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- PDB-1gyd: Structure of Cellvibrio cellulosa alpha-L-arabinanase -

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Basic information

Entry
Database: PDB / ID: 1gyd
TitleStructure of Cellvibrio cellulosa alpha-L-arabinanase
ComponentsARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
KeywordsARABINANASE / HYDROLASE / 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: 2.05 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: Cellvibrio japonicus 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant / _struct.title
Revision 1.3May 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A


Theoretical massNumber of molelcules
Total (without water)35,9331
Polymers35,9331
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.078, 90.078, 177.217
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: 35933.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO CELLULOSA (bacteria) / Plasmid: PVM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growpH: 8
Details: 10% PEG8000 100MM TRIS-HCL PH8.0, 20% GLYCEROL, pH 8.00
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG800011
2100 mMTris-HCl11pH8.0
320 %(v/v)glycerol11
420 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 27420 / % possible obs: 99.9 % / Redundancy: 6.77 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.95 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.27 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 6.7 %
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRICLINIC STRUCTURE PREVIOUSLY SOLVED

Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.895 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 869 3.2 %RANDOM
Rwork0.205 ---
obs0.207 26420 99.9 %-
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: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å21.47 Å20 Å2
2--2.93 Å20 Å2
3----4.4 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 184 2728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212653
X-RAY DIFFRACTIONr_bond_other_d0.0020.022278
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9273604
X-RAY DIFFRACTIONr_angle_other_deg1.84435313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9315314
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_restr0.0870.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022972
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02578
X-RAY DIFFRACTIONr_nbd_refined0.1850.2436
X-RAY DIFFRACTIONr_nbd_other0.2480.22666
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.21435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4480.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5911.51564
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03122511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61431089
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4224.51091
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: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 68
Rwork0.279 1871
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)
13.5193-0.5085-0.21522.1379-1.45961.66120.0127-1.29260.15970.4009-0.11090.5623-0.1693-1.06290.09820.14250.10970.04981.0366-0.20170.385656.900533.709857.6413
21.9277-0.3786-0.19272.31091.84076.7761-0.1238-0.7560.35710.0517-0.18670.4624-0.5477-1.31840.31050.08070.1844-0.06130.5953-0.21640.37159.233737.788845.2345
32.69810.38811.5271.43750.57244.2069-0.2106-0.42440.3361-0.12290.01040.0403-0.5389-0.50930.20020.02970.0625-0.04260.1399-0.06340.198473.096334.379939.7392
43.81790.072.33811.11010.20944.15350.1169-0.8265-0.38180.1589-0.04430.0410.3603-0.6396-0.07270.0068-0.04030.00630.28670.05360.184276.871823.428449.5754
55.45331.33721.46111.7831-0.32931.80560.1221-1.3843-0.28930.3879-0.03650.20210.2778-0.7741-0.08560.1551-0.060.06550.88060.08050.243668.943323.227662.3007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B31 - 83
2X-RAY DIFFRACTION2B84 - 152
3X-RAY DIFFRACTION3B153 - 211
4X-RAY DIFFRACTION4B212 - 285
5X-RAY DIFFRACTION5B286 - 346
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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