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- PDB-5fip: Discovery and characterization of a novel thermostable and highly... -

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Basic information

Entry
Database: PDB / ID: 5fip
TitleDiscovery and characterization of a novel thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate
ComponentsGH5 CELLULASE
KeywordsHYDROLASE / CELLULASE / GH5
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / membrane => GO:0016020
Similarity search - Function
Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / 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
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / Chem-PG6 / TRIETHYLENE GLYCOL / Glycoside hydrolase family 5
Similarity search - Component
Biological speciesUNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZarafeta, D. / Kissas, D. / Sayer, C. / Gudbergsdottir, S.R. / Ladoukakis, E. / Isupov, M.N. / Chatziioannou, A. / Peng, X. / Littlechild, J.A. / Skretas, G. / Kolisis, F.N.
CitationJournal: Plos One / Year: 2016
Title: Discovery and Characterization of a Thermostable and Highly Halotolerant Gh5 Cellulase from an Icelandic Hot Spring Isolate.
Authors: Zarafeta, D. / Kissas, D. / Sayer, C. / Gudbergsdottir, S.R. / Ladoukakis, E. / Isupov, M.N. / Chatziioannou, A. / Peng, X. / Littlechild, J.A. / Skretas, G. / Kolisis, F.N.
History
DepositionOct 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH5 CELLULASE
B: GH5 CELLULASE
C: GH5 CELLULASE
D: GH5 CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,43559
Polymers149,0594
Non-polymers4,37555
Water10,539585
1
D: GH5 CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,15113
Polymers37,2651
Non-polymers88712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH5 CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,82221
Polymers37,2651
Non-polymers1,55720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GH5 CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6796
Polymers37,2651
Non-polymers4145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: GH5 CELLULASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,78319
Polymers37,2651
Non-polymers1,51818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.340, 137.450, 121.340
Angle α, β, γ (deg.)90.00, 114.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.02375, 0.76308, 0.64587), (0.75, -0.41357, 0.5162), (0.66101, 0.49666, -0.56249)-27.43462, -6.97969, 49.22709
2given(-0.14718, -0.98101, -0.12633), (-0.97826, 0.12551, 0.16507), (-0.14608, 0.14788, -0.97816)2.37281, -4.38749, 49.48969
3given(-0.82234, 0.17145, -0.54255), (0.24592, -0.75277, -0.61062), (-0.51311, -0.63557, 0.57687)3.25112, 22.46666, 19.07273

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GH5 CELLULASE


Mass: 37264.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ICELANDIC HOT SPRING ISOLATE / Source: (natural) UNIDENTIFIED (others) / References: UniProt: I3VS73*PLUS, cellulase

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Non-polymers , 8 types, 640 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.36 Å3/Da / Density % sol: 47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.88→36.38 Å / Num. obs: 126320 / % possible obs: 97.5 % / Observed criterion σ(I): 1.8 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G01

1g01


Resolution: 1.88→36.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.027 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23393 6406 5.1 %RANDOM
Rwork0.1931 ---
obs0.19519 119914 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.88→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10406 0 279 585 11270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.95615315
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15851439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06925.623530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.633151935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9371542
X-RAY DIFFRACTIONr_chiral_restr0.10.21632
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218540
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.7568.0665409
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.09515.0416784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.4238.8545889
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 467 -
Rwork0.334 8123 -
obs--89.83 %

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