PDB-6p2k: Crystal structure of AFV00434, an ancestral GH74 enzyme

ID or keywords:

Entry

Database: PDB / ID: 6p2k

Title

Crystal structure of AFV00434, an ancestral GH74 enzyme

Components

Fibronectin type III domain-containing protein

Keywords

HYDROLASE / GH74 /

glycosyl hydrolase / 7-fold beta-propeller

Function / homology

Function and homology information

Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology

Biological species

Simiduia agarivorans

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.15 Å

Authors

Stogios, P.J. / Skarina, T. / Arnal, G. / Brumer, H. / Savchenko, A.

Funding support

Canada, 1items

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H.

History

Deposition	May 21, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Sep 18, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6p2k.cif.gz	656.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6p2k.ent.gz	535.4 KB	Display	PDB format
PDBx/mmJSON format	6p2k.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/p2/6p2k ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2k	HTTPS FTP

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Related structure data

Related structure data	6p2lC 6p2mC 6p2nC 6p2oC C: citing same article (ref.)
Similar structure data	5cdq-d 7082 21522 5cdn-d 5cdo-d 4bof-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#52 - Apr 2004 Growth Hormone similarity (1) #185 - May 2015 Titin similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Fibronectin type III domain-containing protein

B: Fibronectin type III domain-containing protein

hetero molecules

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

1

B: Fibronectin type III domain-containing protein

hetero molecules

B: Fibronectin type III domain-containing protein

hetero molecules

B: Fibronectin type III domain-containing protein

hetero molecules

A: Fibronectin type III domain-containing protein

hetero molecules

A: Fibronectin type III domain-containing protein

hetero molecules

A: Fibronectin type III domain-containing protein

hetero molecules

defined by software
529 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	8_544	-z,x-1/2,-y-1/2	1
crystal symmetry operation	11_545	y+1/2,-z-1/2,-x	1
crystal symmetry operation	3_545	-x,y-1/2,-z+1/2	1
crystal symmetry operation	6_445	z-1/2,-x-1/2,-y	1
crystal symmetry operation	9_545	y,z-1,x	1

Unit cell

Length a, b, c (Å)	173.427, 173.427, 173.427
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

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Protein , 1 types, 2 molecules AB

#1: Protein	Fibronectin type III domain-containing protein Mass: 85372.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simiduia agarivorans (strain DSM 21679 / JCM 13881 / BCRC 17597 / SA1) (bacteria) Strain: DSM 21679 / JCM 13881 / BCRC 17597 / SA1 / Gene: M5M_16515 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4KQN2

#1: Protein

Fibronectin type III domain-containing protein

Mass: 85372.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Simiduia agarivorans (strain DSM 21679 / JCM 13881 / BCRC 17597 / SA1) (bacteria)
Strain: DSM 21679 / JCM 13881 / BCRC 17597 / SA1 / Gene: M5M_16515 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4KQN2

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Non-polymers , 6 types, 1743 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol Mass: 634.751 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₈H₅₈O₁₅
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1714 / 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: 2.55 Å³/Da / Density % sol: 51.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25 mM zinc acetate, 20% (w/v) PEG3350, 1.5 (w/v) MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.15→40 Å / Num. obs: 94257 / % possible obs: 99.8 % / Redundancy: 5.7 % / R_merge(I) obs: 0.072 / R_pim(I) all: 0.032 / Net I/σ(I): 22.2
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.849 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4568 / CC_1/2: 0.676 / R_pim(I) all: 0.441 / % possible all: 97.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.15_3448: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.15→38.779 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.17

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2041	4654	2.92 %	RANDOM
R_work	0.1539	-	-	-
obs	0.1553	93430	86.81 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.15→38.779 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12052	0	150	1714	13916

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	12561
X-RAY DIFFRACTION	f_angle_d	0.663	17109
X-RAY DIFFRACTION	f_dihedral_angle_d	16.68	4352
X-RAY DIFFRACTION	f_chiral_restr	0.049	1733
X-RAY DIFFRACTION	f_plane_restr	0.004	2250

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 (%)
2.15-2.1739	0.2741	77	0.2376	2640	X-RAY DIFFRACTION	44
2.1739-2.1994	0.2973	91	0.2322	3067	X-RAY DIFFRACTION	52
2.1994-2.2263	0.2618	103	0.2226	3349	X-RAY DIFFRACTION	57
2.2263-2.2544	0.2162	112	0.2245	3583	X-RAY DIFFRACTION	60
2.2544-2.2841	0.2949	110	0.2238	3681	X-RAY DIFFRACTION	62
2.2841-2.3154	0.2884	113	0.2268	3892	X-RAY DIFFRACTION	66
2.3154-2.3485	0.2923	131	0.2156	4219	X-RAY DIFFRACTION	72
2.3485-2.3835	0.2723	138	0.2129	4596	X-RAY DIFFRACTION	78
2.3835-2.4207	0.2877	143	0.2229	4953	X-RAY DIFFRACTION	83
2.4207-2.4604	0.2815	159	0.217	5283	X-RAY DIFFRACTION	89
2.4604-2.5028	0.258	173	0.1934	5615	X-RAY DIFFRACTION	94
2.5028-2.5484	0.2048	161	0.1899	5612	X-RAY DIFFRACTION	95
2.5484-2.5974	0.2509	168	0.1895	5610	X-RAY DIFFRACTION	96
2.5974-2.6504	0.1961	183	0.1888	5722	X-RAY DIFFRACTION	96
2.6504-2.708	0.2622	169	0.1852	5703	X-RAY DIFFRACTION	96
2.708-2.771	0.242	168	0.1872	5693	X-RAY DIFFRACTION	96
2.771-2.8402	0.2531	172	0.1841	5749	X-RAY DIFFRACTION	96
2.8402-2.917	0.213	177	0.1724	5705	X-RAY DIFFRACTION	97
2.917-3.0028	0.2376	172	0.1649	5761	X-RAY DIFFRACTION	97
3.0028-3.0997	0.2154	179	0.1626	5747	X-RAY DIFFRACTION	97
3.0997-3.2104	0.1997	169	0.1606	5736	X-RAY DIFFRACTION	97
3.2104-3.3389	0.2233	171	0.149	5818	X-RAY DIFFRACTION	97
3.3389-3.4908	0.1875	172	0.1373	5797	X-RAY DIFFRACTION	98
3.4908-3.6747	0.1644	165	0.1269	5814	X-RAY DIFFRACTION	98
3.6747-3.9047	0.1795	177	0.1189	5892	X-RAY DIFFRACTION	99
3.9047-4.2058	0.1532	179	0.1151	5887	X-RAY DIFFRACTION	99
4.2058-4.6285	0.1579	186	0.1026	5884	X-RAY DIFFRACTION	99
4.6285-5.2968	0.1487	175	0.1051	5888	X-RAY DIFFRACTION	99
5.2968-6.6679	0.1637	180	0.1378	5930	X-RAY DIFFRACTION	100
6.6679-38.7857	0.2092	181	0.1538	5798	X-RAY DIFFRACTION	98

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	5.8931	0.0654	-3.6643	0.1681	0.1987	2.8024	-0.0902	0.1899	-0.0465	-0.0011	0.0761	0.1461	-0.1756	-0.3796	0.0054	0.2327	0.081	-0.0219	0.2412	-0.0398	0.2333	3.3402	-17.3912	37.202
2	0.5757	-0.046	0.059	0.7625	0.239	0.677	0.0195	0.1033	-0.0038	-0.1036	-0.0293	0.1056	-0.0854	-0.0828	0.0095	0.1709	0.0256	-0.0049	0.1762	-0.0246	0.1713	18.4484	-30.252	30.4245
3	0.7028	0.0468	-0.4906	0.2481	0.1401	0.9042	0.0639	-0.0621	0.0914	0.0366	-0.042	0.1117	-0.1005	-0.0971	-0.0274	0.1817	0.046	0.012	0.2179	-0.0387	0.2357	3.4031	-19.179	57.0096
4	2.1673	1.1515	1.463	1.1545	1.2168	2.6299	0.2395	-0.2729	-0.0259	0.2676	-0.2896	0.2574	0.2948	-0.5439	0.0443	0.2282	-0.0451	0.057	0.3776	-0.0522	0.3315	-16.8663	-35.7467	68.4116
5	1.5102	0.6994	-0.0356	1.0271	0.1192	1.6737	0.1	0.1057	0.0284	-0.0317	-0.0832	0.2469	-0.0287	-0.4058	-0.0329	0.1849	0.0644	-0.0287	0.4534	-0.0725	0.4079	-21.5624	-30.301	44.8872
6	3.048	-0.086	1.1833	3.9707	-1.7185	1.1783	-0.0133	0.0518	0.5533	0.3019	-0.0604	0.6057	-0.2448	-0.6011	-0.0344	0.2517	0.1162	-0.035	0.4562	-0.1206	0.3787	-18.1295	-17.372	50.2
7	6.908	3.3555	0.4732	4.3361	-0.3456	1.0699	-0.1486	-0.2139	0.6065	0.119	0.0656	-0.1019	-0.1813	-0.0629	0.0261	0.2296	0.0481	-0.0497	0.1509	-0.0349	0.212	2.1642	-42.7053	-0.1907
8	2.2685	-1.551	-0.1285	2.4246	0.4002	1.3422	0.2475	0.4911	0.9979	-0.6027	-0.2542	-0.8458	-0.3815	-0.0304	-0.0676	0.4593	-0.0179	0.1538	0.2683	0.2472	0.6888	16.692	-35.9924	-15.8089
9	1.577	0.1516	0.3609	1.0139	0.3499	0.4342	-0.0355	-0.072	0.0259	-0.0086	0.0079	-0.1217	-0.0665	0.042	0.0153	0.1456	0.0014	0.0008	0.1379	0.0175	0.1147	0.0897	-61.2188	-5.6997
10	1.6906	-0.7613	0.095	1.5704	0.1988	0.8066	-0.047	0.0111	-0.1366	-0.1291	0.0096	0.3155	-0.0328	-0.1395	0.0362	0.1528	0.0012	-0.0451	0.1893	-0.0138	0.1967	-25.4088	-66.2472	-19.6984
11	1.9712	0.6792	0.335	2.64	-0.4311	1.3022	-0.0835	-0.0568	0.3542	0.0117	0.0023	0.2078	-0.324	-0.1747	0.0844	0.2676	0.0967	-0.0522	0.2142	-0.0383	0.2819	-24.4531	-42.9762	-11.9652
12	7.2423	0.4382	-3.2605	2.5737	-1.2266	7.7955	-0.2604	-0.4131	-0.1987	0.302	0.0388	0.4168	0.1191	-0.4769	0.1594	0.2634	0.0621	0.0139	0.1834	-0.0378	0.2275	-21.3524	-53.1293	0.6805

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:36)
2	X-RAY DIFFRACTION	2	(chain A and resid 37:310)
3	X-RAY DIFFRACTION	3	(chain A and resid 311:536)
4	X-RAY DIFFRACTION	4	(chain A and resid 537:622)
5	X-RAY DIFFRACTION	5	(chain A and resid 623:755)
6	X-RAY DIFFRACTION	6	(chain A and resid 756:779)
7	X-RAY DIFFRACTION	7	(chain B and resid 2:49)
8	X-RAY DIFFRACTION	8	(chain B and resid 50:321)
9	X-RAY DIFFRACTION	9	(chain B and resid 322:508)
10	X-RAY DIFFRACTION	10	(chain B and resid 509:632)
11	X-RAY DIFFRACTION	11	(chain B and resid 633:751)
12	X-RAY DIFFRACTION	12	(chain B and resid 752:779)

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