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- PDB-5gm4: Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 in... -

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Basic information

Entry
Database: PDB / ID: 5gm4
TitleCrystal structure of FI-CMCase from Aspergillus aculeatus F-50 in complex with cellotetrose
ComponentsEndoglucanase-1
KeywordsHYDROLASE/INHIBITOR / substrate binding / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cellotetraose / Endoglucanase-1
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHuang, J.W. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Crystal structure and genetic modifications of FI-CMCase from Aspergillus aculeatus F-50
Authors: Huang, J.W. / Liu, W. / Lai, H.L. / Cheng, Y.S. / Zheng, Y. / Li, Q. / Sun, H. / Kuo, C.J. / Guo, R.T. / Chen, C.C.
History
DepositionJul 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase-1
B: Endoglucanase-1
C: Endoglucanase-1
D: Endoglucanase-1
E: Endoglucanase-1
F: Endoglucanase-1
G: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,48022
Polymers166,0467
Non-polymers5,43515
Water21,3841187
1
A: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers23,7211
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9100 Å2
MethodPISA
2
B: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers23,7211
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9170 Å2
MethodPISA
3
C: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers23,7211
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-13 kcal/mol
Surface area9190 Å2
MethodPISA
4
D: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers23,7211
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9160 Å2
MethodPISA
5
E: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6765
Polymers23,7211
Non-polymers9554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9110 Å2
MethodPISA
6
F: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3872
Polymers23,7211
Non-polymers6671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9170 Å2
MethodPISA
7
G: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4833
Polymers23,7211
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.907, 85.278, 106.025
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endoglucanase-1 / Cellulase / Endo-1 / 4-beta-glucanase / Endoglucanase I / FI-CMCase


Mass: 23720.842 Da / Num. of mol.: 7 / Fragment: UNP residues 19-237 / Mutation: E202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P22669, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.56 % / Mosaicity: 0.573 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: lithium sulfate, HEPES, zinc acetate,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→25 Å / Num. obs: 118911 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.037 / Rrim(I) all: 0.075 / Χ2: 1.348 / Net I/av σ(I): 28.671 / Net I/σ(I): 11.6 / Num. measured all: 480843
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.92-1.9940.4050.8881100
1.99-2.074.10.2880.9471100
2.07-2.164.10.2160.9661100
2.16-2.284.10.1620.9821100
2.28-2.424.10.1310.9861100
2.42-2.614.10.10.9911100
2.61-2.874.10.0740.9941100
2.87-3.284.10.0550.9961100
3.28-4.133.90.050.996199.8
4.13-253.90.0370.998199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KS4

1ks4


Resolution: 1.92→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.435 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 5636 4.7 %RANDOM
Rwork0.1556 ---
obs0.158 113259 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 29.236 Å2 / Biso min: 14.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å21.45 Å2
2--1.13 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11740 0 355 1187 13282
Biso mean--36.08 36.13 -
Num. residues----1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212458
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210718
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9317100
X-RAY DIFFRACTIONr_angle_other_deg0.723324694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85751522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92124.935539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.193151666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8151521
X-RAY DIFFRACTIONr_chiral_restr0.0980.21929
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214245
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023076
X-RAY DIFFRACTIONr_mcbond_it3.2572.7456109
X-RAY DIFFRACTIONr_mcbond_other3.2552.7456108
X-RAY DIFFRACTIONr_mcangle_it3.9544.17624
LS refinement shellResolution: 1.922→1.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 434 -
Rwork0.212 8288 -
all-8722 -
obs--99.65 %

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