PDB-6qzo: Crystal structure of DyP-type peroxidase from Cellulomonas bogoriensis

ID or keywords:

Entry

Database: PDB / ID: 6qzo

Title

Crystal structure of DyP-type peroxidase from Cellulomonas bogoriensis

Components

Peroxidase

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

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

Biological species

Cellulomonas bogoriensis 69B4 = DSM 16987 (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Rozeboom, H.J. / Fraaije, M.W.

Citation

Journal: Molecules / Year: 2019
Title: Characterization of a New DyP-Peroxidase from the Alkaliphilic Cellulomonad, Cellulomonas bogoriensis.
Authors: Habib, M.H. / Rozeboom, H.J. / Fraaije, M.W.

History

Deposition	Mar 12, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qzo.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qz/6qzo ftp://data.pdbj.org/pub/pdb/validation_reports/qz/6qzo	HTTPS FTP

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Related structure data

Related structure data	5jxuS S: Starting model for refinement
Similar structure data	5jxu-d 2y4f-d 3o72-1 3o72-2 3uyl-d 2y4e-d 6gzw-d 5map-d 5hne-d 4gt2-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5jxuS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peroxidase

B: Peroxidase

C: Peroxidase

D: Peroxidase

E: Peroxidase

F: Peroxidase

G: Peroxidase

H: Peroxidase

hetero molecules

337 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Peroxidase

B: Peroxidase

hetero molecules

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

2

C: Peroxidase

D: Peroxidase

hetero molecules

defined by author&software
84.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Peroxidase

F: Peroxidase

hetero molecules

defined by author&software
84.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Peroxidase

H: Peroxidase

hetero molecules

defined by author&software
84.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	173.989, 173.989, 283.003
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 23 - 383 / Label seq-ID: 23 - 383

NCS ensembles :

#1: Protein	Peroxidase Mass: 41456.465 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas bogoriensis 69B4 = DSM 16987 (bacteria) Gene: N869_13850 / Variant: wild type / Plasmid: pBAD-His-SUMO-CboDyp / Production host: Escherichia coli (E. coli) / Variant (production host): NEB 10-beta / References: UniProt: A0A0A0BZU2
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 432 / 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: 3.7 Å³/Da / Density % sol: 67 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG300, 0.1M Tris pH 8.5, 5% PEG8000 and 10% glycerol

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Data collection

Diffraction

Mean temperature: 110 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å

Detector

Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.509
1	1	-K, -H, -L	2	0.491

Reflection

Resolution: 2.4→58.9 Å / Num. obs: 184630 / % possible obs: 97.9 % / Redundancy: 9.9 % / B_iso Wilson estimate: 23.2 Å² / CC_1/2: 0.985 / R_pim(I) all: 0.119 / Net I/σ(I): 7

Reflection shell

Resolution: 2.4→2.44 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9000 / CC_1/2: 0.463 / R_pim(I) all: 0.569 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JXU

5jxu

Resolution: 2.4→58.87 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.922 / SU B: 6.869 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26718	9264	5 %	RANDOM
R_work	0.24209	-	-	-
obs	0.24334	175363	97.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 24.296 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.95 Å²	0 Å²	0 Å²
2-	-	4.95 Å²	0 Å²
3-	-	-	-9.9 Å²

Refinement step

Cycle: 1 / Resolution: 2.4→58.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22160	0	354	433	22947

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	23113
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	21245
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.679	31704
X-RAY DIFFRACTION	r_angle_other_deg	1.242	1.589	48863
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.104	5	2880
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.392	19.583	1344
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.945	15	3376
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.307	15	288
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	2888
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	26688
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	5312
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.738	1.65	11544
X-RAY DIFFRACTION	r_mcbond_other	0.737	1.65	11542
X-RAY DIFFRACTION	r_mcangle_it	1.321	2.473	14416
X-RAY DIFFRACTION	r_mcangle_other	1.321	2.473	14416
X-RAY DIFFRACTION	r_scbond_it	0.603	1.72	11568
X-RAY DIFFRACTION	r_scbond_other	0.603	1.721	11569
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.063	2.555	17289
X-RAY DIFFRACTION	r_long_range_B_refined	2.484	18.795	24664
X-RAY DIFFRACTION	r_long_range_B_other	2.47	18.792	24643
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11334	0.07
1	2	B	11334	0.07
2	1	A	11336	0.07
2	2	C	11336	0.07
3	1	A	11377	0.06
3	2	D	11377	0.06
4	1	A	11352	0.07
4	2	E	11352	0.07
5	1	A	11378	0.07
5	2	F	11378	0.07
6	1	A	11300	0.07
6	2	G	11300	0.07
7	1	A	11306	0.07
7	2	H	11306	0.07
8	1	B	11404	0.06
8	2	C	11404	0.06
9	1	B	11445	0.05
9	2	D	11445	0.05
10	1	B	11448	0.06
10	2	E	11448	0.06
11	1	B	11380	0.06
11	2	F	11380	0.06
12	1	B	11457	0.06
12	2	G	11457	0.06
13	1	B	11398	0.07
13	2	H	11398	0.07
14	1	C	11482	0.05
14	2	D	11482	0.05
15	1	C	11410	0.06
15	2	E	11410	0.06
16	1	C	11343	0.07
16	2	F	11343	0.07
17	1	C	11368	0.06
17	2	G	11368	0.06
18	1	C	11388	0.06
18	2	H	11388	0.06
19	1	D	11417	0.06
19	2	E	11417	0.06
20	1	D	11416	0.06
20	2	F	11416	0.06
21	1	D	11390	0.06
21	2	G	11390	0.06
22	1	D	11469	0.06
22	2	H	11469	0.06
23	1	E	11484	0.06
23	2	F	11484	0.06
24	1	E	11450	0.06
24	2	G	11450	0.06
25	1	E	11437	0.06
25	2	H	11437	0.06
26	1	F	11412	0.05
26	2	G	11412	0.05
27	1	F	11464	0.05
27	2	H	11464	0.05
28	1	G	11367	0.07
28	2	H	11367	0.07

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.597	655	-
R_work	0.51	12754	-
obs	-	-	96.19 %

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	0.8045	-0.1497	0.0446	0.336	-0.0897	0.7539	-0.0032	-0.0607	0.0519	0.0366	0.0279	0.0032	-0.0955	-0.0373	-0.0246	0.0605	0.0077	-0.0016	0.0837	-0.0133	0.0271	47.128	94.484	74.807
2	0.5998	-0.311	0.1394	0.3679	-0.0683	0.527	0.0194	0.0316	0.0512	-0.0075	-0.0166	-0.0353	-0.0578	0.0491	-0.0027	0.0267	-0.0065	0.0004	0.0814	0.0078	0.0284	62.18	86.252	45.388
3	0.6275	0.2785	0.1376	0.4209	0.0434	0.5664	0.021	-0.0361	0.0146	0.0179	-0.0071	0.0246	-0.0458	-0.0224	-0.0139	0.0324	0.0035	0.0032	0.0806	-0.0132	0.0285	116.13	88.337	40.966
4	0.8935	0.1605	0.0825	0.2446	0.0742	0.8574	0.0053	0.0831	0.0529	-0.0327	0.0155	-0.0142	-0.1457	0.0943	-0.0208	0.0821	-0.0182	0.0032	0.1085	0.0101	0.041	130.858	97.145	11.556
5	0.9121	0.0812	0.2252	0.1725	0.011	0.5767	0.0225	-0.0695	-0.0289	0.0176	0.0115	0.0119	-0.0094	0.004	-0.0339	0.0556	0.0211	-0.0233	0.0999	-0.0048	0.0469	80.829	81.477	-6.204
6	1.076	-0.137	0.2356	0.2953	0.0658	0.6892	0.0147	0.1729	-0.0443	-0.0307	-0.0016	-0.0162	0.0128	0.1902	-0.0131	0.0943	0.02	-0.0151	0.216	-0.0123	0.048	98.391	81.768	-35.47
7	0.9295	0.1325	0.2236	0.2406	-0.0997	0.8901	0.0501	-0.1685	-0.0165	0.0206	0.0221	0.039	0.0191	-0.2321	-0.0722	0.0909	-0.0309	-0.0223	0.2236	0.0258	0.0629	80.507	81.187	121.812
8	0.9674	-0.0924	0.315	0.2124	0.0058	0.5645	0.0102	0.0543	-0.0343	-0.0103	0.0115	-0.0043	0.0012	-0.0014	-0.0216	0.0539	-0.0258	-0.0209	0.0988	0.0058	0.0366	98.094	82.017	92.524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	23 - 383
2	X-RAY DIFFRACTION	2	B	23 - 383
3	X-RAY DIFFRACTION	3	C	23 - 383
4	X-RAY DIFFRACTION	4	D	23 - 383
5	X-RAY DIFFRACTION	5	E	23 - 383
6	X-RAY DIFFRACTION	6	F	23 - 383
7	X-RAY DIFFRACTION	7	G	23 - 383
8	X-RAY DIFFRACTION	8	H	23 - 383

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