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- PDB-4cj0: Crystal structure of CelD in complex with affitin E12 -

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Basic information

Entry
Database: PDB / ID: 4cj0
TitleCrystal structure of CelD in complex with affitin E12
Components
  • E12 AFFITIN
  • ENDOGLUCANASE DCellulase
KeywordsHYDROLASE/DE NOVO PROTEIN / HYDROLASE-DE NOVO PROTEIN COMPLEX / GLYCOSIDASE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Clostridium cellulosome enzymes repeated domain signature. ...Glycosyl hydrolases family 9 (GH9) active site signature 1. / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9, His active site / Glycosyl hydrolases family 9 (GH9) active site signature 2. / Glycosyl hydrolases family 9, Asp/Glu active sites / Glycosyl hydrolases family 9 (GH9) active site signature 3. / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCorrea, A. / Pacheco, S. / Mechaly, A.E. / Obal, G. / Behar, G. / Mouratou, B. / Oppezzo, P. / Alzari, P.M. / Pecorari, F.
CitationJournal: Plos One / Year: 2014
Title: Potent and Specific Inhibition of Glycosidases by Small Artificial Binding Proteins (Affitins)
Authors: Correa, A. / Pacheco, S. / Mechaly, A.E. / Obal, G. / Behar, G. / Mouratou, B. / Oppezzo, P. / Alzari, P.M. / Pecorari, F.
History
DepositionDec 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2May 16, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE D
B: E12 AFFITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,79712
Polymers79,0592
Non-polymers73810
Water15,601866
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-45.6 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.633, 87.633, 97.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ENDOGLUCANASE D / Cellulase / EGD / CELD / CELLULASE D / ENDO-1 / 4-BETA-GLUCANASE


Mass: 69774.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: P0C2S4, cellulase
#2: Protein E12 AFFITIN


Mass: 9284.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 4 types, 876 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.81 Å3/Da / Density % sol: 56.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Type: ESRF / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→48.71 Å / Num. obs: 292047 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLC

1clc


Resolution: 1.1→43.85 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.536 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.12546 14749 5.1 %RANDOM
Rwork0.10679 ---
obs0.10773 277269 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.1→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 40 866 5585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194871
X-RAY DIFFRACTIONr_bond_other_d0.0050.024400
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9316628
X-RAY DIFFRACTIONr_angle_other_deg1.839310105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92524.351239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47715743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6351523
X-RAY DIFFRACTIONr_chiral_restr0.1460.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025640
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021191
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr9.77139271
X-RAY DIFFRACTIONr_sphericity_free34.2775217
X-RAY DIFFRACTIONr_sphericity_bonded15.86959800
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 1127 -
Rwork0.169 20011 -
obs--96.4 %
Refinement TLS params.

T23: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.001-0.00010.00020.0009-0.00010.0005-0.000100000-0.0001000.002200.00010.002208.092849.7716-1.2032
20.25960.00410.14290.00130.00450.0826-0.0162-0.01220.03190.001-0.00120.0007-0.0063-0.00760.01750.0038-0.0003-0.00170.00490.00468.925971.874116.4684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 575
2X-RAY DIFFRACTION2B2 - 66

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