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- PDB-4zg8: Crystal structure of Endoglucanase from Perinereis brevicirris -

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Basic information

Entry
Database: PDB / ID: 4zg8
TitleCrystal structure of Endoglucanase from Perinereis brevicirris
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / Cellulase / Endoglucanase / Polychaete / Annelid
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
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 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase ...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 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPerinereis brevicirris (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsFewings, R.S. / Swiderska, A. / Sanchez-Weatherby, J. / Sorensen, T.L.-M. / Schnorr, K.M. / Kneale, G.G. / McGeehan, J.E.
CitationJournal: To Be Published
Title: Biophysical and structural characterisation of the endoglucanase from Perinereis brevicirris
Authors: Fewings, R.S.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,51114
Polymers93,6302
Non-polymers88112
Water19,4201078
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1567
Polymers46,8151
Non-polymers3416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3557
Polymers46,8151
Non-polymers5406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.600, 110.340, 113.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endoglucanase / Cellulase


Mass: 46814.984 Da / Num. of mol.: 2 / Fragment: UNP residues 19-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Perinereis brevicirris (invertebrata) / Gene: pnbEG / Production host: Aspergillus oryzae (mold) / References: UniProt: F2Z7L1, cellulase

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Non-polymers , 5 types, 1090 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1078 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100 mM Bis-Tris, pH5.5, 300 mM NaCl 25% PEG 3350 / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→22.41 Å / Num. obs: 188755 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.7 / Num. measured all: 906572 / Scaling rejects: 148
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
1.39-1.414.80.82.24440292820.69799.9
7.62-22.415.20.05520.6653712460.99196.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.08 Å22.41 Å
Translation6.08 Å22.41 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WC3

3wc3


Resolution: 1.39→22.41 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.136 / WRfactor Rwork: 0.1051 / FOM work R set: 0.8998 / SU B: 2.037 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0415 / SU Rfree: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1479 9289 4.9 %RANDOM
Rwork0.1098 ---
obs0.1117 179248 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.44 Å2 / Biso mean: 17.625 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--2.72 Å2-0 Å2
3----1.92 Å2
Refinement stepCycle: final / Resolution: 1.39→22.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 51 1078 7732
Biso mean--33.48 34.7 -
Num. residues----851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197042
X-RAY DIFFRACTIONr_bond_other_d0.0020.026091
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9289646
X-RAY DIFFRACTIONr_angle_other_deg1.067314024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29224.409372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5915979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3891542
X-RAY DIFFRACTIONr_chiral_restr0.1160.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021786
X-RAY DIFFRACTIONr_mcbond_it1.8691.4693502
X-RAY DIFFRACTIONr_mcbond_other1.8651.4683501
X-RAY DIFFRACTIONr_mcangle_it2.1632.2184406
X-RAY DIFFRACTIONr_rigid_bond_restr2.654313133
X-RAY DIFFRACTIONr_sphericity_free41.4375286
X-RAY DIFFRACTIONr_sphericity_bonded14.951513716
LS refinement shellResolution: 1.391→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 714 -
Rwork0.223 13142 -
all-13856 -
obs--99.7 %

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