PDB-7orx: Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxyb...

ID or keywords:

Entry

Database: PDB / ID: 7orx

Title

Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase

Components

Probable benzoylformate decarboxylase

Keywords

OXIDOREDUCTASE / benzoylformate decarboxylase / thaimine diphosphate / Rhodococcus jostii RHA1 / lignin degradation

Function / homology

Function and homology information

benzoylformate decarboxylase activity / acetolactate synthase / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function

Biological species

Rhodococcus jostii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Wilkinson, R.C. / Fulop, V.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M025772/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M003523/1	United Kingdom

Citation

Journal: Biochemistry / Year: 2019
Title: Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from
Authors: Wei, Z. / Wilkinson, R.C. / Rashid, G.M.M. / Brown, D. / Fulop, V. / Bugg, T.D.H.

History

Deposition	Jun 6, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 16, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7orx.cif.gz	731.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7orx.ent.gz		Display	PDB format
PDBx/mmJSON format	7orx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7orx_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7orx_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7orx_validation.xml.gz	71.4 KB	Display
Data in CIF	7orx_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/7orx ftp://data.pdbj.org/pub/pdb/validation_reports/or/7orx	HTTPS FTP

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Related structure data

Related structure data	6qsiS S: Starting model for refinement
Similar structure data	1yno-1 4mzx-1 2v3w-d 4jud-1 1pi3-1 3fsj-1 4jua-1 5dgd-1 1po7-1 4mpp-1 Search similar-shape structures by Omokage search (details) 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 (12) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

AAA: Probable benzoylformate decarboxylase

BBB: Probable benzoylformate decarboxylase

CCC: Probable benzoylformate decarboxylase

DDD: Probable benzoylformate decarboxylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	123.500, 132.240, 138.700
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	2	Chains AAA CCC
3	3	Chains AAA DDD
4	4	Chains BBB CCC
5	5	Chains BBB DDD
6	6	Chains CCC DDD

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Probable benzoylformate decarboxylase Mass: 55524.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: MATVSEVTYELLRARGLTTVFGNPGSNELPFLSGMPDDFRYVLGLHEGAVLSMADGYSLV TGEATLVNLHAASGSGNAMGALTNSVYSHSPLVVTAGQQVRSTIGQEVMLSNVDAGTLMK PLVKWSSEPTCAEDVPRTINQAIHTALLPAKGPVYVSVPYDDWAAEAPPESAGLLAREVH ...Details: MATVSEVTYELLRARGLTTVFGNPGSNELPFLSGMPDDFRYVLGLHEGAVLSMADGYSLV TGEATLVNLHAASGSGNAMGALTNSVYSHSPLVVTAGQQVRSTIGQEVMLSNVDAGTLMK PLVKWSSEPTCAEDVPRTINQAIHTALLPAKGPVYVSVPYDDWAAEAPPESAGLLAREVH SAASLSGDQINDLIETLESATNPVLVLGPAVDADRANADAVLLAEKLRAPVWIAPSPSRC PFPTRHPSFRGVLPAGVADLSKTLEGHDLILVVGAPVFRYHQYVPGNYLPGGARLIHVTD DGGEAARAPIGEAYVAPVGSTLEILANMVKPSDRSPLPPLGDFEEAVSVGAGLDPAQLFA LVRAGAPDDAIYVNESTSTSDAFWSQMDLSHQGSYYFPASGGLGFGLPAAVGAQLASPDR QVIGLIGDGSANYGITALWSAAQYKIPVVIIILNNGTYGALRGFSKILNTGETPGLDVPG IDFVHLAEGYGVRGTAVATAEDFTTAFKSALAADAPTLIEVRTNFDES Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria) Strain: RHA1 / Gene: RHA1_ro02985 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SCE8, benzoylformate decarboxylase
#2: Chemical	ChemComp-TPP / THIAMINE DIPHOSPHATE Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₉N₄O₇P₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52 % / Description: square plates
Crystal grow	Temperature: 300 K / Method: vapor diffusion / pH: 6.5 Details: 0.16 M ammonium sulfate, 20% PEG8000, 0.1 mM Mes pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97948 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97948 Å / Relative weight: 1
Reflection	Resolution: 2.6→123.5 Å / Num. obs: 70459 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10 % / CC_1/2: 0.997 / R_merge(I) obs: 0.154 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.6→2.74 Å / Redundancy: 10.2 % / R_merge(I) obs: 2.187 / Num. unique obs: 10199 / CC_1/2: 0.461 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6QSI

6qsi

Resolution: 2.6→90.423 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.811 / SU B: 36.895 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R: 0.952 / ESU R Free: 0.297
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2329	2975	4.222 %
R_work	0.1946	67484	-
all	0.196	-	-
obs	0.1963	70459	99.99 %

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: 81.639 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.019 Å²	0 Å²	0 Å²
2-	-	-3.673 Å²	0 Å²
3-	-	-	-1.346 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→90.423 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15556	0	108	63	15727

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	16037
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14659
X-RAY DIFFRACTION	r_angle_refined_deg	1.803	1.637	21983
X-RAY DIFFRACTION	r_angle_other_deg	1.339	1.563	33979
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.853	5	2108
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.876	22.423	714
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.527	15	2254
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.073	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	2115
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	18363
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3165
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	3017
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	13393
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	7850
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	7101
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	248
X-RAY DIFFRACTION	r_metal_ion_refined	0.298	0.2	19
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.248	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.254	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.432	3.4	8444
X-RAY DIFFRACTION	r_mcbond_other	2.432	3.399	8443
X-RAY DIFFRACTION	r_mcangle_it	4.016	5.096	10548
X-RAY DIFFRACTION	r_mcangle_other	4.016	5.097	10549
X-RAY DIFFRACTION	r_scbond_it	2.702	3.683	7593
X-RAY DIFFRACTION	r_scbond_other	2.678	3.678	7585
X-RAY DIFFRACTION	r_scangle_it	4.288	5.415	11435
X-RAY DIFFRACTION	r_scangle_other	4.288	5.416	11436
X-RAY DIFFRACTION	r_lrange_it	8.05	40.246	16725
X-RAY DIFFRACTION	r_lrange_other	8.051	40.247	16725
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.042	0.05	15939
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.037	0.05	15909
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.035	0.05	15965
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.041	0.05	15945
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.038	0.05	15973
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.037	0.05	15933

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.668	0.377	189	0.361	4975	X-RAY DIFFRACTION	100
2.668-2.741	0.384	199	0.337	4819	X-RAY DIFFRACTION	100
2.741-2.82	0.365	192	0.328	4688	X-RAY DIFFRACTION	100
2.82-2.907	0.342	179	0.294	4546	X-RAY DIFFRACTION	100
2.907-3.002	0.324	179	0.282	4445	X-RAY DIFFRACTION	100
3.002-3.107	0.279	183	0.258	4259	X-RAY DIFFRACTION	100
3.107-3.224	0.273	214	0.255	4103	X-RAY DIFFRACTION	100
3.224-3.356	0.275	157	0.214	3980	X-RAY DIFFRACTION	100
3.356-3.505	0.237	155	0.198	3833	X-RAY DIFFRACTION	100
3.505-3.676	0.203	171	0.182	3647	X-RAY DIFFRACTION	100
3.676-3.874	0.195	180	0.16	3455	X-RAY DIFFRACTION	100
3.874-4.109	0.169	152	0.14	3293	X-RAY DIFFRACTION	100
4.109-4.392	0.181	158	0.142	3080	X-RAY DIFFRACTION	100
4.392-4.743	0.184	145	0.144	2904	X-RAY DIFFRACTION	100
4.743-5.194	0.212	144	0.159	2651	X-RAY DIFFRACTION	100
5.194-5.805	0.242	113	0.175	2435	X-RAY DIFFRACTION	100
5.805-6.699	0.186	84	0.161	2178	X-RAY DIFFRACTION	100
6.699-8.195	0.167	75	0.152	1863	X-RAY DIFFRACTION	100
8.195-11.547	0.174	84	0.178	1446	X-RAY DIFFRACTION	100
11.547-90.423	0.715	22	0.315	884	X-RAY DIFFRACTION	99.2333

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	1.598	-0.2534	-0.3472	2.389	-1.1066	2.3426	0.0119	-0.1299	0.281	0.0649	0.0248	-0.0656	-0.0498	0.0698	-0.0367	0.0058	-0.029	-0.0486	0.8119	-0.011	0.9448	43.066	-25.889	-15.745
2	2.3887	-0.3116	-0.1886	0.9979	-0.3131	0.9404	-0.01	-0.2046	-0.2017	0.1444	0.0156	0.205	0.2425	0.0857	-0.0056	0.1332	0.0069	0.0339	0.813	0.1515	0.8899	34.251	-53.804	-7.654
3	2.8293	0.0632	-0.6881	1.4301	-0.4696	1.7034	-0.0648	-0.1104	-0.1897	-0.1365	0.0421	0.3331	0.095	0.025	0.0227	0.0604	0.0518	-0.0693	0.6707	0.0172	0.9023	34.665	-45.957	-40.164
4	0.997	0.2835	-0.1625	2.1456	-0.6155	0.8485	-0.062	-0.1286	0.0611	-0.118	0.0553	-0.0988	0.0074	0.2289	0.0067	0.0232	0.0345	0.0173	0.8695	0.0033	0.8048	61.17	-31.601	-43.422
5	1.8579	-0.1238	0.2441	1.1804	0.6617	3.263	0.1253	-0.1963	0.1863	0.0072	-0.0806	0.1199	-0.1444	-0.3614	-0.0447	0.1438	0.0062	-0.0367	0.6579	-0.0229	0.9083	19.41	-9.703	-39.38
6	0.8878	-0.2812	-0.097	0.8607	0.3663	0.8904	0.058	0.1649	-0.0816	0.1262	-0.0981	0.1352	-0.0054	-0.0896	0.04	0.0826	0.0562	-0.129	0.7404	-0.0062	0.9077	10.737	-22.51	-59.609
7	0.8298	-0.5318	-0.0543	1.2901	1.0865	2.7789	0.1196	-0.1244	-0.217	-0.0252	-0.044	0.1248	0.1334	0.036	-0.0756	0.0557	-0.0244	0.0622	0.7209	-0.0165	0.9963	8.974	-32.242	-27.629
8	1.2038	0.0861	0.8725	1.0849	0.1269	1.5166	-0.0073	-0.1693	0.1487	0.1351	0.0024	-0.0089	-0.2497	-0.115	0.0049	0.1103	0.0008	0.1603	0.8077	-0.1272	0.913	9.979	-5.993	-12.403

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 181
2	X-RAY DIFFRACTION	2	ALL	AAA	182 - 528
3	X-RAY DIFFRACTION	3	ALL	BBB	2 - 181
4	X-RAY DIFFRACTION	4	ALL	BBB	182 - 528
5	X-RAY DIFFRACTION	5	ALL	CCC	-2 - 181
6	X-RAY DIFFRACTION	6	ALL	CCC	182 - 528
7	X-RAY DIFFRACTION	7	ALL	DDD	2 - 181
8	X-RAY DIFFRACTION	8	ALL	DDD	182 - 528

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