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- PDB-2x8t: Crystal Structure of the Abn2 H318A mutant -

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Basic information

Entry
Database: PDB / ID: 2x8t
TitleCrystal Structure of the Abn2 H318A mutant
ComponentsENDO-ALPHA-1,5-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
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: 1.79 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 1.3Sep 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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-ARABINANASE
B: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,26312
Polymers105,5722
Non-polymers69110
Water8,809489
1
A: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0725
Polymers52,7861
Non-polymers2864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-ALPHA-1,5-ARABINANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1917
Polymers52,7861
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 57.370, 85.480
Angle α, β, γ (deg.)82.10, 88.21, 63.61
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52786.117 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

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Non-polymers , 7 types, 499 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 318 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 318 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: 2.13 Å3/Da / Density % sol: 42.36 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / Details: 65% MPD 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.79→46.5 Å / Num. obs: 76283 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 13.42 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.7
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 72.2

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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: 1.79→31.79 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3664 5.1 %
Rwork0.158 --
obs0.16 72418 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.18 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0122 Å20.6967 Å2-2.2925 Å2
2---2.497 Å2-3.5842 Å2
3---3.5092 Å2
Refinement stepCycle: LAST / Resolution: 1.79→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6999 0 39 489 7527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017404
X-RAY DIFFRACTIONf_angle_d1.18510059
X-RAY DIFFRACTIONf_dihedral_angle_d17.8652652
X-RAY DIFFRACTIONf_chiral_restr0.0891034
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7933-1.81370.29681470.24692402X-RAY DIFFRACTION47
1.8137-1.8350.23221810.21133448X-RAY DIFFRACTION67
1.835-1.85740.25851850.21243878X-RAY DIFFRACTION73
1.8574-1.88090.25152080.21434168X-RAY DIFFRACTION82
1.8809-1.90560.25572730.20864866X-RAY DIFFRACTION94
1.9056-1.93180.26152340.18744989X-RAY DIFFRACTION95
1.9318-1.95930.22362380.18674847X-RAY DIFFRACTION94
1.9593-1.98860.22092660.18315070X-RAY DIFFRACTION95
1.9886-2.01970.21642460.174799X-RAY DIFFRACTION96
2.0197-2.05280.21742310.16465059X-RAY DIFFRACTION96
2.0528-2.08820.19332940.16624876X-RAY DIFFRACTION95
2.0882-2.12610.20052530.1584983X-RAY DIFFRACTION96
2.1261-2.1670.20512760.15284940X-RAY DIFFRACTION96
2.167-2.21120.19612830.15265001X-RAY DIFFRACTION97
2.2112-2.25930.18133190.15814860X-RAY DIFFRACTION96
2.2593-2.31180.21652250.15865051X-RAY DIFFRACTION96
2.3118-2.36960.18262540.14785002X-RAY DIFFRACTION97
2.3696-2.43370.18182700.15914999X-RAY DIFFRACTION97
2.4337-2.50530.20342840.16055008X-RAY DIFFRACTION97
2.5053-2.58610.20392730.16535046X-RAY DIFFRACTION97
2.5861-2.67850.21832460.16224956X-RAY DIFFRACTION97
2.6785-2.78570.19292380.16265015X-RAY DIFFRACTION97
2.7857-2.91230.2022810.15955088X-RAY DIFFRACTION97
2.9123-3.06580.18212490.15215061X-RAY DIFFRACTION97
3.0658-3.25770.15222540.14725017X-RAY DIFFRACTION97
3.2577-3.50890.16082620.12915024X-RAY DIFFRACTION97
3.5089-3.86150.12843190.12155032X-RAY DIFFRACTION97
3.8615-4.4190.13793190.12315008X-RAY DIFFRACTION97
4.419-5.56260.162570.13734997X-RAY DIFFRACTION97
5.5626-31.79710.18862740.17864988X-RAY DIFFRACTION96
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)
10.1745-0.0975-0.05850.3979-0.15390.2029-0.0182-0.03020.0098-0.0094-0.0165-0.0948-0.0040.01430.04760.0326-0.0039-0.00570.0426-0.00280.04720.041210.593730.3744
20.10320.0303-0.10650.11970.00670.1887-0.06120.0460.0034-0.01960.02380.07420.0831-0.04830.0033-0.01530.0140.0035-0.0105-0.0086-0.0302-24.4813-1.015965.8662
30.1310.1322-0.1010.1957-0.06170.1760.04020.00420.0912-0.07820.02270.1316-0.0377-0.0722-0.03620.01440.0402-0.02670.00420.01780.0532-17.661528.893918.8654
40.1909-0.1323-0.01990.19530.08240.1251-0.0072-0.01060.07380.02590.0365-0.07680.00790.024-0.02970.0206-0.00050.00160.0172-0.0110.0311-4.309816.062174.6292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 30:350)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 30:350)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 351:469)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 351:469)

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