PDB-4pva: Crystal structure of GH62 hydrolase from thermophilic fungus Scyt...

ID or keywords:

Entry

Database: PDB / ID: 4pva

Title

Crystal structure of GH62 hydrolase from thermophilic fungus Scytalidium thermophilum

Components

GH62 hydrolase

Keywords

HYDROLASE / Arabinofuranosidase / arabinofuranohydrolase / GH62 hydrolase / fungal genomics / arabinoxylan / lignocellulose degradation

Function / homology

Function and homology information

L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region
Similarity search - Function

Biological species

Scytalidium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.23 Å

Authors

Nocek, B. / Kaur, A.P. / Xu, X. / Cui, H. / Savchenko, A.

Citation

Journal: Microb Biotechnol / Year: 2015
Title: Functional and structural diversity in GH62 alpha-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum.
Authors: Kaur, A.P. / Nocek, B.P. / Xu, X. / Lowden, M.J. / Leyva, J.F. / Stogios, P.J. / Cui, H. / Di Leo, R. / Powlowski, J. / Tsang, A. / Savchenko, A.

History

Deposition	Mar 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2015	Group: Database references
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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	4pva.cif.gz	159.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4pva.ent.gz	123.6 KB	Display	PDB format
PDBx/mmJSON format	4pva.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pva_validation.pdf.gz	437.7 KB	Display	wwPDB validaton report
Full document	4pva_full_validation.pdf.gz	438.1 KB	Display
Data in XML	4pva_validation.xml.gz	22.3 KB	Display
Data in CIF	4pva_validation.cif.gz	33.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/4pva ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pva	HTTPS FTP

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Related structure data

Related structure data	4pvi
Similar structure data	5ag3-1 3cxu-2 4ufp-1 1t1i-d 4y9s-2 4ufn-2 1is9-d 4ufp-2 4uhb-2 3cxu-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

Deposited unit

A: GH62 hydrolase

hetero molecules

39.8 kDa, 1 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)	72.004, 72.004, 61.215
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	GH62 hydrolase Mass: 39198.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytalidium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059U759*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H₂O
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: 2.34 Å³/Da / Density % sol: 47.37 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 2.2 M ammonium di-hydrate phosphate, 12% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.23→28 Å / Num. all: 103224 / Num. obs: 97754 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / R_merge(I) obs: 0.044 / Net I/σ(I): 30
Reflection shell	Resolution: 1.23→1.25 Å / % possible all: 52.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
MLPHARE		phasing
DM		model building
ARP/wARP		model building
CCP4		model building
REFMAC	5.7.0029	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.23→27.49 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.974 / SU B: 1.17 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16211	4442	5 %	RANDOM
R_work	0.14298	-	-	-
obs	0.1439	84561	86.93 %	-
all	-	89003	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.531 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0.06 Å²	0 Å²
2-	-	0.06 Å²	0 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.23→27.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2638	0	31	514	3183

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.02	2816
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2486
X-RAY DIFFRACTION	r_angle_refined_deg	1.897	1.942	3866
X-RAY DIFFRACTION	r_angle_other_deg	1.1	3	5726
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.645	5	344
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.786	24.83	147
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.671	15	402
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.346	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	397
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	3279
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	696
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.233→1.265 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.315	59	-
R_work	0.291	1176	-
obs	-	-	16.32 %

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	1.273	-0.0317	-0.0811	1.2926	-0.2195	0.9703	-0.0406	-0.1354	0.0171	-0.0244	0.0627	-0.1111	-0.0433	0.1106	-0.0221	0.0361	0.0157	-0.0071	0.0896	-0.0061	0.0562	-1.8728	1.0227	2.862
2	3.0248	-0.3539	0.1831	0.1469	0.1956	0.4712	-0.0791	-0.0975	-0.2491	0.0761	0.0306	0.0758	0.1353	0.0074	0.0485	0.055	0.0063	0.0325	0.049	0.0741	0.125	-28.8293	-13.3196	2.7445
3	0.3713	-0.0266	0.0121	0.4824	-0.0982	0.0388	-0.0665	-0.1329	-0.0615	0.0218	0.1267	0.1551	-0.0127	-0.0337	-0.0602	0.0255	0.0316	0.0264	0.0888	0.0649	0.0948	-29.3	1.5084	6.5268
4	1.6682	0.0659	0.3162	2.5573	0.1141	0.0688	-0.1766	-0.3145	-0.1082	0.2573	0.2008	0.3741	-0.0289	-0.0627	-0.0242	0.0549	0.0731	0.0696	0.1426	0.0874	0.1008	-34.5089	5.0312	13.094
5	0.6641	-0.2099	0.1309	0.4121	-0.0329	0.0498	-0.0345	-0.0044	0.0054	-0.0072	0.0479	0.1356	0.014	0.0188	-0.0134	0.045	-0.005	-0.0113	0.0483	0.0107	0.0827	-28.6519	13.3269	-8.5517
6	6.1268	-3.1082	2.1092	20.712	8.0956	5.1168	0.2459	0.6037	0.6429	-0.5021	-0.2219	-0.8281	-0.0953	0.2541	-0.024	0.0488	0.037	0.0199	0.1401	0.0002	0.1277	-16.4505	26.6109	9.0685
7	0.5928	-0.4738	-0.1311	0.4193	0.2192	0.9603	-0.0362	-0.0145	0.0803	0.0114	0.0459	-0.024	-0.0297	0.0399	-0.0098	0.0525	-0.009	-0.0099	0.0567	0.0226	0.0951	-22.9591	18.6261	-5.451
8	0.4548	-0.2053	0.0159	0.5279	0.184	0.6875	-0.0078	-0.0149	0.0128	-0.0213	0.0556	-0.0083	0.0057	0.0423	-0.0478	0.0451	0.0106	0.0063	0.0626	0.0012	0.0484	-12.532	8.3751	-6.4645
9	4.7688	-7.3945	1.6114	12.5682	0.4939	12.9987	0.6158	0.262	-0.0488	-0.8877	-0.5693	-0.2061	0.5812	0.3131	-0.0465	0.1719	0.049	-0.0066	0.1536	0.1199	0.2262	-13.5163	-8.0574	-14.1198
10	1.0094	0.4043	0.1572	1.1612	0.6359	0.376	-0.0061	-0.0212	0.0683	-0.0592	0.0377	0.0001	-0.0154	0.0224	-0.0316	0.0566	-0.0015	0.0144	0.0601	-0.0035	0.0645	-9.0734	9.0734	-6.3333
11	0.4894	-0.1763	0.1063	0.4453	0.0339	0.0598	-0.0202	-0.037	-0.0032	-0.0385	0.0736	-0.0703	-0.0022	0.0132	-0.0534	0.0511	0.0086	0.0032	0.0629	-0.0117	0.078	-7.0261	1.9477	-5.5742
12	4.7202	2.0026	2.755	3.054	-6.0689	25.3839	0.1158	-0.1831	-0.6293	-0.3367	-0.1399	-0.3978	1.2976	0.0776	0.024	0.1684	0.078	0.0798	0.1257	0.1866	0.3167	-14.0224	-15.108	-3.0737
13	0.494	-0.0341	-0.0571	0.667	0.249	0.2067	-0.0499	-0.1201	-0.056	0.025	0.0911	0.0186	0.0116	-0.0091	-0.0412	0.0477	0.0263	0.0048	0.0807	0.0263	0.0491	-15.1907	1.2837	4.5989
14	6.8034	-3.2406	-0.3441	10.0859	1.5046	1.5278	-0.0119	0.5289	-0.4368	-0.3091	0.1011	0.3499	-0.0026	0.1823	-0.0892	0.0577	-0.018	-0.0097	0.0855	-0.0376	0.072	-25.7394	-13.9128	-12.9958
15	2.4167	0.543	1.0963	0.3007	0.44	1.038	-0.0375	-0.0359	-0.1749	0.0275	0.0573	0.0355	0.0214	-0.0084	-0.0197	0.0446	0.0116	0.0086	0.0372	0.0345	0.0775	-19.7407	-8.6377	-1.0844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-7 - 35
2	X-RAY DIFFRACTION	2	A	36 - 52
3	X-RAY DIFFRACTION	3	A	53 - 137
4	X-RAY DIFFRACTION	4	A	138 - 147
5	X-RAY DIFFRACTION	5	A	148 - 177
6	X-RAY DIFFRACTION	6	A	178 - 182
7	X-RAY DIFFRACTION	7	A	183 - 219
8	X-RAY DIFFRACTION	8	A	220 - 254
9	X-RAY DIFFRACTION	9	A	255 - 259
10	X-RAY DIFFRACTION	10	A	260 - 268
11	X-RAY DIFFRACTION	11	A	269 - 294
12	X-RAY DIFFRACTION	12	A	295 - 299
13	X-RAY DIFFRACTION	13	A	300 - 332
14	X-RAY DIFFRACTION	14	A	333 - 338
15	X-RAY DIFFRACTION	15	A	339 - 350

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