PDB-9jp7: 4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni ...

ID or keywords:

Entry

Database: PDB / ID: 9jp7

Title

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

Components

4,5-dihydroxyphthalate decarboxylase

Keywords

LYASE / Decarboxylase

Function / homology

4,5-dihydroxyphthalate decarboxylase / 4,5-dihydroxyphthalate decarboxylase activity / SsuA/THI5-like / NMT1/THI5 like / 4,5-dihydroxyphthalate decarboxylase

Function and homology information

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.05 Å

Authors

Kumar, K.A. / Kumar, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: 4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)
Authors: Kumar, K.A.

History

Deposition	Sep 25, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 30, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jp7.cif.gz	677.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jp/9jp7 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/9jp7	HTTPS FTP

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Related structure data

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: 4,5-dihydroxyphthalate decarboxylase

B: 4,5-dihydroxyphthalate decarboxylase

C: 4,5-dihydroxyphthalate decarboxylase

D: 4,5-dihydroxyphthalate decarboxylase

hetero molecules

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

1

A: 4,5-dihydroxyphthalate decarboxylase

B: 4,5-dihydroxyphthalate decarboxylase

hetero molecules

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

2

C: 4,5-dihydroxyphthalate decarboxylase

D: 4,5-dihydroxyphthalate decarboxylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.045, 270.201, 113.627
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ASN	ASN	SER	SER	2 - 328	22 - 348
2	1	1	ASN	ASN	SER	SER	2 - 328	22 - 348
3	2	2	MET	MET	TYR	TYR	1 - 324	21 - 344
4	2	2	MET	MET	TYR	TYR	1 - 324	21 - 344
5	3	3	MET	MET	ILE	ILE	1 - 329	21 - 349
6	3	3	MET	MET	ILE	ILE	1 - 329	21 - 349
7	4	4	ASN	ASN	TYR	TYR	2 - 324	22 - 344
8	4	4	ASN	ASN	TYR	TYR	2 - 324	22 - 344
9	5	5	ASN	ASN	ILE	ILE	2 - 329	22 - 349
10	5	5	ASN	ASN	ILE	ILE	2 - 329	22 - 349
11	6	6	MET	MET	GLU	GLU	1 - 325	21 - 345
12	6	6	MET	MET	GLU	GLU	1 - 325	21 - 345

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	4,5-dihydroxyphthalate decarboxylase Mass: 39402.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD2040 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B7WQU9, 4,5-dihydroxyphthalate decarboxylase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.12 Å³/Da / Density % sol: 60.55 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 3.05→26.44 Å / Num. obs: 37226 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC_1/2: 0.978 / Net I/σ(I): 6.3
Reflection shell	Resolution: 3.05→3.19 Å / Num. unique obs: 4585 / CC_1/2: 0.911

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
CrysalisPro		data reduction
CrysalisPro		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.05→25.221 Å / Cor.coef. F_o:F_c: 0.836 / Cor.coef. F_o:F_c free: 0.738 / SU B: 52.263 / SU ML: 0.401 / Cross valid method: FREE R-VALUE / ESU R Free: 0.569 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.3352	1829	4.915 %
R_work	0.2635	35385	-
all	0.267	-	-
obs	-	37214	98.063 %

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: 30.756 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.901 Å²	-0 Å²	0 Å²
2-	-	2.143 Å²	0 Å²
3-	-	-	-0.242 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→25.221 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10283	0	4	163	10450

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	10552
X-RAY DIFFRACTION	r_angle_refined_deg	1.496	1.666	14333
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.584	5	1282
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.462	5	106
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.832	10	1718
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.327	10	503
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	1546
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8194
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	4901
X-RAY DIFFRACTION	r_nbtor_refined	0.318	0.2	7154
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	383
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.236	0.2	116
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.045	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.111	2.977	5149
X-RAY DIFFRACTION	r_mcangle_it	3.409	5.349	6424
X-RAY DIFFRACTION	r_scbond_it	2.154	3.087	5403
X-RAY DIFFRACTION	r_scangle_it	3.482	5.611	7909
X-RAY DIFFRACTION	r_lrange_it	6.815	30.007	15889
X-RAY DIFFRACTION	r_rigid_bond_restr	3.979	3	10552
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.093	0.05	10676
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.084	0.05	10698
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.112	0.05	9565
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.078	0.05	10677
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.109	0.05	9554
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.105	0.05	9522

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	0.09335	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09335	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08435	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08435	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11218	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11218	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07765	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07765	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.10888	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.10888	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10511	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10511	0.05008

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
3.05-3.128	0.372	117	0.268	2614	0.273	2734	0.929	0.966	99.8903	0.253
3.128-3.212	0.356	122	0.293	2510	0.296	2632	0.908	0.95	100	0.274
3.212-3.304	0.323	119	0.244	2487	0.248	2607	0.929	0.963	99.9616	0.224
3.304-3.404	0.34	131	0.247	2359	0.252	2526	0.921	0.965	98.5748	0.219
3.404-3.513	0.432	119	0.282	2231	0.288	2432	0.912	0.953	96.6283	0.247
3.513-3.634	0.363	114	0.349	2265	0.35	2386	0.939	0.958	99.7066	0.347
3.634-3.768	0.511	134	0.451	2167	0.454	2302	0.913	0.945	99.9566	0.452
3.768-3.919	0.378	106	0.296	2037	0.3	2216	0.918	0.952	96.7058	0.258
3.919-4.088	0.474	102	0.375	1725	0.38	2120	0.925	0.947	86.1792	0.303
4.088-4.282	0.34	120	0.261	1845	0.266	2032	0.921	0.956	96.7028	0.237
4.282-4.507	0.321	87	0.268	1852	0.271	1943	0.884	0.95	99.7941	0.261
4.507-4.771	0.28	89	0.195	1706	0.199	1849	0.956	0.978	97.0795	0.172
4.771-5.087	0.211	90	0.169	1639	0.171	1737	0.978	0.983	99.5394	0.15
5.087-5.476	0.23	79	0.147	1552	0.151	1632	0.972	0.988	99.9387	0.133
5.476-5.971	0.254	63	0.18	1456	0.183	1519	0.973	0.985	100	0.161
5.971-6.629	0.232	62	0.168	1318	0.171	1380	0.975	0.987	100	0.153
6.629-7.568	0.198	59	0.158	1197	0.16	1256	0.978	0.986	100	0.145
7.568-9.067	0.21	44	0.134	1032	0.137	1077	0.966	0.989	99.9072	0.127
9.067-12.067	0.118	48	0.107	822	0.108	871	0.992	0.994	99.8852	0.107
12.067-25.221	0.281	24	0.25	566	0.251	609	0.969	0.971	96.8801	0.246

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