PDB-7mks: Crystal structure of the GH12 domain from Acidothermus cellulolyt...

ID or keywords:

Entry

Database: PDB / ID: 7mks

Title

Crystal structure of the GH12 domain from Acidothermus cellulolyticus GuxA bound to cellobiose

Components

Glycoside hydrolase, family 6

Keywords

HYDROLASE / GH12

Function / homology

Function and homology information

cellulose binding / cellulase activity / cellulose catabolic process
Similarity search - Function

Biological species

Acidothermus cellulolyticus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Lunin, V.V.

Funding support

United States, 1items

Organization	Grant number	Country
Department of Energy (DOE, United States)	Funding provided by the BioEnergy Science Center (BESC) and the Center for Bioenergy Innovation (CBI), from the U.S. Department of Energy Bioenergy Research Centers supported by the Office of Biological and Environmental Research in the DOE Office of Science	United States

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus.
Authors: Hengge, N.N. / Mallinson, S.J.B. / Pason, P. / Lunin, V.V. / Alahuhta, M. / Chung, D. / Himmel, M.E. / Westpheling, J. / Bomble, Y.J.

History

Deposition	Apr 26, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 22, 2022	Group: Database references / Category: citation / citation_author 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
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7mks.cif.gz	77.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7mks_validation.pdf.gz	838.8 KB	Display	wwPDB validaton report
Full document	7mks_full_validation.pdf.gz	839.5 KB	Display
Data in XML	7mks_validation.xml.gz	15.1 KB	Display
Data in CIF	7mks_validation.cif.gz	23.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mk/7mks ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mks	HTTPS FTP

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Related structure data

Related structure data	7mkrC 3b7mS S: Starting model for refinement C: citing same article (ref.)
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	#217 - Jan 2018 Opioid Receptors similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

AAA: Glycoside hydrolase, family 6

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	66.235, 66.235, 127.176
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-306- CL
2	1	AAA-688- HOH

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein

Glycoside hydrolase, family 6 / GuxA

Mass: 25652.828 Da / Num. of mol.: 1 / Fragment: GH12 domain (UNP residues 836-1071)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acidothermus cellulolyticus (bacteria) / Gene: Acel_0615 / Production host:

Caldicellulosiruptor bescii (bacteria) / References: UniProt: A0LSH8

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 6 types, 339 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.14 Å³/Da / Density % sol: 60.82 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 10% PEG8000, 0.2 M zinc chloride, 0.1 M sodium cacodylate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.542 Å
Detector	Type: Bruker Platinum 135 / Detector: CCD / Date: Feb 28, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.542 Å / Relative weight: 1
Reflection	Resolution: 1.85→34.1 Å / Num. obs: 28178 / % possible obs: 99.7 % / Redundancy: 1.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.038 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.85→1.89 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.292 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2727 / CC_1/2: 0.755 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3B7M

3b7m

Resolution: 1.85→34.1 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.95 / SU B: 1.895 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1649	1418	5.035 %
R_work	0.1328	26747	-
all	0.134	-	-
obs	-	28165	99.565 %

Solvent computation

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

Displacement parameters

B_iso mean: 13.253 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.156 Å²	-0.078 Å²	-0 Å²
2-	-	-0.156 Å²	0 Å²
3-	-	-	0.506 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→34.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1773	0	45	328	2146

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	1996
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1659
X-RAY DIFFRACTION	r_angle_refined_deg	1.776	1.651	2763
X-RAY DIFFRACTION	r_angle_other_deg	1.61	1.577	3882
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	15.337	5.235	277
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.094	24.872	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.494	15	262
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	7.112	15	5
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.322	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	290
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2582
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	403
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	327
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	1509
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	907
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	822
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	222
X-RAY DIFFRACTION	r_metal_ion_refined	0.176	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.442	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.344	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.241	0.2	25
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.018	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.307	1.251	1047
X-RAY DIFFRACTION	r_mcbond_other	1.279	1.239	1043
X-RAY DIFFRACTION	r_mcangle_it	1.966	1.855	1329
X-RAY DIFFRACTION	r_mcangle_other	1.965	1.86	1330
X-RAY DIFFRACTION	r_scbond_it	1.901	1.373	949
X-RAY DIFFRACTION	r_scbond_other	1.9	1.374	950
X-RAY DIFFRACTION	r_scangle_it	2.767	2.006	1434
X-RAY DIFFRACTION	r_scangle_other	2.766	2.007	1435
X-RAY DIFFRACTION	r_lrange_it	5.377	15.574	2255
X-RAY DIFFRACTION	r_lrange_other	5.376	15.579	2256

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 (%)
1.85-1.898	0.246	95	0.216	1856	X-RAY DIFFRACTION	95.4034
1.898-1.95	0.196	107	0.162	1916	X-RAY DIFFRACTION	99.8027
1.95-2.006	0.18	99	0.15	1826	X-RAY DIFFRACTION	99.6893
2.006-2.068	0.151	89	0.126	1797	X-RAY DIFFRACTION	99.8941
2.068-2.136	0.159	90	0.125	1759	X-RAY DIFFRACTION	99.9459
2.136-2.211	0.138	98	0.119	1695	X-RAY DIFFRACTION	100
2.211-2.294	0.173	88	0.114	1615	X-RAY DIFFRACTION	99.9413
2.294-2.388	0.161	89	0.118	1580	X-RAY DIFFRACTION	100
2.388-2.493	0.17	70	0.118	1517	X-RAY DIFFRACTION	100
2.493-2.615	0.135	73	0.109	1456	X-RAY DIFFRACTION	100
2.615-2.756	0.177	73	0.118	1391	X-RAY DIFFRACTION	100
2.756-2.923	0.15	71	0.118	1310	X-RAY DIFFRACTION	100
2.923-3.124	0.159	68	0.118	1241	X-RAY DIFFRACTION	100
3.124-3.374	0.159	71	0.12	1147	X-RAY DIFFRACTION	100
3.374-3.694	0.158	76	0.128	1059	X-RAY DIFFRACTION	99.7364
3.694-4.128	0.139	53	0.127	972	X-RAY DIFFRACTION	99.7082
4.128-4.763	0.156	29	0.113	897	X-RAY DIFFRACTION	99.7845
4.763-5.823	0.132	29	0.14	750	X-RAY DIFFRACTION	100
5.823-8.193	0.234	27	0.214	607	X-RAY DIFFRACTION	100
8.193-34.1	0.229	23	0.274	356	X-RAY DIFFRACTION	98.1865

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Protein / Sugars , 2 types, 2 molecules AAA

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