PDB-8zj3: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c...

ID or keywords:

Entry

Database: PDB / ID: 8zj3

Title

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 4-Hydroxybenzoate.

Components

4-hydroxythreonine-4-phosphate dehydrogenase

Keywords

LYASE / Metal-dependent oxidative Decarboxylase / OXIDOREDUCTASE / Lyase.

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 / P-HYDROXYBENZOIC ACID / 4-hydroxythreonine-4-phosphate dehydrogenase

Function and homology information

Biological species

Comamonas testosteroni KF-1 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.9 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 4-Hydroxybenzoate.
Authors: Kumar, K.A. / Pahwa, D.

History

Deposition	May 14, 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: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zj3.cif.gz	590.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8zj3.ent.gz	412.9 KB	Display	PDB format
PDBx/mmJSON format	8zj3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zj3_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8zj3_full_validation.pdf.gz	2 MB	Display
Data in XML	8zj3_validation.xml.gz	47.5 KB	Display
Data in CIF	8zj3_validation.cif.gz	65.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zj/8zj3 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zj3	HTTPS FTP

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Related structure data

Related structure data	8zhy 8zi8 8zin 8zj0
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-hydroxythreonine-4-phosphate dehydrogenase

B: 4-hydroxythreonine-4-phosphate dehydrogenase

C: 4-hydroxythreonine-4-phosphate dehydrogenase

D: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

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

1

A: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

D: 4-hydroxythreonine-4-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
66.6 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
66.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.831, 94.332, 168.433
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	3 - 314
2	1	1	THR	THR	GLN	GLN	2 - 313	3 - 314
3	2	2	MET	MET	PRO	PRO	1 - 314	2 - 315
4	2	2	MET	MET	PRO	PRO	1 - 314	2 - 315
5	3	3	MET	MET	PRO	PRO	1 - 314	2 - 315
6	3	3	MET	MET	PRO	PRO	1 - 314	2 - 315
7	4	4	THR	THR	PRO	PRO	2 - 314	3 - 315
8	4	4	THR	THR	PRO	PRO	2 - 314	3 - 315
9	5	5	THR	THR	GLN	GLN	2 - 313	3 - 314
10	5	5	THR	THR	GLN	GLN	2 - 313	3 - 314
11	6	6	MET	MET	PRO	PRO	1 - 314	2 - 315
12	6	6	MET	MET	PRO	PRO	1 - 314	2 - 315

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: 33059.090 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, 230 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PHB / P-HYDROXYBENZOIC ACID Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.61 Å³/Da / Density % sol: 53.22 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4

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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: Aug 23, 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: 2.5→26.61 Å / Num. obs: 31086 / % possible obs: 98.3 % / Redundancy: 12.8 % / CC_1/2: 0.981 / R_merge(I) obs: 0.2 / R_pim(I) all: 0.113 / R_rim(I) all: 0.218 / Χ²: 0.97 / Net I/σ(I): 6.4
Reflection shell	Resolution: 2.5→2.58 Å / Redundancy: 9.7 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / Num. unique obs: 4103 / CC_1/2: 0.898 / R_rim(I) all: 0.61 / % possible all: 87.1

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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: 2.9→20.001 Å / Cor.coef. F_o:F_c: 0.883 / Cor.coef. F_o:F_c free: 0.831 / SU B: 46.776 / SU ML: 0.377 / Cross valid method: FREE R-VALUE / ESU R Free: 0.468
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2793	1613	5.189 %
R_work	0.2383	29473	-
all	0.24	-	-
obs	-	31086	98.931 %

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: 0.786 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.828 Å²	-0 Å²	0 Å²
2-	-	7.171 Å²	-0 Å²
3-	-	-	-2.343 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→20.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9183	0	27	220	9430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9347
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9207
X-RAY DIFFRACTION	r_angle_refined_deg	1.485	1.802	12715
X-RAY DIFFRACTION	r_angle_other_deg	0.514	1.722	21160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.552	5	1247
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.192	5	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.353	10	1529
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.846	10	345
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1544
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11009
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1903
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1896
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	8435
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	4429
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	5114
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.203	0.2	234
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.108	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.07	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.181	0.2	159
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0	0.05	5006
X-RAY DIFFRACTION	r_mcbond_other	0	0.05	5006
X-RAY DIFFRACTION	r_mcangle_it	0	0.09	6247
X-RAY DIFFRACTION	r_mcangle_other	0	0.09	6248
X-RAY DIFFRACTION	r_scbond_it	0.04	0.05	4341
X-RAY DIFFRACTION	r_scbond_other	0.04	0.05	4342
X-RAY DIFFRACTION	r_scangle_it	0.056	0.093	6468
X-RAY DIFFRACTION	r_scangle_other	0.056	0.093	6469
X-RAY DIFFRACTION	r_lrange_it	8.94	0.721	9666
X-RAY DIFFRACTION	r_lrange_other	8.756	0.574	9657
X-RAY DIFFRACTION	r_rigid_bond_restr	0.454	3	18554
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.111	0.05	8849
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.115	0.05	8815
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.101	0.05	8914
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.119	0.05	8719
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.116	0.05	8758
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.114	0.05	8749

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	0.11075	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.11075	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11481	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11481	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10137	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10137	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.11912	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.11912	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.1155	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.1155	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.11418	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.11418	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
2.9-2.974	0.407	100	0.323	2154	0.327	2254	0.916	0.939	100	0.314
2.974-3.053	0.358	103	0.313	2072	0.315	2178	0.905	0.935	99.8623	0.303
3.053-3.14	0.399	122	0.308	1987	0.313	2109	0.89	0.938	100	0.299
3.14-3.234	0.327	80	0.308	1996	0.309	2080	0.923	0.939	99.8077	0.299
3.234-3.337	0.312	115	0.282	1879	0.284	1997	0.932	0.941	99.8498	0.278
3.337-3.451	0.329	111	0.278	1839	0.281	1953	0.92	0.945	99.8464	0.274
3.451-3.577	0.274	82	0.261	1808	0.262	1891	0.938	0.954	99.9471	0.257
3.577-3.718	0.338	86	0.268	1724	0.272	1813	0.931	0.952	99.8345	0.267
3.718-3.877	0.276	97	0.252	1650	0.253	1752	0.946	0.958	99.7146	0.251
3.877-4.059	0.258	82	0.228	1581	0.23	1671	0.947	0.963	99.5212	0.229
4.059-4.269	0.212	83	0.186	1506	0.188	1611	0.975	0.977	98.6344	0.187
4.269-4.515	0.226	77	0.195	1437	0.197	1524	0.966	0.971	99.3438	0.199
4.515-4.809	0.22	68	0.178	1346	0.18	1439	0.973	0.98	98.2627	0.185
4.809-5.169	0.226	83	0.184	1257	0.187	1355	0.969	0.978	98.893	0.19
5.169-5.625	0.263	68	0.211	1171	0.214	1256	0.957	0.978	98.6465	0.217
5.625-6.228	0.309	68	0.218	1096	0.224	1172	0.953	0.975	99.3174	0.227
6.228-7.078	0.24	54	0.192	969	0.195	1028	0.976	0.981	99.5136	0.199
7.078-8.409	0.187	57	0.144	829	0.147	911	0.984	0.988	97.2558	0.155
8.409-10.963	0.209	49	0.145	683	0.149	754	0.976	0.989	97.0822	0.159
10.963-20.001	0.264	28	0.221	484	0.223	541	0.98	0.982	94.6396	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	0.5034	-0.1992	-0.0635	1.4668	1.1088	2.9778	0.0192	0.0931	0.0349	0.0143	-0.1962	0.1764	-0.099	-0.209	0.1769	0.2713	-0.0098	-0.0077	0.0405	-0.0052	0.3381	-50.1259	-20.981	-3.7221
2	1.1931	0.3001	0.3799	0.5882	0.6089	3.181	-0.0117	-0.1112	0.1292	0.0189	-0.1116	0.054	-0.0516	-0.0889	0.1233	0.3354	0.0212	-0.0221	0.3612	0.0346	0.397	-6.8239	-25.5233	-6.3724
3	1.5025	-0.2205	-0.7363	0.8191	-0.4005	1.8824	-0.0464	-0.0306	-0.3029	-0.1054	0.0491	-0.1241	0.1368	0.1142	-0.0027	0.3586	-0.0882	-0.0694	0.3463	-0.0185	0.4089	-0.2917	-31.5935	33.0978
4	0.956	-0.1691	-0.8117	0.9326	0.2224	2.5361	-0.0985	0.1369	-0.1157	0.1004	0.0107	-0.0117	0.1282	-0.0763	0.0878	0.3103	0.0019	-0.0455	0.0222	-0.0189	0.2998	-42.1618	-32.1403	40.4408

Refinement TLS group

Selection: ALL

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