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- PDB-2x8s: Crystal Structure of the Abn2 D171A mutant in complex with arabin... -

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Basic information

Entry
Database: PDB / ID: 2x8s
TitleCrystal Structure of the Abn2 D171A mutant in complex with arabinotriose
ComponentsENDO-ALPHA-1,5-L-ARABINANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / extracellular region / metal ion binding
Similarity search - Function
Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / : / 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 ...Extracellular endo-alpha-(1->5)-L-arabinanase, C-terminal / C-terminal lipocalin-like domain / Lipocalin - #10 / : / 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 / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Extracellular endo-alpha-(1->5)-L-arabinanase 2 / Extracellular endo-alpha-(1->5)-L-arabinanase 2
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsdeSanctis, D. / Inacio, J.M. / Lindley, P.F. / de Sa-Nogueira, I. / Bento, I.
CitationJournal: FEBS J. / Year: 2010
Title: New Evidence for the Role of Calcium in the Glycosidase Reaction of Gh43 Arabinanases.
Authors: De Sanctis, D. / Inacio, J.M. / Lindley, P.F. / De Sa-Nogueira, I. / Bento, I.
History
DepositionMar 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" 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. THE SHEETS PRESENTED AS "BF" 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: ENDO-ALPHA-1,5-L-ARABINANASE
B: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,38519
Polymers105,4762
Non-polymers1,90917
Water12,448691
1
A: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5867
Polymers52,7381
Non-polymers8486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,79912
Polymers52,7381
Non-polymers1,06111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.950, 57.985, 85.595
Angle α, β, γ (deg.)96.14, 91.77, 117.34
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.96281, -0.04159, -0.26695), (-0.0046, 0.99046, -0.13771), (0.27013, -0.13136, -0.95382)
Vector: 37.6219, -2.32137, 89.19862)

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ENDO-ALPHA-1,5-L-ARABINANASE / ENDO-ALPHA- ARABINANASE


Mass: 52738.098 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B3FRL6, UniProt: P42293*PLUS, arabinan endo-1,5-alpha-L-arabinanase
#2: Polysaccharide alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-5LArafa1-5LArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a211h-1a_1-4]/1-1-1/a5-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][a-L-Araf]{[(5+1)][a-L-Araf]{[(5+1)][a-L-Araf]{}}}LINUCSPDB-CARE

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Non-polymers , 8 types, 706 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 171 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 171 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 38.93 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.06725
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06725 Å / Relative weight: 1
ReflectionResolution: 1.5→84.8 Å / Num. obs: 133640 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X8F

2x8f


Resolution: 1.5→24.595 Å / SU ML: 0.21 / σ(F): 2.01 / Phase error: 14.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1666 6372 4.96 %
Rwork0.1473 --
obs0.1482 128476 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.573 Å2 / ksol: 0.375 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→24.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 119 691 7808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177485
X-RAY DIFFRACTIONf_angle_d1.40310165
X-RAY DIFFRACTIONf_dihedral_angle_d18.5912735
X-RAY DIFFRACTIONf_chiral_restr0.1261030
X-RAY DIFFRACTIONf_plane_restr0.0061314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.22922200.19614195X-RAY DIFFRACTION93
1.517-1.53490.20872360.194190X-RAY DIFFRACTION94
1.5349-1.55360.21181930.17894162X-RAY DIFFRACTION93
1.5536-1.57330.19552250.16894210X-RAY DIFFRACTION95
1.5733-1.5940.19142130.1644213X-RAY DIFFRACTION93
1.594-1.61580.19692220.16614235X-RAY DIFFRACTION95
1.6158-1.63890.18852030.1614184X-RAY DIFFRACTION94
1.6389-1.66330.18772090.15274286X-RAY DIFFRACTION95
1.6633-1.68930.18932440.14724188X-RAY DIFFRACTION94
1.6893-1.7170.17122200.14124231X-RAY DIFFRACTION96
1.717-1.74660.14352340.13084266X-RAY DIFFRACTION95
1.7466-1.77840.14932190.13724238X-RAY DIFFRACTION96
1.7784-1.81260.16822140.13584268X-RAY DIFFRACTION95
1.8126-1.84950.15812270.1364245X-RAY DIFFRACTION95
1.8495-1.88970.15072340.13524251X-RAY DIFFRACTION96
1.8897-1.93370.14542420.13474281X-RAY DIFFRACTION96
1.9337-1.9820.16292050.12964299X-RAY DIFFRACTION96
1.982-2.03560.1652220.13324292X-RAY DIFFRACTION97
2.0356-2.09550.15052500.13264271X-RAY DIFFRACTION97
2.0955-2.1630.15821910.13634362X-RAY DIFFRACTION97
2.163-2.24030.15572260.13534331X-RAY DIFFRACTION97
2.2403-2.32990.15142300.144273X-RAY DIFFRACTION97
2.3299-2.43590.17052470.14694312X-RAY DIFFRACTION97
2.4359-2.56420.17881990.15424360X-RAY DIFFRACTION97
2.5642-2.72470.17552340.15784391X-RAY DIFFRACTION98
2.7247-2.93470.15872140.15124356X-RAY DIFFRACTION98
2.9347-3.22950.15722540.1474364X-RAY DIFFRACTION98
3.2295-3.69540.16092340.1334385X-RAY DIFFRACTION98
3.6954-4.65070.13162370.12264384X-RAY DIFFRACTION99
4.6507-24.59840.16512050.14924417X-RAY DIFFRACTION98
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)
10.8195-0.21560.00760.87270.28340.8379-0.0049-0.04710.0083-0.0042-0.03250.0992-0.0121-0.051-00.0428-0.00470.00790.05230.00360.0479-2.1446-10.335831.2645
20.5156-0.0336-0.16560.7048-0.01110.41450.04410.0322-0.1519-0.1318-0.0077-0.20150.10620.1462-00.13390.03480.01350.135-0.01280.145915.7777-28.470919.7325
30.89860.3543-0.10170.6929-0.15130.6372-0.04730.046-0.0151-0.0260.028-0.0376-0.02290.007500.04230.0054-0.00320.03860.00050.036622.78551.19767.1001
40.77680.2822-0.05740.7031-0.02620.219-0.01750.0366-0.096-0.02290.06230.10790.0357-0.035300.0809-0.0031-0.00050.08450.01520.09712.3565-15.815175.6152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 28:350)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 351:470)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 28:350)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 351:470)

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