PDB-4gs1: Crystal structure of DyP-type peroxidase from Thermobifida cellul...

ID or keywords:

Entry

Database: PDB / ID: 4gs1

Title

Crystal structure of DyP-type peroxidase from Thermobifida cellulosilytica

Components

DyP-type peroxidase

Keywords

OXIDOREDUCTASE / ferridoxin-like

Function / homology

Function and homology information

dye decolorizing peroxidase / peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Thermobifida cellulosilytica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Lukk, T. / Hetta, A.M.A. / Jones, A. / Solbiati, J. / Majumdar, S. / Cronan, J.E. / Gerlt, J.A. / Nair, S.K.

Citation

Journal: To be Published
Title: DyP-type peroxidases from Stretptomyces and Thermobifida can modify organosolv lignin.
Authors: Lukk, T. / Hetta, A.M.A. / Jones, A. / Solbiati, J. / Majumdar, S. / Cronan, J.E. / Gerlt, J.A. / Nair, S.K.

History

Deposition	Aug 27, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gs1.cif.gz	316.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4gs1.ent.gz	254 KB	Display	PDB format
PDBx/mmJSON format	4gs1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4gs1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4gs1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4gs1_validation.xml.gz	37.9 KB	Display
Data in CIF	4gs1_validation.cif.gz	58.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gs/4gs1 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/4gs1	HTTPS FTP

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Related structure data

Related structure data	4grcC 4gt2C 4gu7C 2gvkS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fzr-1 2y4d-d 1dhk-d 4pkh-1 5nbs-1 2eab-1 4g2t-1 2ead-2 4ut4-2 5mjh-d 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 (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: DyP-type peroxidase

B: DyP-type peroxidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.680, 91.190, 110.550
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	DyP-type peroxidase Mass: 42414.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida cellulosilytica (bacteria) Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: U3KRF5*PLUS, dye decolorizing peroxidase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 915 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.78 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution was at 15 mg/mL, containing 20 mM Tris and 150 mM NaCl. Mother liqueur contained 170 mM (NH4)2SO4, 25.5% PEG 4,000 and 15% (w/v) glycerol, pH 7.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97857 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 15, 2012

Radiation

Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.7→20 Å / Num. obs: 97818 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / B_iso Wilson estimate: 28.602 Å² / R_sym value: 0.068 / Net I/σ(I): 12.93

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	Diffraction-ID	% possible all
1.7-1.74	0.477	2.6	49758	13894	1	99.9
1.74-1.79	0.393	3.44	54641	13624	1	99.9
1.79-1.84	0.313	4.45	56183	13184	1	100
1.84-1.9	0.243	5.64	55014	12868	1	100
1.9-1.96	0.183	7.28	53103	12413	1	99.9
1.96-2.03	0.147	8.84	51517	12006	1	100
2.03-2.11	0.119	10.63	49939	11644	1	100
2.11-2.19	0.098	12.67	47963	11138	1	100
2.19-2.29	0.088	13.87	46103	10695	1	100
2.29-2.4	0.079	15.54	44251	10249	1	100
2.4-2.53	0.073	16.54	42103	9738	1	99.9
2.53-2.69	0.066	18.48	39741	9193	1	100
2.69-2.87	0.062	19.96	37456	8645	1	100
2.87-3.1	0.057	21.8	34831	8049	1	100
3.1-3.4	0.054	23.42	32082	7408	1	100
3.4-3.8	0.052	24.82	29088	6720	1	99.9
3.8-4.39	0.051	25.55	25543	5901	1	100
4.39-5.38	0.052	25.96	21502	4970	1	100
5.38-7.6	0.052	25.56	16647	3856	1	99.9
7.6-20	0.053	26.14	8291	1981	1	94.2

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.8_1066	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2GVK

2gvk

Resolution: 1.7→19.914 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.9127 / SU ML: 0.14 / σ(F): 2.03 / Phase error: 15.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1738	4891	5 %	random
R_work	0.1457	-	-	-
all	0.171	97913	-	-
obs	0.1471	97818	99.98 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 89.74 Å² / B_iso mean: 24.7093 Å² / B_iso min: 7.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→19.914 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5673	0	108	915	6696

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6006
X-RAY DIFFRACTION	f_angle_d	1.109	8222
X-RAY DIFFRACTION	f_chiral_restr	0.079	872
X-RAY DIFFRACTION	f_plane_restr	0.006	1121
X-RAY DIFFRACTION	f_dihedral_angle_d	13.376	2207

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.7-1.7193	0.2395	161	0.1932	3071	3232
1.7193-1.7396	0.2168	159	0.177	3020	3179
1.7396-1.7608	0.2427	162	0.1764	3080	3242
1.7608-1.783	0.2071	162	0.169	3074	3236
1.783-1.8065	0.194	162	0.162	3072	3234
1.8065-1.8312	0.2143	161	0.1581	3063	3224
1.8312-1.8574	0.1819	162	0.1534	3070	3232
1.8574-1.8851	0.2159	160	0.1468	3053	3213
1.8851-1.9145	0.1875	162	0.1487	3072	3234
1.9145-1.9459	0.1933	162	0.1444	3088	3250
1.9459-1.9794	0.1649	161	0.1452	3046	3207
1.9794-2.0153	0.1914	162	0.1562	3092	3254
2.0153-2.0541	0.1838	161	0.1428	3052	3213
2.0541-2.0959	0.1927	163	0.1452	3086	3249
2.0959-2.1415	0.1824	162	0.147	3095	3257
2.1415-2.1912	0.1726	161	0.1456	3054	3215
2.1912-2.2459	0.1948	164	0.1514	3116	3280
2.2459-2.3066	0.1701	162	0.1442	3085	3247
2.3066-2.3744	0.1851	162	0.1437	3059	3221
2.3744-2.4509	0.1937	162	0.1541	3093	3255
2.4509-2.5383	0.1961	164	0.1542	3111	3275
2.5383-2.6397	0.1775	163	0.1496	3094	3257
2.6397-2.7595	0.1702	165	0.1562	3135	3300
2.7595-2.9046	0.1707	162	0.1577	3085	3247
2.9046-3.086	0.1789	165	0.1557	3121	3286
3.086-3.3232	0.1872	164	0.1487	3129	3293
3.3232-3.6558	0.154	166	0.1367	3156	3322
3.6558-4.1806	0.1273	166	0.1274	3152	3318
4.1806-5.251	0.1537	168	0.1174	3190	3358
5.251-19.9156	0.1623	175	0.1516	3313	3488

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	0.3831	-0.4253	0.2568	0.6259	-0.3534	0.3185	0.027	0.0609	0.1133	0.0743	-0.1243	-0.1911	-0.0905	0.1484	-0.0195	0.1392	-0.0254	-0.0232	0.1637	0.0343	0.1565	24.5556	1.3991	-9.5507
2	0.4979	-0.1555	0.0891	0.4066	-0.0319	0.631	0.0221	-0.0411	-0.0128	0.0472	-0.035	-0.0199	0.0133	0.0227	0	0.119	-0.0142	-0.0155	0.1159	0.0137	0.1019	14.3489	-8.0319	-1.1088
3	0.4482	0.1536	0.2233	0.3076	0.0044	0.4747	0.0512	-0.0243	-0.0785	0.0483	-0.0686	-0.0484	0.0679	0.0143	0.0022	0.129	-0.0246	-0.0248	0.1181	0.0378	0.1131	12.1869	-14.0464	2.5073
4	0.0533	0.0248	-0.0797	-0.0396	-0.0045	0.0896	-0.1364	-0.2008	0.2328	0.0682	-0.0407	0.1105	-0.4831	-0.1951	-0.0004	0.2774	0.0482	-0.0076	0.1534	-0.0354	0.1955	-2.2076	19.4201	-7.253
5	0.2506	-0.2392	0.1509	0.2997	-0.2617	0.1543	0.0057	-0.107	-0.0677	0.15	0.0111	0.223	0.0608	-0.1112	-0.0071	0.1333	-0.0157	0.0615	0.1894	-0.013	0.2273	-17.4412	0.2682	-14.1437
6	0.0761	-0.0703	0.046	0.1135	0.0385	0.0119	0.0111	-0.1045	-0.1672	0.0896	0.1082	0.0701	-0.0979	-0.1961	0	0.1605	-0.0026	0.018	0.1637	-0.0018	0.1879	-9.6456	6.0202	-9.4052
7	0.2453	-0.023	-0.1354	0.6954	-0.2456	0.1418	-0.0216	0.0326	-0.0502	0.0305	0.0332	0.0779	0.0761	-0.0657	-0	0.1024	-0.0151	0.0147	0.1243	-0.0119	0.1363	-8.9291	1.2692	-20.814
8	0.2335	0.3834	0.0101	0.3754	-0.1826	0.1649	0.0537	0.053	0.1316	0.1635	-0.0751	0.0486	-0.135	-0.014	0.0008	0.1686	0.0234	0.0113	0.1038	-0.004	0.1516	4.0898	20.7618	-19.1474
9	0.1584	0.287	-0.0081	0.3306	-0.1271	0.1805	-0.0222	0.0131	0.0894	-0.0262	0.0586	0.1339	0.0218	-0.1021	0.0396	0.0988	0.0389	-0.0018	0.1609	0.0134	0.2055	-14.7926	12.3963	-27.0542
10	0.0404	0.0937	0.0384	0.0622	0.0332	0.0401	0.0218	0.1187	-0.1758	-0.1982	-0.0928	-0.2926	0.1304	0.3493	-0.0001	0.1428	0.0288	0.0276	0.2036	0.0208	0.1739	19.4805	10.2754	-31.9043
11	0.0812	0.0717	-0.0038	0.0494	-0.045	0.0315	0.0751	0.0206	0.0843	0.0073	-0.1284	-0.1337	-0.2299	0.1418	0	0.1769	0.0003	-0.0035	0.1589	0.0426	0.1668	13.6635	26.6079	-28.2473
12	0.2583	0.1002	0.0036	0.239	-0.104	0.4559	0.0194	0.0154	-0.0071	-0.1042	-0.035	-0.0333	0.0423	0.0568	0.0445	0.1117	0.039	0.0119	0.0924	0.0168	0.0993	7.7736	14.5238	-32.7016
13	0.1829	0.326	0.1095	0.7749	-0.1698	0.3203	-0.0441	0.0774	0.0003	0.0109	0.0346	0.1182	-0.0091	-0.1001	-0.0002	0.1122	0.033	0.0057	0.131	0.0142	0.1344	-6.9635	10.1131	-28.1498

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 53:151)	A
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 152:319)	A
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 320:427)	A
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 53:82)	B
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 83:123)	B
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 124:151)	B
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 152:218)	B
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 219:256)	B
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 257:282)	B
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 283:299)	B
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 300:319)	B
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 320:368)	B
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 369:428)	B

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