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- PDB-4kca: Crystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine R... -

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Basic information

Entry
Database: PDB / ID: 4kca
TitleCrystal Structure of Endo-1,5-alpha-L-arabinanase from a Bovine Ruminal Metagenomic Library
ComponentsEndo-1,5-alpha-L-arabinanase
KeywordsHYDROLASE / beta-propeller / GH43 / glycoside hydrolase / arabinanase
Function / homology
Function and homology information


Lipocalin - #10 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Lipocalin / Glutaredoxin / Glutaredoxin / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSantos, C.R. / Polo, C.C. / Costa, M.C.M.F. / Nascimento, A.F.Z. / Wong, D.W.S. / Murakami, M.T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.
Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. ...Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. / Squina, F.M. / Wong, D.W. / Murakami, M.T.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Endo-1,5-alpha-L-arabinanase
B: Endo-1,5-alpha-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,03669
Polymers152,8102
Non-polymers8,22567
Water15,043835
1
A: Endo-1,5-alpha-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,70836
Polymers76,4051
Non-polymers4,30335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,5-alpha-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,32733
Polymers76,4051
Non-polymers3,92232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.909, 114.318, 167.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-1,5-alpha-L-arabinanase


Mass: 76405.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle)
Description: THE SAMPLE SEQUENCE WAS IDENTIFIED FROM A DNA LIBRARY CONSTRUCTED FROM BOVINE RUMEN FLUID (WONG ET AL., 2008)
Production host: Escherichia coli (E. coli) / References: arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium Malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.429 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.429 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 147570 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.231 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21565 7377 5 %RANDOM
Rwork0.18704 ---
obs0.18846 140105 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20 Å2
2--0.52 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9889 0 77 835 10801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0210175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.94113838
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92551270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44424.664461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.403151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4511534
X-RAY DIFFRACTIONr_chiral_restr0.1450.21466
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217876
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_it2.0272.6165086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9653.9086354
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9382.8315089
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_restr1.852310175
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 528 -
Rwork0.311 9691 -
obs--92.86 %
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)
10.1872-0.015-0.09650.05010.02390.31170.003-0.0364-0.03160.01080.002-0.00740.00130.0311-0.0050.0525-0.00930.01470.03190.00680.018514.079537.564933.8682
20.12910.10220.04040.08460.03990.3533-0.0290.05750.0246-0.02810.05450.0178-0.05710.0158-0.02550.084-0.04190.00740.04720.00610.0113.949260.7657-11.4262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 638
2X-RAY DIFFRACTION1A701 - 735
3X-RAY DIFFRACTION1A801 - 1220
4X-RAY DIFFRACTION2B4 - 640
5X-RAY DIFFRACTION2B701 - 732
6X-RAY DIFFRACTION2B801 - 1215

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