PDB-8zi8: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c...

ID or keywords:

Entry

Database: PDB / ID: 8zi8

Title

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,5-Dihydroxybenzoate.

Components

4-hydroxythreonine-4-phosphate dehydrogenase

Keywords

LYASE / Metal-dependent oxidative Decarboxylase / OXIDOREDUCTASE

Function / homology

4-hydroxythreonine-4-phosphate dehydrogenase / 4-hydroxythreonine-4-phosphate dehydrogenase activity / PdxA family / Pyridoxal phosphate biosynthetic protein PdxA / NAD binding / metal ion binding / CARBON DIOXIDE / 2,5-dihydroxybenzoic acid / 4-hydroxythreonine-4-phosphate dehydrogenase

Function and homology information

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Kumar, K.A. / Pahwa, D. / Kumar, P.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 2,5-Dihydroxybenzoate.
Authors: Kumar, K.A. / Pahwa, D.

History

Deposition	May 13, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_struct_assembly ...pdbx_entry_details / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zi8.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8zi8.ent.gz	659.2 KB	Display	PDB format
PDBx/mmJSON format	8zi8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zi8_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8zi8_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8zi8_validation.xml.gz	26.8 KB	Display
Data in CIF	8zi8_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zi/8zi8 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/8zi8	HTTPS FTP

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Related structure data

Related structure data	8zhy
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	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: 4-hydroxythreonine-4-phosphate dehydrogenase

B: 4-hydroxythreonine-4-phosphate dehydrogenase

C: 4-hydroxythreonine-4-phosphate dehydrogenase

D: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

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

1

D: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

A: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

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

2

B: 4-hydroxythreonine-4-phosphate dehydrogenase

C: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.549, 94.717, 166.714
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P22₁2₁

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	THR	THR	GLN	GLN	2 - 313	22 - 333
2	1	1	THR	THR	GLN	GLN	2 - 313	22 - 333
3	2	2	MET	MET	GLY	GLY	1 - 311	21 - 331
4	2	2	MET	MET	GLY	GLY	1 - 311	21 - 331
5	3	3	MET	MET	PRO	PRO	1 - 314	21 - 334
6	3	3	MET	MET	PRO	PRO	1 - 314	21 - 334
7	4	4	THR	THR	GLY	GLY	2 - 311	22 - 331
8	4	4	THR	THR	GLY	GLY	2 - 311	22 - 331
9	5	5	THR	THR	GLN	GLN	2 - 313	22 - 333
10	5	5	THR	THR	GLN	GLN	2 - 313	22 - 333
11	6	6	MET	MET	GLY	GLY	1 - 311	21 - 331
12	6	6	MET	MET	GLY	GLY	1 - 311	21 - 331

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

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Protein , 1 types, 4 molecules ABCD

#1: Protein	4-hydroxythreonine-4-phosphate dehydrogenase Mass: 35159.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD2128 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B7WRJ7, 4-hydroxythreonine-4-phosphate dehydrogenase

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Non-polymers , 6 types, 131 molecules

#2: Chemical	ChemComp-CO2 / CARBON DIOXIDE Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GTQ / 2,5-dihydroxybenzoic acid Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₆O₄
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.59 Å³/Da / Density meas: 0.485 Mg/m³ / Density % sol: 52.57 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 4% v/v Tacsimate pH 6.0 12% 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: Jan 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.65→27.23 Å / Num. obs: 40549 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC_1/2: 0.993 / Net I/σ(I): 6.9
Reflection shell	Resolution: 2.65→2.76 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4526 / CC_1/2: 0.788 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
CrysalisPro		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→24.001 Å / Cor.coef. F_o:F_c: 0.885 / Cor.coef. F_o:F_c free: 0.837 / SU B: 37.263 / SU ML: 0.342 / Cross valid method: FREE R-VALUE / ESU R Free: 0.392
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2949	2000	4.941 %
R_work	0.2604	38475	-
all	0.262	-	-
obs	-	40475	99.663 %

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: 3.479 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.439 Å²	-0 Å²	0 Å²
2-	-	3.645 Å²	-0 Å²
3-	-	-	-1.206 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→24.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9184	0	40	121	9345

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	9362
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9198
X-RAY DIFFRACTION	r_angle_refined_deg	1.343	1.803	12732
X-RAY DIFFRACTION	r_angle_other_deg	0.471	1.722	21138
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.183	5	1248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.009	6	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.377	10	1530
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.806	10	347
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1541
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11039
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1909
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	1984
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	8379
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	4567
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4953
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	203
X-RAY DIFFRACTION	r_metal_ion_refined	0.132	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.158	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.165	0.2	192
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.214	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	0.682	0.324	5007
X-RAY DIFFRACTION	r_mcbond_other	0.681	0.324	5007
X-RAY DIFFRACTION	r_mcangle_it	1.128	0.583	6250
X-RAY DIFFRACTION	r_mcangle_other	1.128	0.583	6251
X-RAY DIFFRACTION	r_scbond_it	0.677	0.351	4355
X-RAY DIFFRACTION	r_scbond_other	0.677	0.351	4356
X-RAY DIFFRACTION	r_scangle_it	1.115	0.636	6482
X-RAY DIFFRACTION	r_scangle_other	1.115	0.636	6483
X-RAY DIFFRACTION	r_lrange_it	4.122	3.985	38524
X-RAY DIFFRACTION	r_lrange_other	4.01	3.973	38509
X-RAY DIFFRACTION	r_rigid_bond_restr	3.649	3	18560
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.105	0.05	9152
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.104	0.05	9064
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.079	0.05	9297
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.125	0.05	8872
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.114	0.05	9070
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.101	0.05	9028

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	0.10457	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10457	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10415	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10415	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07925	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07925	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12469	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12469	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.1141	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.1141	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10102	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10102	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
2.65-2.718	0.306	130	0.318	2816	0.317	2947	0.919	0.929	99.9661	0.311
2.718-2.791	0.298	134	0.307	2710	0.307	2848	0.942	0.939	99.8596	0.301
2.791-2.871	0.315	139	0.305	2632	0.305	2772	0.914	0.935	99.9639	0.294
2.871-2.958	0.367	145	0.302	2546	0.305	2693	0.908	0.94	99.9257	0.288
2.958-3.054	0.302	126	0.279	2495	0.28	2622	0.933	0.947	99.9619	0.266
3.054-3.159	0.312	128	0.27	2410	0.272	2538	0.929	0.95	100	0.255
3.159-3.276	0.308	134	0.264	2309	0.266	2443	0.941	0.954	100	0.251
3.276-3.407	0.345	115	0.279	2265	0.282	2381	0.915	0.947	99.958	0.264
3.407-3.556	0.275	109	0.255	2157	0.256	2268	0.948	0.957	99.9118	0.241
3.556-3.725	0.362	83	0.296	2076	0.298	2159	0.924	0.945	100	0.287
3.725-3.921	0.29	89	0.279	2030	0.279	2120	0.947	0.955	99.9528	0.269
3.921-4.152	0.296	104	0.244	1849	0.247	1965	0.945	0.96	99.3893	0.223
4.152-4.429	0.27	96	0.234	1764	0.236	1863	0.954	0.962	99.839	0.22
4.429-4.771	0.25	104	0.21	1648	0.213	1761	0.958	0.972	99.4889	0.193
4.771-5.206	0.277	74	0.229	1538	0.231	1612	0.949	0.968	100	0.212
5.206-5.786	0.292	68	0.25	1416	0.252	1484	0.959	0.968	100	0.234
5.786-6.618	0.293	65	0.288	1263	0.289	1329	0.953	0.956	99.9248	0.275
6.618-7.955	0.236	69	0.202	1083	0.204	1153	0.972	0.978	99.9133	0.19
7.955-10.679	0.217	50	0.16	892	0.163	943	0.975	0.986	99.894	0.144
10.679-24.001	0.313	38	0.259	576	0.263	637	0.956	0.971	96.3893	0.244

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	0.2052	0.2358	-0.0846	1.2992	-1.4005	3.9406	0.0571	-0.0558	0.0139	0.049	-0.1409	-0.1247	-0.1295	0.2744	0.0838	0.2014	0.0024	-0.0019	0.1221	-0.0101	0.2872	49.8354	26.4022	3.9289
2	1.1576	-0.5193	-0.0714	0.4401	0.0478	3.6998	0.0845	0.2567	0.0063	-0.2026	-0.1137	-0.0105	-0.0315	-0.3521	0.0292	0.3067	0.043	-0.023	0.7888	-0.0176	0.4805	6.7914	21.0615	6.5251
3	2.0437	-0.0222	-1.5525	0.8127	0.5228	1.5894	-0.1337	-0.1204	-0.1192	0.33	0.1555	0.0307	0.2751	-0.0326	-0.0218	0.5024	0.1622	-0.1129	0.9418	-0.0123	0.4899	0.5484	16.396	-32.7104
4	0.7275	0.0972	-0.6827	0.6191	-0.3673	3.2366	-0.0972	-0.0537	-0.0735	-0.1826	0.0052	0.1241	0.2594	0.0302	0.0919	0.3498	-0.0229	-0.0922	0.0073	0.0009	0.3071	42.4437	14.8941	-40.1156

Refinement TLS group

Selection: ALL

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