PDB-8zj0: Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in c...

ID or keywords:

Entry

Database: PDB / ID: 8zj0

Title

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3-Hydroxybenzoate.

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-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 3-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: 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

-
Download

PDBx/mmCIF format	8zj0.cif.gz	583.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8zj0.ent.gz	405.4 KB	Display	PDB format
PDBx/mmJSON format	8zj0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zj/8zj0 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/8zj0	HTTPS FTP

-
Related structure data

Related structure data	8zhy 8zi8 8zin
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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
70.6 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
70.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.734, 94.273, 166.395
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	ALA	ALA	2 - 312	22 - 332
2	1	1	THR	THR	ALA	ALA	2 - 312	22 - 332
3	2	2	MET	MET	ALA	ALA	1 - 312	21 - 332
4	2	2	MET	MET	ALA	ALA	1 - 312	21 - 332
5	3	3	MET	MET	GLN	GLN	1 - 313	21 - 333
6	3	3	MET	MET	GLN	GLN	1 - 313	21 - 333
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	ALA	ALA	2 - 312	22 - 332
10	5	5	THR	THR	ALA	ALA	2 - 312	22 - 332
11	6	6	MET	MET	ALA	ALA	1 - 312	21 - 332
12	6	6	MET	MET	ALA	ALA	1 - 312	21 - 332

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: 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
#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-3HB / 3-HYDROXYBENZOIC ACID Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density meas: 0.496 Mg/m³ / Density % sol: 52.36 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Potassium sodium tartrate tetrahydrate 20% w/v Polyethylene glycol 3,350 pH 7.4

-
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: Dec 14, 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: 2.9→26.429 Å / Num. obs: 30906 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC_1/2: 0.974 / Χ²: 1.03 / Net I/σ(I): 5
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / Num. unique obs: 4437 / CC_1/2: 0.824 / Χ²: 0.78

-
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→26.429 Å / Cor.coef. F_o:F_c: 0.866 / Cor.coef. F_o:F_c free: 0.826 / WR_factor R_free: 0.266 / WR_factor R_work: 0.235 / SU B: 49.458 / SU ML: 0.402 / Average fsc free: 0.944 / Average fsc work: 0.9569 / 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	0.2823	1408	4.572 %
R_work	0.2489	29385	-
all	0.25	-	-
obs	-	30793	99.412 %

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: 0.541 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.006 Å²	0 Å²	-0 Å²
2-	-	2.563 Å²	-0 Å²
3-	-	-	-0.557 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→26.429 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9176	0	15	87	9278

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.012	9346
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9185
X-RAY DIFFRACTION	r_angle_refined_deg	2.519	1.806	12740
X-RAY DIFFRACTION	r_angle_other_deg	0.475	1.723	21105
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.376	5	1245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.264	5	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.337	10	1532
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.351	10	347
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1541
X-RAY DIFFRACTION	r_chiral_restr_other	0.012	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11005
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1907
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1865
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	8470
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	4496
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	4987
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	155
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.191	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.01	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.229	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	141
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.239	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0	0.05	4998
X-RAY DIFFRACTION	r_mcbond_other	0	0.05	4998
X-RAY DIFFRACTION	r_mcangle_it	0	0.09	6237
X-RAY DIFFRACTION	r_mcangle_other	0	0.09	6238
X-RAY DIFFRACTION	r_scbond_it	0.731	0.056	4348
X-RAY DIFFRACTION	r_scbond_other	0.731	0.056	4349
X-RAY DIFFRACTION	r_scangle_it	0.738	0.097	6503
X-RAY DIFFRACTION	r_scangle_other	0.738	0.097	6504
X-RAY DIFFRACTION	r_lrange_it	2.264	0.519	9662
X-RAY DIFFRACTION	r_lrange_other	2.264	0.519	9663
X-RAY DIFFRACTION	r_rigid_bond_restr	5.724	3	18531
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.092	0.05	9192
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.093	0.05	9161
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.098	0.05	9156
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.097	0.05	9058
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	9097
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.097	0.05	9065

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	0.09178	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09178	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09252	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.09252	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09836	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09836	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.09662	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.09662	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0924	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0924	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09726	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09726	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
2.9-2.974	0.386	96	0.329	2120	0.331	2217	0.925	0.933	99.9549	0.325
2.974-3.055	0.36	110	0.311	2062	0.313	2173	0.904	0.934	99.954	0.303
3.055-3.142	0.423	104	0.309	2016	0.314	2120	0.896	0.934	100	0.301
3.142-3.237	0.251	79	0.284	1974	0.283	2056	0.959	0.945	99.8541	0.274
3.237-3.342	0.317	101	0.267	1894	0.27	1995	0.931	0.953	100	0.257
3.342-3.457	0.316	105	0.254	1841	0.257	1948	0.942	0.956	99.8973	0.242
3.457-3.585	0.244	64	0.258	1784	0.257	1851	0.956	0.954	99.8379	0.246
3.585-3.729	0.303	78	0.304	1722	0.304	1800	0.936	0.95	100	0.294
3.729-3.891	0.296	82	0.25	1659	0.253	1743	0.94	0.959	99.8853	0.238
3.891-4.077	0.28	87	0.245	1575	0.247	1669	0.952	0.961	99.5806	0.231
4.077-4.292	0.218	68	0.213	1529	0.213	1598	0.964	0.97	99.9374	0.201
4.292-4.545	0.264	56	0.223	1444	0.225	1503	0.954	0.967	99.8004	0.212
4.545-4.848	0.256	58	0.209	1339	0.211	1409	0.968	0.975	99.1483	0.196
4.848-5.222	0.198	69	0.203	1277	0.203	1349	0.98	0.975	99.7776	0.195
5.222-5.698	0.247	56	0.215	1171	0.217	1233	0.965	0.974	99.5134	0.208
5.698-6.334	0.269	54	0.212	1086	0.215	1142	0.96	0.974	99.8249	0.202
6.334-7.245	0.249	42	0.203	976	0.205	1024	0.963	0.974	99.4141	0.195
7.245-8.711	0.215	52	0.161	814	0.165	880	0.97	0.984	98.4091	0.156
8.711-11.7	0.223	30	0.174	664	0.176	717	0.978	0.985	96.7922	0.176
11.7-26.429	0.259	17	0.272	438	0.271	491	0.946	0.964	92.668	0.273

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	0.4024	-0.4199	-0.4599	1.462	1.4089	3.1354	0.0028	0.1025	0.0444	0.0233	-0.2461	0.2186	-0.1105	-0.2806	0.2433	0.2297	0.011	-0.0075	0.1404	0.0086	0.2888	-49.979	-21.0005	-3.7386
2	1.0851	0.6367	0.6223	0.8797	0.7745	3.8087	0.0291	-0.0631	0.1332	0.0584	-0.1273	0.1237	0.0347	-0.0754	0.0982	0.2583	0.0272	-0.0217	0.4699	0.0348	0.354	-6.8132	-25.6176	-6.3724
3	1.9061	-0.3293	-1.1517	0.7533	-0.5417	1.9062	-0.0255	-0.1571	-0.1898	-0.1426	0.1157	-0.0744	0.1285	0.1302	-0.0901	0.3298	-0.1536	-0.0826	0.5245	0.0186	0.346	-0.2404	-31.0588	32.4375
4	1.0841	-0.2672	-0.7815	0.9144	0.5127	2.6598	-0.1161	0.0597	-0.0865	0.1809	0.0114	-0.0073	0.1814	-0.0143	0.1046	0.2999	0.0137	-0.0263	0.0052	-0.005	0.2495	-42.1881	-32.1476	40.006

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi