PDB-7eiw: Human histidine decarboxylase mutant Y334F reacted with histidine

ID or keywords:

Entry

Database: PDB / ID: 7eiw

Title

Human histidine decarboxylase mutant Y334F reacted with histidine

Components

Histidine decarboxylase

Keywords

LYASE / Pyridoxal-dependent decarboxylase

Function / homology

Function and homology information

histamine biosynthetic process / histidine decarboxylase / histidine decarboxylase activity / Histidine catabolism / L-histidine catabolic process / L-histidine metabolic process / catecholamine biosynthetic process / pyridoxal phosphate binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Komori, H.

Funding support

Japan, 1items

Citation

Journal: J Biol Macromol / Year: 2021
Title: Structural analysis of the HDC Y334F mutant
Authors: Komori, H. / Nitta, Y.

History

Deposition	Apr 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2023	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	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	7eiw.cif.gz	350.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7eiw.ent.gz	276.7 KB	Display	PDB format
PDBx/mmJSON format	7eiw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7eiw_validation.pdf.gz	465 KB	Display	wwPDB validaton report
Full document	7eiw_full_validation.pdf.gz	474.7 KB	Display
Data in XML	7eiw_validation.xml.gz	34.7 KB	Display
Data in CIF	7eiw_validation.cif.gz	47.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/7eiw ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7eiw	HTTPS FTP

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Related structure data

Related structure data	7eixC 7eiyC 4e1oS S: Starting model for refinement 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

Deposited unit

A: Histidine decarboxylase

B: Histidine decarboxylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.902, 57.654, 117.647
Angle α, β, γ (deg.)	90.000, 106.297, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Histidine decarboxylase / HDC Mass: 54314.172 Da / Num. of mol.: 2 / Mutation: C180S, C418S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDC / Production host: Escherichia coli (E. coli) / References: UniProt: P19113, histidine decarboxylase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.09 Å³/Da / Density % sol: 41.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.1 M Tris-HCl (pH 8.5), 28% (w/v) PEG 3350, 0.2 M lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 52603 / % possible obs: 99.6 % / Redundancy: 3.7 % / R_merge(I) obs: 0.069 / Net I/σ(I): 20.6
Reflection shell	Resolution: 2.1→2.18 Å / R_merge(I) obs: 0.431 / Num. unique obs: 5121

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4E1O

4e1o

Resolution: 2.1→33.223 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.928 / WR_factor R_free: 0.24 / WR_factor R_work: 0.199 / SU B: 15.764 / SU ML: 0.192 / Average fsc free: 0.8474 / Average fsc work: 0.8684 / Cross valid method: FREE R-VALUE / ESU R: 0.286 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2521	2679	5.095 %
R_work	0.2119	49904	-
all	0.214	-	-
obs	-	52583	99.435 %

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: 46.105 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.775 Å²	-0 Å²	2.994 Å²
2-	-	-0.971 Å²	-0 Å²
3-	-	-	-1.328 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→33.223 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7431	0	30	151	7612

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	7697
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7229
X-RAY DIFFRACTION	r_angle_refined_deg	1.319	1.638	10451
X-RAY DIFFRACTION	r_angle_other_deg	1.152	1.574	16664
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.921	5	942
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.93	21.535	404
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.301	15	1302
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.055	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	983
X-RAY DIFFRACTION	r_chiral_restr_other	0.039	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	8628
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1804
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	1609
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.175	0.2	6854
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	3684
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3589
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	267
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.024	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.229	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.215	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.26	4.032	3744
X-RAY DIFFRACTION	r_mcbond_other	1.258	4.032	3743
X-RAY DIFFRACTION	r_mcangle_it	2.043	6.04	4676
X-RAY DIFFRACTION	r_mcangle_other	2.043	6.04	4677
X-RAY DIFFRACTION	r_scbond_it	1.167	4.213	3953
X-RAY DIFFRACTION	r_scbond_other	1.161	4.214	3950
X-RAY DIFFRACTION	r_scangle_it	1.954	6.265	5769
X-RAY DIFFRACTION	r_scangle_other	1.954	6.266	5770
X-RAY DIFFRACTION	r_lrange_it	3.533	46.936	8620
X-RAY DIFFRACTION	r_lrange_other	3.527	46.927	8611

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
2.1-2.154	0.351	183	0.336	3500	0.337	3882	0.552	0.577	94.8738	0.3
2.154-2.213	0.336	209	0.323	3527	0.324	3776	0.643	0.676	98.9407	0.29
2.213-2.277	0.331	168	0.275	3482	0.278	3657	0.767	0.807	99.8086	0.242
2.277-2.347	0.278	195	0.256	3326	0.258	3522	0.843	0.85	99.9716	0.223
2.347-2.423	0.306	170	0.241	3315	0.244	3485	0.862	0.873	100	0.208
2.423-2.508	0.289	159	0.227	3208	0.23	3367	0.879	0.899	100	0.197
2.508-2.602	0.28	159	0.221	3060	0.224	3219	0.888	0.913	100	0.19
2.602-2.707	0.26	163	0.226	2918	0.228	3082	0.883	0.91	99.9676	0.197
2.707-2.827	0.305	144	0.23	2876	0.234	3020	0.883	0.911	100	0.203
2.827-2.964	0.267	150	0.221	2674	0.224	2824	0.891	0.919	100	0.197
2.964-3.123	0.306	133	0.22	2632	0.224	2765	0.882	0.912	100	0.202
3.123-3.31	0.24	128	0.207	2437	0.209	2565	0.917	0.931	100	0.193
3.31-3.537	0.229	115	0.206	2314	0.207	2431	0.933	0.94	99.9177	0.198
3.537-3.816	0.241	137	0.196	2143	0.199	2282	0.928	0.94	99.9124	0.191
3.816-4.175	0.208	108	0.189	1971	0.19	2079	0.944	0.947	100	0.191
4.175-4.659	0.198	109	0.168	1803	0.17	1914	0.955	0.961	99.8955	0.176
4.659-5.362	0.222	80	0.168	1623	0.17	1703	0.954	0.966	100	0.177
5.362-6.524	0.253	77	0.192	1358	0.195	1435	0.916	0.955	100	0.203
6.524-9.054	0.21	60	0.177	1083	0.178	1144	0.945	0.961	99.9126	0.19
9.054-33.223	0.239	32	0.211	650	0.213	702	0.958	0.962	97.151	0.231

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	0.3249	-0.218	-0.2612	0.2341	0.4506	1.1609	-0.0612	0.0491	0.0184	0.135	-0.0719	0.045	0.3059	-0.1625	0.133	0.1256	-0.0534	0.0709	0.026	-0.0247	0.051	-22.8796	-7.3843	-22.0227
2	0.1174	-0.1535	-0.2028	0.4389	0.2244	0.3579	-0.0351	-0.0243	0.0458	0.0461	0.1146	-0.0472	0.0605	0.0285	-0.0795	0.0157	-0.0009	-0.0067	0.0652	-0.0314	0.0571	0.2982	-13.1638	-35.4843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 477
2	X-RAY DIFFRACTION	2	ALL	B	1 - 476

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