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- PDB-3qr3: Crystal Structure of Cel5A (EG2) from Hypocrea jecorina (Trichode... -

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Basic information

Entry
Database: PDB / ID: 3qr3
TitleCrystal Structure of Cel5A (EG2) from Hypocrea jecorina (Trichoderma reesei)
ComponentsEndoglucanase EG-II
KeywordsHYDROLASE / Tim Barrel / Endoglucanase
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) ...CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsLee, T.M. / Farrow, M.F. / Kaiser, J.T. / Arnold, F.H. / Mayo, S.L.
CitationJournal: Protein Sci. / Year: 2011
Title: A structural study of Hypocrea jecorina Cel5A.
Authors: Lee, T.M. / Farrow, M.F. / Arnold, F.H. / Mayo, S.L.
History
DepositionFeb 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Endoglucanase EG-II
B: Endoglucanase EG-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,62020
Polymers73,1782
Non-polymers1,44218
Water9,062503
1
A: Endoglucanase EG-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,50212
Polymers36,5891
Non-polymers91311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase EG-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1188
Polymers36,5891
Non-polymers5297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.953, 84.593, 90.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:72 )
211chain B and (resseq 1:72 )
112chain A and (resseq 74:98 )
212chain B and (resseq 74:98 )
113chain A and (resseq 100:327 )
213chain B and (resseq 100:327 )

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.999999, -0.000893, -0.001316), (-0.000914, -0.999872, -0.015986), (-0.001302, 0.015988, -0.999871)-41.404701, 84.738602, 24.535999
2given(0.999971, 0.000889, 0.007513), (0.00106, -0.999742, -0.022693), (0.00749, 0.0227, -0.999714)-41.620201, 84.681702, 23.655001
3given(0.999996, -0.002926, 0.000319), (-0.002922, -0.999908, -0.013247), (0.000358, 0.013246, -0.999912)-41.298199, 84.840103, 24.594801
DetailsBIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

#1: Protein Endoglucanase EG-II / EGLII / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 36589.031 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Gene: Cel5A, egl2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07982, cellulase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate, 1 M Magnesium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2011 / Details: Rh coated mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→39.77 Å / Num. all: 40013 / Num. obs: 40013 / % possible obs: 98.8 % / Redundancy: 12.5 % / Rsym value: 0.081 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.05-2.169.80.2682.80.268192.4
2.16-2.2913.30.2173.40.217199.9
2.29-2.4512.90.1694.20.169199.9
2.45-2.6513.20.1375.10.1371100
2.65-2.913.20.10660.106199.9
2.9-3.2412.70.0837.10.083199.9
3.24-3.74130.0638.70.0631100
3.74-4.5812.60.049100.0491100
4.58-6.4812.50.05100.05199.9
6.48-39.76712.10.0411.80.04199.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2.05→39.767 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.969 / SU ML: 0.24 / σ(F): 1.41 / Phase error: 26.7 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2048 1968 4.94 %
Rwork0.1631 --
obs0.1652 39858 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.326 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.7709 Å20 Å2-0 Å2
2--14.0092 Å20 Å2
3----5.2383 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4966 0 74 503 5543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075182
X-RAY DIFFRACTIONf_angle_d0.9877081
X-RAY DIFFRACTIONf_dihedral_angle_d17.9441731
X-RAY DIFFRACTIONf_chiral_restr0.072771
X-RAY DIFFRACTIONf_plane_restr0.003927
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A560X-RAY DIFFRACTIONPOSITIONAL
12B560X-RAY DIFFRACTIONPOSITIONAL0.028
21A177X-RAY DIFFRACTIONPOSITIONAL
22B177X-RAY DIFFRACTIONPOSITIONAL0.026
31A1718X-RAY DIFFRACTIONPOSITIONAL
32B1718X-RAY DIFFRACTIONPOSITIONAL0.023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.26631240.20632242X-RAY DIFFRACTION84
2.1013-2.15810.22821500.17442687X-RAY DIFFRACTION100
2.1581-2.22160.27641310.16592731X-RAY DIFFRACTION100
2.2216-2.29340.21041540.16152678X-RAY DIFFRACTION100
2.2934-2.37530.23971270.15452722X-RAY DIFFRACTION100
2.3753-2.47040.23881330.16792690X-RAY DIFFRACTION99
2.4704-2.58280.24011330.16412735X-RAY DIFFRACTION100
2.5828-2.7190.22731420.16262708X-RAY DIFFRACTION100
2.719-2.88930.2071370.16692738X-RAY DIFFRACTION100
2.8893-3.11230.22241510.17162734X-RAY DIFFRACTION99
3.1123-3.42530.19251430.17232748X-RAY DIFFRACTION100
3.4253-3.92060.16481310.14822785X-RAY DIFFRACTION100
3.9206-4.9380.14861540.12522779X-RAY DIFFRACTION100
4.938-39.77490.17061580.16072913X-RAY DIFFRACTION100

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