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- PDB-5gm3: Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 -

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Basic information

Entry
Database: PDB / ID: 5gm3
TitleCrystal structure of FI-CMCase from Aspergillus aculeatus F-50
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
CACODYLATE ION / Endoglucanase-1
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,62914
Polymers47,5582
Non-polymers1,07112
Water10,521584
1
A: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3808
Polymers23,7791
Non-polymers6017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2496
Polymers23,7791
Non-polymers4705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.215, 75.089, 188.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 4 - 220 / Label seq-ID: 2 - 218

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.033906, -0.997237, 0.066094), (-0.992271, -0.025691, 0.121401), (-0.119367, -0.069699, -0.990401)-30.82667, -68.006622, -56.113369

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Components

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


Mass: 23778.877 Da / Num. of mol.: 2 / Fragment: UNP residues 19-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: P22669, cellulase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.42 % / Mosaicity: 0.425 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium cacodylate, PEG 8000, 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: Sep 27, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→25 Å / Num. obs: 70687 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/av σ(I): 27.317 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.6-1.666.40.4590.904197.3
1.66-1.726.80.3650.9421100
1.72-1.86.80.2730.9651100
1.8-1.96.80.2120.9771100
1.9-2.026.60.1550.9861100
2.02-2.176.50.1170.991199.9
2.17-2.396.40.0990.9931100
2.39-2.746.40.0840.994199.9
2.74-3.446.10.0630.996199.8
3.44-256.40.0470.998199.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KS4

1ks4


Resolution: 1.59→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.367 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3644 5.2 %RANDOM
Rwork0.157 ---
obs0.1587 66978 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.39 Å2 / Biso mean: 20.211 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0 Å2-0 Å2
2---0.46 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: final / Resolution: 1.59→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 28 584 3975
Biso mean--26.93 31.28 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023479
X-RAY DIFFRACTIONr_bond_other_d00.023031
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9014765
X-RAY DIFFRACTIONr_angle_other_deg0.70236951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5925435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80625156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20715480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.444156
X-RAY DIFFRACTIONr_chiral_restr0.1020.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.024079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02879
X-RAY DIFFRACTIONr_mcbond_it2.3091.7811746
X-RAY DIFFRACTIONr_mcbond_other2.3091.7811745
X-RAY DIFFRACTIONr_mcangle_it2.932.6582179
Refine LS restraints NCSNumber: 1669 / Type: TIGHT THERMAL / Rms dev position: 2.75 Å / Weight position: 0.5
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 280 -
Rwork0.238 4626 -
all-4906 -
obs--94.77 %

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