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- PDB-2x8f: Native structure of Endo-1,5-alpha-L-arabinanases from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 2x8f
TitleNative structure of Endo-1,5-alpha-L-arabinanases from Bacillus subtilis
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 / Lipocalin ...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 / SAD / Resolution: 1.9 Å
Authorsde Sanctis, 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 9, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_symmetry / _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 "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)107,12223
Polymers105,4802
Non-polymers1,64121
Water10,575587
1
A: ENDO-ALPHA-1,5-L-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50011
Polymers52,7401
Non-polymers76010
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)53,62212
Polymers52,7401
Non-polymers88211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.975, 57.645, 86.272
Angle α, β, γ (deg.)82.31, 87.97, 63.66
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.96568, -0.03475, 0.25738), (-0.00069, 0.99135, 0.13127), (-0.25972, 0.12659, -0.95735)
Vector: -36.06733, 2.37353, 98.11938)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52740.027 Da / Num. of mol.: 2
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

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Non-polymers , 8 types, 608 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.46 % / Description: NONE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→84.5 Å / Num. obs: 67116 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→19.62 Å / SU ML: 0.6 / σ(F): 0.85 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 3232 5.1 %
Rwork0.141 --
obs0.143 63738 85.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.76 Å2 / ksol: 0.41 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7002 0 100 587 7689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157476
X-RAY DIFFRACTIONf_angle_d1.47110139
X-RAY DIFFRACTIONf_dihedral_angle_d19.1632720
X-RAY DIFFRACTIONf_chiral_restr0.1111025
X-RAY DIFFRACTIONf_plane_restr0.0071303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.23491430.16952761X-RAY DIFFRACTION61
1.9216-1.94420.21171500.16562955X-RAY DIFFRACTION67
1.9442-1.96780.20131450.16863430X-RAY DIFFRACTION77
1.9678-1.99270.23372170.15863794X-RAY DIFFRACTION84
1.9927-2.01890.21591480.15173743X-RAY DIFFRACTION85
2.0189-2.04660.21642110.14523816X-RAY DIFFRACTION86
2.0466-2.07580.18742230.13683873X-RAY DIFFRACTION86
2.0758-2.10670.17662040.14073744X-RAY DIFFRACTION86
2.1067-2.13960.18211890.13293858X-RAY DIFFRACTION87
2.1396-2.17460.19622410.1343793X-RAY DIFFRACTION86
2.1746-2.21210.17672310.13123831X-RAY DIFFRACTION87
2.2121-2.25220.18872120.13283811X-RAY DIFFRACTION87
2.2522-2.29550.18141880.1273889X-RAY DIFFRACTION87
2.2955-2.34230.17731990.13133880X-RAY DIFFRACTION88
2.3423-2.39310.18442190.13013871X-RAY DIFFRACTION87
2.3931-2.44870.17432240.12833865X-RAY DIFFRACTION88
2.4487-2.50980.17192220.13863920X-RAY DIFFRACTION88
2.5098-2.57750.20621860.1443827X-RAY DIFFRACTION88
2.5775-2.65320.18682390.1433935X-RAY DIFFRACTION89
2.6532-2.73860.19561900.13774000X-RAY DIFFRACTION88
2.7386-2.83620.19362060.14453855X-RAY DIFFRACTION89
2.8362-2.94940.18772390.14593903X-RAY DIFFRACTION89
2.9494-3.08320.20731960.13813997X-RAY DIFFRACTION89
3.0832-3.2450.16311790.13824010X-RAY DIFFRACTION89
3.245-3.44730.16681870.12843984X-RAY DIFFRACTION89
3.4473-3.71180.14872280.12733907X-RAY DIFFRACTION90
3.7118-4.08230.1392040.12333979X-RAY DIFFRACTION89
4.0823-4.66610.13432150.12013842X-RAY DIFFRACTION88
4.6661-5.85280.16192300.13793750X-RAY DIFFRACTION84
5.8528-19.62190.17232200.17254116X-RAY DIFFRACTION93
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)
10.6572-0.1540.00480.5688-0.15440.68480.0007-0.0041-0.0099-0.0147-0.0166-0.05020.00250.036500.1363-0.0042-0.00080.1314-0.00790.13023.106917.817635.7234
20.78190.1805-0.00480.49240.08260.4997-0.01480.00520.0019-0.00310.00320.01840.017-0.0112-00.1271-0.00080.00220.10990.00290.1246-21.63046.140971.9465
30.4971-0.05540.17840.6815-0.09180.35560.04030.03290.1199-0.1006-0.01630.1534-0.1017-0.1293-00.2030.03680.00140.20590.01330.2049-15.035936.094924.5064
40.71020.10850.09640.53530.03940.2401-0.00250.00790.08120.01250.03-0.06-0.01740.0351-00.1621-0.00680.00150.1563-0.00310.1625-1.314623.392580.2583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 28:350)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 28:350)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 351:469)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 351:469)

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