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- PDB-6gjf: Ancestral endocellulase Cel5A -

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Basic information

Entry
Database: PDB / ID: 6gjf
TitleAncestral endocellulase Cel5A
ComponentsENDOGLUCANASECellulase
KeywordsHYDROLASE / ancestral reconstructed / cellulase
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGavira, J.A. / Perez-Jimenez, R. / Barruetabena-Garate, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-74875-P Spain
CitationJournal: Commun Chem / Year: 2019
Title: Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis
Authors: Barruetabena-Garate, N. / Alonso-Lerma, B. / Galera-Prat, A. / Joudeh, N. / Barandiaran, L. / Aldazabal, L. / Arbulu, M. / Alcalde, M. / De Sancho, D. / Gavira, J.A. / Carrion-Vazquez, M. / Perez-Jimenez, R.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE
B: ENDOGLUCANASE
C: ENDOGLUCANASE
D: ENDOGLUCANASE
E: ENDOGLUCANASE
F: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,81640
Polymers201,7226
Non-polymers2,09434
Water37,4172077
1
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,29711
Polymers33,6201
Non-polymers67710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9757
Polymers33,6201
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8905
Polymers33,6201
Non-polymers2694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8205
Polymers33,6201
Non-polymers2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0378
Polymers33,6201
Non-polymers4167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7974
Polymers33,6201
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.436, 235.636, 74.562
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
ENDOGLUCANASE / Cellulase


Mass: 33620.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: ancestral reconstructed / Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: cellulase

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Non-polymers , 5 types, 2111 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2077 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris hydrochloride pH 8.5, 30% w/v PEG 4K
PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→71.08 Å / Num. obs: 310126 / % possible obs: 99.43 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06782 / Rpim(I) all: 0.04339 / Rrim(I) all: 0.08074 / Net I/σ(I): 9.79
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4738 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 30944 / CC1/2: 0.787 / Rpim(I) all: 0.3056 / Rrim(I) all: 0.5655 / % possible all: 99.29

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pzv

3pzv


Resolution: 1.45→71.08 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.29
RfactorNum. reflection% reflection
Rfree0.1532 15359 4.95 %
Rwork0.118 --
obs0.1197 310076 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 32.57 Å2
Displacement parametersBiso mean: 19.71 Å2
Refinement stepCycle: LAST / Resolution: 1.45→71.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14226 0 131 2080 16437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815755
X-RAY DIFFRACTIONf_angle_d1.01321531
X-RAY DIFFRACTIONf_dihedral_angle_d14.9745854
X-RAY DIFFRACTIONf_chiral_restr0.0792193
X-RAY DIFFRACTIONf_plane_restr0.0072871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.24675520.18559855X-RAY DIFFRACTION99
1.4665-1.48370.24664960.17299732X-RAY DIFFRACTION99
1.4837-1.50180.21634950.15389808X-RAY DIFFRACTION99
1.5018-1.52080.2055410.15219811X-RAY DIFFRACTION99
1.5208-1.54090.22734860.15119801X-RAY DIFFRACTION99
1.5409-1.5620.2135280.14739727X-RAY DIFFRACTION99
1.562-1.58430.17815490.13539741X-RAY DIFFRACTION99
1.5843-1.60790.1875070.12779879X-RAY DIFFRACTION99
1.6079-1.63310.19584950.13039721X-RAY DIFFRACTION99
1.6331-1.65980.19045140.1269951X-RAY DIFFRACTION99
1.6598-1.68850.18434610.11869758X-RAY DIFFRACTION99
1.6885-1.71920.17265110.11519876X-RAY DIFFRACTION100
1.7192-1.75220.16985140.11399736X-RAY DIFFRACTION99
1.7522-1.7880.17094920.11539877X-RAY DIFFRACTION100
1.788-1.82690.17035510.1179845X-RAY DIFFRACTION100
1.8269-1.86940.16925000.11689788X-RAY DIFFRACTION100
1.8694-1.91610.16195340.10799868X-RAY DIFFRACTION99
1.9161-1.96790.15625190.10829710X-RAY DIFFRACTION99
1.9679-2.02590.1535440.10569825X-RAY DIFFRACTION100
2.0259-2.09130.14595190.10869795X-RAY DIFFRACTION100
2.0913-2.1660.14714670.10369923X-RAY DIFFRACTION100
2.166-2.25270.14435090.10689901X-RAY DIFFRACTION100
2.2527-2.35530.15065450.10759763X-RAY DIFFRACTION100
2.3553-2.47940.13014970.19868X-RAY DIFFRACTION100
2.4794-2.63480.12854740.1039850X-RAY DIFFRACTION100
2.6348-2.83820.14254850.11189902X-RAY DIFFRACTION99
2.8382-3.12390.14675230.11699804X-RAY DIFFRACTION100
3.1239-3.57590.13535140.12339861X-RAY DIFFRACTION100
3.5759-4.50510.1265040.10969876X-RAY DIFFRACTION99
4.5051-71.16910.14845330.14079865X-RAY DIFFRACTION99

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