - 126	129 - 132
3	4	ALA	ALA	LEU	LEU	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	128 - 189	134 - 195
3	5	GLU	GLU	ILE	ILE	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	191 - 212	197 - 218
3	6	GLN	GLN	SER	SER	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	214 - 364	220 - 370
3	7	ALA	ALA	GLU	GLU	(chain 'C' and (resid 2 through 27 or resid 29...	C	C	370 - 398	376 - 404
4	1	HIS	HIS	PHE	PHE	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	2 - 27	8 - 33
4	2	ASN	ASN	ASP	ASP	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	29 - 105	35 - 111
4	3	TRP	TRP	ASP	ASP	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	123 - 126	129 - 132
4	4	ALA	ALA	LEU	LEU	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	128 - 189	134 - 195
4	5	GLU	GLU	ILE	ILE	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	191 - 212	197 - 218
4	6	GLN	GLN	SER	SER	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	214 - 364	220 - 370
4	7	ALA	ALA	GLU	GLU	(chain 'D' and (resid 2 through 27 or resid 29...	D	D	370 - 398	376 - 404

#1: Protein	Saccharopine dehydrogenase Mass: 45880.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093 (bacteria) Strain: 102618 / Gene: NCTC11637_00022 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X5A3P4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEC 3350, calcium acetate hydrate, Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.2→30 Å / Num. obs: 98370 / % possible obs: 99.8 % / Redundancy: 3.6 % / B_iso Wilson estimate: 31.73 Å² / CC_1/2: 0.993 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4869 / CC_1/2: 0.661 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold 2-gerenated model

Resolution: 2.2→29.98 Å / SU ML: 0.2557 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2222	4975	5.06 %
R_work	0.1846	93315	-
obs	0.1865	98290	99.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 36.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12142	0	0	425	12567

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	12398
X-RAY DIFFRACTION	f_angle_d	0.8999	16805
X-RAY DIFFRACTION	f_chiral_restr	0.0573	1886
X-RAY DIFFRACTION	f_plane_restr	0.0054	2158
X-RAY DIFFRACTION	f_dihedral_angle_d	18.6305	7387

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 (%)
2.2-2.23	0.3031	160	0.2506	3043	X-RAY DIFFRACTION	97.95
2.23-2.25	0.3048	141	0.2453	3108	X-RAY DIFFRACTION	100
2.25-2.28	0.307	169	0.2479	3086	X-RAY DIFFRACTION	99.94
2.28-2.31	0.2889	180	0.2293	3030	X-RAY DIFFRACTION	99.94
2.31-2.34	0.2938	165	0.2234	3093	X-RAY DIFFRACTION	100
2.34-2.37	0.27	157	0.2168	3083	X-RAY DIFFRACTION	99.97
2.37-2.4	0.2531	141	0.2214	3092	X-RAY DIFFRACTION	99.97
2.4-2.44	0.3219	144	0.2187	3156	X-RAY DIFFRACTION	100
2.44-2.48	0.2787	143	0.2173	3088	X-RAY DIFFRACTION	99.94
2.48-2.52	0.2409	169	0.2195	3081	X-RAY DIFFRACTION	100
2.52-2.56	0.2344	143	0.2175	3123	X-RAY DIFFRACTION	99.91
2.56-2.61	0.2989	175	0.2131	3061	X-RAY DIFFRACTION	99.97
2.61-2.66	0.2535	178	0.21	3071	X-RAY DIFFRACTION	99.91
2.66-2.71	0.2542	175	0.2075	3102	X-RAY DIFFRACTION	99.94
2.71-2.77	0.249	172	0.2045	3076	X-RAY DIFFRACTION	99.94
2.77-2.84	0.2457	183	0.2058	3087	X-RAY DIFFRACTION	100
2.84-2.91	0.2429	160	0.2118	3088	X-RAY DIFFRACTION	99.94
2.91-2.99	0.2476	175	0.2129	3116	X-RAY DIFFRACTION	99.97
2.99-3.07	0.2768	176	0.2004	3101	X-RAY DIFFRACTION	99.97
3.07-3.17	0.2386	166	0.1988	3108	X-RAY DIFFRACTION	99.91
3.17-3.29	0.2389	172	0.1999	3115	X-RAY DIFFRACTION	99.97
3.29-3.42	0.2182	168	0.1869	3111	X-RAY DIFFRACTION	99.97
3.42-3.57	0.2016	172	0.1744	3118	X-RAY DIFFRACTION	99.97
3.57-3.76	0.1943	185	0.1589	3124	X-RAY DIFFRACTION	99.91
3.76-4	0.1966	162	0.1593	3131	X-RAY DIFFRACTION	99.85
4-4.3	0.1597	153	0.1436	3152	X-RAY DIFFRACTION	99.73
4.3-4.74	0.1657	162	0.1317	3154	X-RAY DIFFRACTION	99.58
4.74-5.42	0.1844	164	0.1413	3190	X-RAY DIFFRACTION	99.53
5.42-6.81	0.2009	186	0.1796	3153	X-RAY DIFFRACTION	99.11
6.81-29.98	0.2006	179	0.1864	3274	X-RAY DIFFRACTION	97.54

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	1.30445719281	0.342389698109	-0.175562981926	2.5735986137	0.594774829264	2.32165737941	0.0248404396228	0.0473000708126	0.173801240761	-0.181401233472	-0.0151231762408	0.0757541488978	-0.110796196699	-0.158395113318	-0.00462365257748	0.160135815796	0.0379046413984	0.00562542332754	0.153735718372	0.052563032835	0.206708666552	20.0787154538	47.3372961659	-0.546639730959
2	2.27919793255	-0.768026675459	0.41718941551	1.04248213498	-0.0202980616267	0.54133315613	-0.0837738150794	-0.199405061988	-0.274944009306	0.0811495825987	0.112025807394	0.213461383235	0.0971892983089	-0.132731161673	-0.039503915769	0.24477671908	-0.0175239944925	0.0484812991797	0.214376758753	0.0758464698532	0.238901267658	2.13710447626	40.3533382022	8.06497402856
3	4.8692549607	1.95487292058	-0.0975288259949	4.02822543807	-0.297979952059	3.1251645275	-0.0589785472561	0.107697908246	-0.0785222365137	-0.486051268212	0.0889394030941	-0.0652004505689	0.226425642476	0.0424479103848	-0.0221474052438	0.244697086617	0.0275113272812	-0.0256446825589	0.119671571274	-0.000935987539954	0.157941632185	-39.4405641444	76.3246978699	-22.2269187267
4	1.8642439146	0.934665505089	-0.63282722304	2.39616673316	-0.47220608234	4.60440041808	0.102406956273	-0.203691967534	0.144443699113	0.012930281597	-0.0584814613296	-0.120528432997	-0.176004286743	0.139746671207	0.0455467558155	0.192790274279	0.0121492105223	-0.0181302240208	0.133798401337	-0.0391445151022	0.278686350415	-36.3256538105	90.6193163527	-11.8985614236
5	1.5795866191	-0.490980167212	0.607953992633	1.01405553251	-0.365202836124	0.902055337336	-0.0434984192966	-0.436220810225	0.0878172981549	0.101131128299	0.0471785101537	-0.0442275673353	-0.0243241630038	-0.145437137528	-0.0069754040157	0.204268097442	-0.029847586292	0.0131435539459	0.267966619335	0.00231137100456	0.223739898702	-36.0242854053	70.232155192	2.63640493944
6	2.3944901602	0.689177377423	0.00170917451746	2.50047116454	0.33382259311	2.52524804358	0.0478998300439	-0.343576652167	0.541832050561	0.0481182540778	0.00590878434723	0.579136924346	-0.21826843686	-0.585983097787	-0.0905248017881	0.152603244598	0.038159505667	0.0042138375757	0.38527672153	-0.0283302157625	0.416027093007	-52.3233856631	81.1422686307	-3.72233507957
7	1.93643552864	0.179293527451	0.264692621881	1.2452302363	0.953613846928	3.5342399358	0.0615593781371	0.0398059676805	0.0181929115037	-0.108820898185	0.0758489813908	-0.100810365735	-0.134993835124	0.0431631387787	-0.142709992645	0.252042647199	0.0309699404029	-0.00628351984667	0.188819200172	-0.0143655328123	0.197050729493	10.2988810884	33.0554327947	-29.2326380844
8	1.54653774072	-1.22430975075	-0.0418248881968	3.31235650579	-0.371925286408	0.758763807247	0.169357436667	0.320850887553	0.0872591758283	-0.528141944966	-0.137974969919	-0.233563908846	0.187364001196	0.0182746757816	-0.0434014423972	0.366860700003	0.0741443266518	-0.0174468500514	0.482332303508	-0.0528105325043	0.242214452077	-2.77893428711	38.7732256904	-52.9402906335
9	1.25445403088	-0.554807452084	0.788894361372	1.07945289687	-0.456576511497	0.792210367045	0.0669106400611	0.136004386026	-0.0561190897536	-0.18740260684	-0.00502141441403	-0.0452130127368	0.152057349337	-0.0730913515059	-0.0501141321569	0.265710326146	-0.00463742070751	0.00367833702417	0.317119175768	-0.0634748063075	0.200073126637	0.238538888127	32.2783256227	-40.9310430921
10	3.725583765	0.438072014816	-1.15155296875	2.03981853341	0.556954000849	4.07654754283	0.0114353725653	0.229716610524	0.371558109491	-0.32073187763	0.0779276082203	-0.65414812913	-0.416372288312	0.529617291864	-0.120473136849	0.295091944163	-0.110298057781	0.0231193407105	0.283298744851	0.0597665259106	0.425564452273	-17.5463550715	94.2530488202	-49.2688387267
11	5.1026328708	1.07317198273	-1.43118068049	2.27973709649	-0.202800118442	3.9728492252	0.0523446269201	-0.181324223993	-0.0292525915855	0.00204702064882	-0.0853722763375	-0.274561608143	-0.056942613409	0.232831060544	0.0120940107142	0.285676958198	0.00568768103019	-0.0555955759139	0.197371805782	0.0274129992503	0.255230445265	-30.6500764041	91.5943168616	-37.6133534284
12	0.986682388926	-0.658519368356	-0.128134818575	2.18896309797	0.0384711279673	1.04304926792	0.0257563312235	0.250010543928	0.0101185700812	-0.193439049067	-0.0031700337511	0.0482948662831	-0.0331551478965	-0.00847735695901	-0.011592249288	0.215267515667	-0.0188776074238	-0.043228160019	0.317921022999	0.00259774391168	0.192004487561	-32.0700329502	75.3364202246	-52.5771824882

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 145 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 146 through 399 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 2 through 64 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 65 through 132 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 133 through 359 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 360 through 399 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 157 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 158 through 267 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 268 through 399 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 64 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 65 through 132 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 133 through 399 )

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