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- PDB-1gyh: Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant -

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Basic information

Entry
Database: PDB / ID: 1gyh
TitleStructure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant
ComponentsARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
KeywordsHYDROLASE / ARABINANASE / PROPELLER / CATALYSIS / CELLVIBRIO / PSEUDOMONAS
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 43, endo-1, 5-alpha-L-arabinosidase / : / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Extracellular exo-alpha-(1->5)-L-arabinofuranosidase ArbA
Similarity search - Component
Biological speciesCELLVIBRIO CELLULOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsNurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has a Novel Five-Blade Beta-Propeller Fold
Authors: Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / Mckie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J.
History
DepositionApr 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
B: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
C: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
D: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
E: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
F: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,09212
Polymers216,8796
Non-polymers2136
Water34,4091910
1
A: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1822
Polymers36,1471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.556, 79.557, 132.402
Angle α, β, γ (deg.)88.83, 89.58, 83.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A / ALPHA-L-ARABINANASE / ABN A / ENDO-1 / 5-ALPHA-L-ARABINANASE A


Mass: 36146.512 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION ASP 158 ALA / Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PVM1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): Tuner
References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1910 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION: ASP 158 ALA
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: 2.2 Å3/Da / Density % sol: 42.9 %
Crystal growpH: 6.5
Details: 18% PEG5000 MME, 4% AMMONIUM SULFATE, 100MM NA-CACODYLATE PH6.5, 20% GLYCEROL, pH 6.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 %(w/v)PEG5000 MME11
24 %(w/v)ammonium sulfate11
3100 mMsodium cacodylate11pH6.5
420 %(v/v)glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 155379 / % possible obs: 97.4 % / Redundancy: 1.89 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.37
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.08 / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Redundancy: 1.9 %
Reflection shell
*PLUS
% possible obs: 89.8 % / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAP FROM AN A P6522 CRYSTAL FORM SOLVED BY MAD

Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.191 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 730 0.5 %RANDOM
Rwork0.147 ---
obs0.147 154093 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.44 Å2-0.34 Å2
2---1.25 Å20.48 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15319 0 6 1910 17235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02115900
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213752
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.92621600
X-RAY DIFFRACTIONr_angle_other_deg1.484332043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00251897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.22187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217815
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023467
X-RAY DIFFRACTIONr_nbd_refined0.1920.22252
X-RAY DIFFRACTIONr_nbd_other0.2570.214879
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.27985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.21180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.2170
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.272
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3111.59426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.899215126
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.92936472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0894.56469
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: 1.89→1.94 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 40
Rwork0.164 9799
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79460.16270.43441.6837-0.20470.72130.0191-0.0423-0.0381-0.03620.0168-0.01460.0167-0.1136-0.03590.02090.00830.03250.0853-0.03790.11830.1420.079-0.053
21.6556-0.77370.23151.5023-0.12681.44610.05950.1543-0.1184-0.0318-0.08670.01140.07620.04730.02730.0103-0.00790.03840.178-0.03790.143419.7598.53789.472
30.30490.2139-0.07122.8554-0.29741.05440.041-0.04670.02470.212-0.0878-0.0779-0.1399-0.00520.04680.1481-0.0384-0.02710.0633-0.01560.141415.87439.10422.25
42.1272-0.8712-0.93311.8950.02421.73580.22550.08890.4208-0.2336-0.0209-0.0355-0.4617-0.1665-0.20460.26290.05880.03660.0755-0.03130.25442.63740.787112.308
50.67860.2172-0.29172.8583-1.72452.3237-0.0209-0.0836-0.07370.2958-0.1489-0.188-0.14150.17160.16980.1407-0.0505-0.05450.1150.01830.164620.0921.03643.191
61.8317-0.24930.63551.8385-1.01921.33110.13350.42510.32720.0046-0.0710.2015-0.1539-0.0201-0.06250.15440.13660.12340.50570.23160.277252.6441.43266.036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 346
2X-RAY DIFFRACTION2B31 - 346
3X-RAY DIFFRACTION3C31 - 346
4X-RAY DIFFRACTION4D31 - 346
5X-RAY DIFFRACTION5E31 - 346
6X-RAY DIFFRACTION6F31 - 346
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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