PDB-9az0: Crystal crystal of FC2591 peroxidase from Frankia casuarinae

ID or keywords:

Entry

Database: PDB / ID: 9az0

Title

Crystal crystal of FC2591 peroxidase from Frankia casuarinae

Components

Dyp-type peroxidase

Keywords

OXIDOREDUCTASE / FERRIDOXIN-LIKE

Function / homology

Function and homology information

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

Biological species

Frankia casuarinae (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Stogios, P.J. / Skarina, T. / Choolaei, Z. / Yakunin, A. / Savchenko, A.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal crystal of FC2591 peroxidase from Frankia casuarinae
Authors: Stogios, P.J.

History

Deposition	Mar 9, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9az0.cif.gz	186.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9az0.ent.gz	126.7 KB	Display	PDB format
PDBx/mmJSON format	9az0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/9az0 ftp://data.pdbj.org/pub/pdb/validation_reports/az/9az0	HTTPS FTP

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Related structure data

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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2) #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)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#220 - Apr 2018
Dehalogenases
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (2)
#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

hetero molecules

41.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	64.434, 71.639, 76.638
Angle α, β, γ (deg.)	90.000, 109.230, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-1049- HOH
2	1	A-1090- HOH
3	1	A-1206- HOH

#1: Protein	Dyp-type peroxidase Mass: 40757.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Frankia casuarinae (bacteria) / Gene: Francci3_2591 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2J9T9
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.22 Å³/Da / Density % sol: 39.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15 mg/mL protein plus 40 mM zinc acetate, 18% (w/v) Polyethylene glycol (PEG) 3350, cryoprotectant paratone oil

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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: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.65→25 Å / Num. obs: 39461 / % possible obs: 99.4 % / Redundancy: 4.1 % / B_iso Wilson estimate: 20.13 Å² / R_merge(I) obs: 0.048 / R_pim(I) all: 0.027 / Net I/σ(I): 28.97
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.389 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1922 / CC_1/2: 0.888 / R_pim(I) all: 0.221 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→24.12 Å / SU ML: 0.2025 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1796	1972	5 %
R_work	0.1441	37489	-
obs	0.1459	39461	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→24.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2647	0	45	704	3396

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	2757
X-RAY DIFFRACTION	f_angle_d	0.9127	3765
X-RAY DIFFRACTION	f_chiral_restr	0.0558	401
X-RAY DIFFRACTION	f_plane_restr	0.0087	508
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3883	985

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 (%)
1.65-1.69	0.2922	128	0.2788	2445	X-RAY DIFFRACTION	91.24
1.69-1.73	0.2547	141	0.2287	2654	X-RAY DIFFRACTION	98.07
1.73-1.78	0.2392	142	0.185	2687	X-RAY DIFFRACTION	98.47
1.78-1.84	0.21	139	0.1619	2654	X-RAY DIFFRACTION	98.76
1.84-1.91	0.2071	140	0.1607	2657	X-RAY DIFFRACTION	99.33
1.91-1.98	0.1935	139	0.1569	2670	X-RAY DIFFRACTION	99.43
1.98-2.07	0.2148	142	0.1658	2700	X-RAY DIFFRACTION	99.61
2.07-2.18	0.2041	142	0.1498	2708	X-RAY DIFFRACTION	99.89
2.18-2.32	0.2268	142	0.146	2692	X-RAY DIFFRACTION	99.93
2.32-2.5	0.1768	142	0.1408	2698	X-RAY DIFFRACTION	100
2.5-2.75	0.1482	142	0.1433	2707	X-RAY DIFFRACTION	100
2.75-3.15	0.1722	143	0.1383	2707	X-RAY DIFFRACTION	100
3.15-3.96	0.1472	144	0.1192	2742	X-RAY DIFFRACTION	99.93
3.96-24.12	0.157	146	0.1284	2768	X-RAY DIFFRACTION	99.9

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	4.46710363405	-2.5296942442	0.954336898723	2.66415970869	0.0980649169065	1.88921792132	0.0183846322244	0.0537372013433	0.136665031304	-0.0536139612541	-0.0731281562533	0.0438769163843	-0.0968173387575	-0.0239357661646	0.0486276687856	0.0807359802203	-0.0284586610295	0.0332202236379	0.103563898633	0.0486598045442	0.0730357501306	9.60408566406	-3.39223832485	14.4537371487
2	4.0779140819	-4.60609068984	2.12543730155	9.9032018079	-4.51568399511	4.07852349799	0.0232257856995	-0.00397211463911	0.171993227713	0.0653924001691	-0.120844572672	-0.334334931951	0.0490920627238	0.296083257803	0.0958886579162	0.10646177222	0.00218750993767	-0.000967352251417	0.151672941451	-0.0318990965667	0.109318298009	22.0728553633	-6.76137963148	15.5657603819
3	0.191887452412	-0.332981141551	0.659974657065	1.60328250667	-2.29482394577	4.63795977351	0.0384524715672	0.0351482525231	-0.0104444726307	-0.0233124322395	-0.0271914744969	-0.0526863007583	-0.124869420862	0.289664429533	0.0254601614837	0.129369768252	-0.0245268923022	0.00837851616694	0.19859808957	-0.00549996516119	0.208065401414	15.740777155	-1.00878646648	8.20960570815
4	0.531022028398	-0.0929705332516	-0.403821328865	1.53086835667	-0.462624056076	0.827919156315	-0.0120446654565	-0.0162090065215	-0.117486302169	-0.0549871528942	-0.0070918422981	0.055027252037	0.195108320283	0.0320792010547	0.0143547460658	0.149757846704	-0.0031005728507	-0.00677510400023	0.14843237384	-0.00105047905947	0.164566461859	5.8717590297	-13.2579657135	19.4851961327
5	1.82240863402	-0.551754199247	1.25821825823	1.4534230135	-1.52757879216	1.97214856382	0.0586762563429	0.050651497811	-0.0179754039895	-0.121840892315	-0.0759397550497	-0.136008370613	0.119566066522	0.177992612111	0.0200006945797	0.189854032966	0.0192597774879	0.0159375469833	0.169412702845	-0.0196105532302	0.162965414951	12.2130630955	-7.82752833046	5.11051449743
6	1.593741397	0.963304400752	-0.702270232876	1.79331645186	0.643802381626	1.65417543783	0.0620448225248	-0.0874931918664	0.117910511236	-0.0555451857338	0.0214346703429	-0.0709861477674	-0.0965800667715	-0.152077399918	-0.0899052631049	0.176125830823	0.0268270746995	-0.00055217780079	0.16250405033	0.010615003671	0.175671577871	-9.37865112517	5.8521779909	8.38542104132
7	4.82068675464	-0.0714611879949	1.82696576837	0.637128925871	-0.120633701967	1.74873211673	-0.123488779331	-0.184982730758	0.427929363961	0.0787470394198	0.0283728438202	-0.0307034144794	-0.0994095881099	-0.0534814022835	0.0974671990688	0.13730213562	-0.0144482987081	0.0166613361405	0.111981073505	0.0054558517661	0.131554322119	1.67365097915	-1.23896167382	24.5952837674
8	2.93695890413	-0.377062792689	-0.297475437115	4.20267627523	2.47612593783	4.29007381352	-0.021761153784	0.348937854425	0.0233923662326	-0.249940285358	-0.0311019854358	0.148473779608	-0.323326626911	-0.173970828496	0.0819971863097	0.125695932855	0.00429824115194	-0.00629182412477	0.186016471292	0.0314847500735	0.116882447826	-22.8290773192	-0.530005692807	14.9250737956
9	1.83921069209	-0.211856802821	-1.70332964885	0.186870555044	-0.145065539534	2.09104461365	-0.0419685453384	0.0506300165207	-0.0392842481906	0.00968237309135	-0.0110809587234	0.0929672155593	0.106873913413	-0.0532925569324	0.0592381715074	0.152202882347	-0.000145131336853	0.00062122348287	0.135600669691	0.00675300736421	0.165210841494	-14.62323514	-4.60275814482	20.5437749895
10	4.44790724017	0.404550144514	0.677913625335	0.440455910937	0.131471745338	0.292911572687	-0.0189810794617	-0.0840425533169	-0.0955840737755	0.0199804716608	0.0153740760746	0.0327951968602	0.0380445382567	0.00413694290329	-0.00639834194862	0.14415792097	-0.000215892570382	0.00186743747893	0.115338828761	0.00441273408638	0.108859695915	1.17448012342	-8.85663177515	21.7631801875

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 30 through 55 )	30 - 55	1 - 26
2	2	chain 'A' and (resid 56 through 78 )	56 - 78	27 - 49
3	3	chain 'A' and (resid 79 through 111 )	79 - 111	50 - 82
4	4	chain 'A' and (resid 112 through 150 )	112 - 150	83 - 121
5	5	chain 'A' and (resid 151 through 178 )	151 - 178	122 - 149
6	6	chain 'A' and (resid 179 through 198 )	179 - 198	150 - 169
7	7	chain 'A' and (resid 199 through 238 )	199 - 238	170 - 209
8	8	chain 'A' and (resid 239 through 275 )	239 - 275	210 - 246
9	9	chain 'A' and (resid 276 through 330 )	276 - 330	247 - 301
10	10	chain 'A' and (resid 331 through 389 )	331 - 389	302 - 360

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