PDB-8zj5: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c...

ID or keywords:

Entry

Database: PDB / ID: 8zj5

Title

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-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 / 3,4-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: 2.8 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 3,4-Dihydroxybenzoate.
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: 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 / _pdbx_struct_oper_list.name ..._pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zj5.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8zj5.ent.gz	739.7 KB	Display	PDB format
PDBx/mmJSON format	8zj5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zj5_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	8zj5_full_validation.pdf.gz	2.1 MB	Display
Data in XML	8zj5_validation.xml.gz	47.7 KB	Display
Data in CIF	8zj5_validation.cif.gz	64.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zj/8zj5 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zj5	HTTPS FTP

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Related structure data

Related structure data	8zhy 8zi8 8zin 8zj0 8zj3
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

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

defined by author&software
Evidence: gel filtration
70.7 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
70.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.041, 94.469, 167.425
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	PRO	PRO	2 - 314	23 - 335
2	1	1	THR	THR	PRO	PRO	2 - 314	23 - 335
3	2	2	MET	MET	ALA	ALA	1 - 312	22 - 333
4	2	2	MET	MET	ALA	ALA	1 - 312	22 - 333
5	3	3	MET	MET	PRO	PRO	1 - 314	22 - 335
6	3	3	MET	MET	PRO	PRO	1 - 314	22 - 335
7	4	4	THR	THR	ALA	ALA	2 - 312	23 - 333
8	4	4	THR	THR	ALA	ALA	2 - 312	23 - 333
9	5	5	THR	THR	PRO	PRO	2 - 314	23 - 335
10	5	5	THR	THR	PRO	PRO	2 - 314	23 - 335
11	6	6	MET	MET	ALA	ALA	1 - 312	22 - 333
12	6	6	MET	MET	ALA	ALA	1 - 312	22 - 333

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-hydroxythreonine-4-phosphate dehydrogenase Mass: 35230.434 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
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID Mass: 154.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₇H₆O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.63 Å³/Da / Density % sol: 53.27 %
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 22, 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: 2.8→24.46 Å / Num. obs: 34601 / % possible obs: 99.6 % / Redundancy: 12.8 % / CC_1/2: 0.97 / R_merge(I) obs: 0.23 / R_rim(I) all: 0.248 / Χ²: 1 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.8→2.94 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.814 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4534 / CC_1/2: 0.759 / R_rim(I) all: 0.89 / Χ²: 0.94 / % 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: 2.8→23.721 Å / Cor.coef. F_o:F_c: 0.834 / Cor.coef. F_o:F_c free: 0.774 / SU B: 44.94 / SU ML: 0.376 / Cross valid method: FREE R-VALUE / ESU R Free: 0.462
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3031	1768	5.115 %
R_work	0.2595	32796	-
all	0.262	-	-
obs	-	34564	99.476 %

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: 21.633 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.942 Å²	-0 Å²	0 Å²
2-	-	2.397 Å²	-0 Å²
3-	-	-	-0.455 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→23.721 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9153	0	26	161	9340

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	9320
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9172
X-RAY DIFFRACTION	r_angle_refined_deg	1.372	1.802	12681
X-RAY DIFFRACTION	r_angle_other_deg	0.462	1.723	21075
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.409	5	1243
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.038	5	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.835	10	1525
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.737	10	344
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1538
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	10984
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1900
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1860
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	8431
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	4465
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	4992
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	224
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.119	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	119
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.248	0.2	10
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.125	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.54	0.302	4990
X-RAY DIFFRACTION	r_mcbond_other	0.54	0.302	4990
X-RAY DIFFRACTION	r_mcangle_it	0.927	0.543	6227
X-RAY DIFFRACTION	r_mcangle_other	0.927	0.543	6228
X-RAY DIFFRACTION	r_scbond_it	0.501	0.325	4330
X-RAY DIFFRACTION	r_scbond_other	0.501	0.325	4329
X-RAY DIFFRACTION	r_scangle_it	0.858	0.59	6454
X-RAY DIFFRACTION	r_scangle_other	0.858	0.59	6454
X-RAY DIFFRACTION	r_lrange_it	5.38	3.059	9723
X-RAY DIFFRACTION	r_lrange_other	5.287	3.052	9719
X-RAY DIFFRACTION	r_rigid_bond_restr	2.462	3	18492
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.081	0.05	9184
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	9004
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.095	0.05	9121
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.089	0.05	8893
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.09	0.05	9082
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.082	0.05	8943

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	0.0808	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0808	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08335	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08335	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09511	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09511	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08882	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08882	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09013	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.09013	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08164	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08164	0.05009

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
2.8-2.872	0.376	118	0.323	2366	0.325	2486	0.912	0.936	99.9195	0.315
2.872-2.949	0.373	103	0.316	2332	0.318	2435	0.89	0.941	100	0.305
2.949-3.033	0.365	128	0.29	2233	0.294	2361	0.919	0.946	100	0.277
3.033-3.125	0.32	114	0.27	2182	0.272	2296	0.932	0.949	100	0.257
3.125-3.226	0.313	117	0.261	2130	0.264	2248	0.934	0.951	99.9555	0.248
3.226-3.337	0.342	124	0.264	2039	0.268	2163	0.923	0.954	100	0.252
3.337-3.46	0.346	108	0.27	1990	0.274	2102	0.918	0.952	99.8097	0.261
3.46-3.598	0.349	101	0.287	1906	0.29	2016	0.913	0.945	99.5536	0.277
3.598-3.754	0.393	103	0.395	1852	0.395	1955	0.928	0.941	100	0.385
3.754-3.933	0.324	100	0.27	1760	0.273	1871	0.929	0.952	99.4121	0.258
3.933-4.139	0.289	92	0.24	1676	0.242	1788	0.943	0.962	98.8814	0.221
4.139-4.382	0.268	78	0.219	1601	0.221	1683	0.939	0.964	99.7623	0.211
4.382-4.673	0.232	81	0.208	1495	0.209	1583	0.965	0.97	99.5578	0.201
4.673-5.031	0.204	79	0.185	1422	0.186	1501	0.981	0.979	100	0.181
5.031-5.487	0.235	62	0.203	1339	0.205	1402	0.972	0.979	99.9287	0.197
5.487-6.094	0.267	66	0.217	1200	0.22	1267	0.952	0.976	99.9211	0.21
6.094-6.96	0.254	66	0.196	1073	0.2	1139	0.969	0.979	100	0.192
6.96-8.347	0.194	57	0.156	930	0.158	995	0.978	0.985	99.196	0.157
8.347-11.135	0.18	42	0.147	761	0.149	816	0.983	0.989	98.4069	0.153
11.135-23.721	0.257	29	0.279	506	0.278	563	0.97	0.976	95.0266	0.27

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	0.6734	-0.085	0.1374	0.9853	0.866	2.5926	0.0326	0.088	0.0416	0.0066	-0.1265	0.1017	-0.0333	-0.1963	0.0939	0.1365	-0.0049	0.0091	0.0604	0.0197	0.1194	-50.3106	-21.0482	-3.7013
2	0.7324	0.3516	0.2434	0.5621	0.7515	3.378	-0.0425	-0.133	0.1053	0.033	-0.1265	0.0906	-0.0847	-0.1711	0.169	0.1721	0.0232	-0.0059	0.2235	0.0302	0.1811	-6.7565	-25.516	-6.4827
3	1.7427	-0.1292	-0.7447	0.6835	-0.29	1.8247	-0.0016	-0.066	-0.2343	-0.0991	0.0322	-0.068	0.1474	0.1628	-0.0306	0.1904	-0.0382	-0.0811	0.1814	-0.0005	0.1759	-0.323	-31.5144	32.7331
4	1.0396	-0.1549	-0.7317	0.6471	0.1544	2.4306	-0.0623	0.0963	-0.1172	0.1068	0.003	-0.0141	0.1306	-0.1143	0.0593	0.1516	-0.0039	-0.0349	0.0108	-0.0158	0.1336	-42.2635	-32.1676	40.2058

Refinement TLS group

Selection: ALL

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