PDB-8ag9: Thermogutta terrifontis endoglucanase of glycoside hydrolase fami...

ID or keywords:

Entry

Database: PDB / ID: 8ag9

Title

Thermogutta terrifontis endoglucanase of glycoside hydrolase family 5 (TtEnd5A)

Components

Endoglucanase

Keywords

HYDROLASE / Thermogutta terrifontis endoglucanase of HG5 family / Cellulase / apo structure

Function / homology

Function and homology information

glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function

Biological species

Thermogutta terrifontis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.56 Å

Authors

Hussain, N. / Mikolajek, H. / Naismith, J.H.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: Thermogutta terrifontis endoglucanase of glycoside hydrolase family 5 (TtEnd5A)
Authors: Hussain, N. / Mikolajek, H. / Naismith, J.H.

History

Deposition	Jul 19, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 17, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ag9.cif.gz	98.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8ag9.ent.gz	68.4 KB	Display	PDB format
PDBx/mmJSON format	8ag9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ag9_validation.pdf.gz	424.1 KB	Display	wwPDB validaton report
Full document	8ag9_full_validation.pdf.gz	424.7 KB	Display
Data in XML	8ag9_validation.xml.gz	16.7 KB	Display
Data in CIF	8ag9_validation.cif.gz	25.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ag/8ag9 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8ag9	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

Deposited unit

A: Endoglucanase

hetero molecules

58.8 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)	59.851, 69.442, 81.094
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Endoglucanase Mass: 58481.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This protein was crystalized in degraded form (192-526 amino acids) after nine months. It was never reproducible. Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: pEHISTEV Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A286RCT9, cellulase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.2 Å³/Da
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M (NH4)2SO4 , 0.1 M HEPES Buffer, 25 %w/v PEG 3350 as precipitant, and protein concentration was 0.18 mM

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.56→48.18 Å / Num. obs: 386442 / % possible obs: 70.24 % / Redundancy: 11.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.014 / R_rim(I) all: 0.051 / Net I/σ(I): 32.2
Reflection shell	Resolution: 1.56→1.59 Å / Redundancy: 1.4 % / R_merge(I) obs: 0.371 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 221 / CC_1/2: 0.8 / R_pim(I) all: 0.33 / R_rim(I) all: 0.499 / % possible all: 9.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.56→48.156 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.963 / SU B: 1.358 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1699	1712	4.991 %
R_work	0.1405	32591	-
all	0.142	-	-
obs	-	34303	70.244 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.724 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.453 Å²	0 Å²	-0 Å²
2-	-	-0.515 Å²	0 Å²
3-	-	-	1.969 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→48.156 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2732	0	15	318	3065

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2904
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2515
X-RAY DIFFRACTION	r_angle_refined_deg	1.186	1.637	3976
X-RAY DIFFRACTION	r_angle_other_deg	0.427	1.554	5861
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.628	5	352
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.477	10	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.97	10	446
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.283	10	159
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	404
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3414
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	642
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	553
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	2354
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1389
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1374
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	234
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.176	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	1.86	1.737	1357
X-RAY DIFFRACTION	r_mcbond_other	1.851	1.737	1357
X-RAY DIFFRACTION	r_mcangle_it	2.652	2.596	1699
X-RAY DIFFRACTION	r_mcangle_other	2.655	2.6	1700
X-RAY DIFFRACTION	r_scbond_it	3.338	2.071	1547
X-RAY DIFFRACTION	r_scbond_other	3.323	2.065	1536
X-RAY DIFFRACTION	r_scangle_it	4.899	2.977	2268
X-RAY DIFFRACTION	r_scangle_other	4.879	2.966	2251
X-RAY DIFFRACTION	r_lrange_it	6.137	29.633	3456
X-RAY DIFFRACTION	r_lrange_other	6.047	25.83	3365

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 (%)
1.6-1.644	0.281	39	0.193	721	X-RAY DIFFRACTION	21.8642
1.644-1.692	0.166	45	0.162	997	X-RAY DIFFRACTION	30.7556
1.692-1.744	0.217	52	0.157	1217	X-RAY DIFFRACTION	38.689
1.744-1.801	0.184	62	0.146	1467	X-RAY DIFFRACTION	47.7663
1.801-1.864	0.19	90	0.136	1669	X-RAY DIFFRACTION	57.4086
1.864-1.934	0.182	105	0.123	1955	X-RAY DIFFRACTION	69.058
1.934-2.013	0.151	120	0.126	2457	X-RAY DIFFRACTION	89.7909
2.013-2.103	0.162	134	0.131	2558	X-RAY DIFFRACTION	97.7842
2.103-2.205	0.182	152	0.133	2479	X-RAY DIFFRACTION	99.5083
2.205-2.324	0.177	123	0.133	2388	X-RAY DIFFRACTION	99.4062
2.324-2.465	0.185	117	0.136	2259	X-RAY DIFFRACTION	99.79
2.465-2.634	0.173	129	0.134	2106	X-RAY DIFFRACTION	99.6878
2.634-2.845	0.17	124	0.137	1983	X-RAY DIFFRACTION	99.8105
2.845-3.115	0.172	90	0.138	1843	X-RAY DIFFRACTION	99.8966
3.115-3.481	0.158	88	0.147	1694	X-RAY DIFFRACTION	99.9439
3.481-4.016	0.143	94	0.133	1484	X-RAY DIFFRACTION	99.9367
4.016-4.91	0.122	53	0.128	1290	X-RAY DIFFRACTION	100
4.91-6.908	0.246	56	0.18	1017	X-RAY DIFFRACTION	100
6.908-48.156	0.195	23	0.181	622	X-RAY DIFFRACTION	99.8452

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