PDB-9dui: Re-refined of Crystal structure of dopa decarboxylase in complex ...

ID or keywords:

Entry

Database: PDB / ID: 9dui

Title

Re-refined of Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa (1JS3) with ketoenamine form of carbidopa

Components

Aromatic-L-amino-acid decarboxylase

Keywords

LYASE / DOPA decarboxylase / carbiDOPA / Parkinson's disease / Vitamin B6

Function / homology

Function and homology information

L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / serotonin biosynthetic process / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process / dopamine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function

Biological species

Sus scrofa (pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.25 Å

Authors

Doukov, I.T. / Berkowitz, B.D.

Funding support

United States, 2items

Citation

Journal: Nat.Struct.Biol. / Year: 2001
Title: Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase.
Authors: Burkhard, P. / Dominici, P. / Borri-Voltattorni, C. / Jansonius, J.N. / Malashkevich, V.N.

History

Deposition	Oct 3, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Remark 0

THIS ENTRY 9DUI REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 1JS3, DETERMINED BY P. ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9dui.cif.gz	501.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9dui.ent.gz		Display	PDB format
PDBx/mmJSON format	9dui.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dui_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9dui_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9dui_validation.xml.gz	47.4 KB	Display
Data in CIF	9dui_validation.cif.gz	65.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/du/9dui ftp://data.pdbj.org/pub/pdb/validation_reports/du/9dui	HTTPS FTP

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Related structure data

Related structure data	47362C 47364C 47366C 9e0mC 9e0oC 9e0qC 9gnsC 1js3 1js6 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: Aromatic-L-amino-acid decarboxylase

B: Aromatic-L-amino-acid 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: Software - PISA

Unit cell

Length a, b, c (Å)	154.360, 154.360, 86.780
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 478 / Label seq-ID: 3 - 479

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Aromatic-L-amino-acid decarboxylase / E.C.4.1.1.28 / AADC / DOPA decarboxylase / DDC Mass: 54028.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: DDC / Organ: kidney / Plasmid: pKKDDC(delta)4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P80041, aromatic-L-amino-acid decarboxylase
#2: Chemical	ChemComp-A1BCS / (2S)-3-(3,4-dihydroxyphenyl)-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)hydrazin-1-yl]-2-methylpropanoic acid Mass: 455.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₃O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.47 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1J3S.
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, MES, ammonium sulfate at pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 0.95 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1993
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95 Å / Relative weight: 1
Reflection	Resolution: 2.25→19.611 Å / Num. obs: 53582 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / B_iso Wilson estimate: 15 Å² / R_sym value: 0.056 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 154 / R_sym value: 0.19 / % possible all: 70.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM		model building
DM		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.25→19.61 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.958 / SU B: 7.863 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1538	2540	4.74 %	RANDOM
R_work	0.1171	51042	-	-
all	0.119	-	-	-
obs	-	53582	95.781 %	-

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: 23.854 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.021 Å²	-0.01 Å²	-0 Å²
2-	-	-0.021 Å²	0 Å²
3-	-	-	0.067 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→19.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	82	579	7945

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	7603
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7188
X-RAY DIFFRACTION	r_angle_refined_deg	1.697	1.821	10313
X-RAY DIFFRACTION	r_angle_other_deg	0.588	1.75	16501
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.434	5	946
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.41	5	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.882	10	1237
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.98	10	338
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1116
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9072
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1840
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	1641
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	7028
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	3845
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	4357
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	569
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.189	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.173	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	2.258	2.413	3743
X-RAY DIFFRACTION	r_mcbond_other	2.256	2.413	3743
X-RAY DIFFRACTION	r_mcangle_it	3.041	5.388	4671
X-RAY DIFFRACTION	r_mcangle_other	3.042	5.391	4672
X-RAY DIFFRACTION	r_scbond_it	5.11	3.461	3860
X-RAY DIFFRACTION	r_scbond_other	5.045	3.44	3850
X-RAY DIFFRACTION	r_scangle_it	7.218	7.266	5632
X-RAY DIFFRACTION	r_scangle_other	7.102	7.225	5621
X-RAY DIFFRACTION	r_lrange_it	8.333	16.967	8970
X-RAY DIFFRACTION	r_lrange_other	8.306	16.651	8867
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.053	0.05	15445

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05293	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.05293	0.05009

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 (%)
2.25-2.308	0.186	154	0.161	2837	X-RAY DIFFRACTION	73.2012
2.308-2.37	0.185	176	0.15	3497	X-RAY DIFFRACTION	92.9168
2.37-2.438	0.182	177	0.148	3506	X-RAY DIFFRACTION	95.9614
2.438-2.512	0.185	159	0.144	3437	X-RAY DIFFRACTION	95.9701
2.512-2.593	0.184	221	0.141	3286	X-RAY DIFFRACTION	96.3726
2.593-2.682	0.191	118	0.138	3298	X-RAY DIFFRACTION	97.1559
2.682-2.782	0.181	187	0.138	3140	X-RAY DIFFRACTION	98.0548
2.782-2.893	0.195	136	0.135	3058	X-RAY DIFFRACTION	97.2594
2.893-3.018	0.184	136	0.13	2947	X-RAY DIFFRACTION	98.0286
3.018-3.162	0.165	136	0.127	2842	X-RAY DIFFRACTION	98.6093
3.162-3.328	0.162	142	0.118	2685	X-RAY DIFFRACTION	98.9499
3.328-3.524	0.163	108	0.112	2605	X-RAY DIFFRACTION	99.1956
3.524-3.758	0.142	108	0.104	2450	X-RAY DIFFRACTION	99.6494
3.758-4.047	0.112	88	0.09	2296	X-RAY DIFFRACTION	99.749
4.047-4.415	0.103	115	0.077	2092	X-RAY DIFFRACTION	99.9095
4.415-4.905	0.098	93	0.076	1928	X-RAY DIFFRACTION	99.9505
4.905-5.605	0.117	108	0.091	1697	X-RAY DIFFRACTION	99.9446
5.605-6.729	0.133	78	0.11	1474	X-RAY DIFFRACTION	99.9356
6.729-9.001	0.117	59	0.105	1181	X-RAY DIFFRACTION	100
9.001-19.61	0.174	41	0.133	786	X-RAY DIFFRACTION	98.9234

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	1.0428	-0.0122	-0.2638	0.8831	-0.0995	1.0594	0.0357	0.0918	0.1077	-0.0528	-0.015	0.0159	-0.1169	-0.0575	-0.0208	0.0177	0.0091	0.0008	0.0153	0.0032	0.0173	43.0338	33.5424	64.8732
2	0.6442	-0.0079	0.0613	1.0716	0.0548	0.9555	-0.0204	-0.0431	-0.0421	0.1544	-0.0006	-0.0711	0.0648	0.0436	0.021	0.0386	0.0013	0.0064	0.006	0.0012	0.0236	49.3578	16.8972	86.4724

Refinement TLS group

Selection: ALL

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