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- PDB-5eff: Crystal structure of an aromatic mutant (F4A) of an alkali thermo... -

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Entry
Database: PDB / ID: 5eff
TitleCrystal structure of an aromatic mutant (F4A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / glycosyl hydrolase family 10 (GH10) / xylanase / (beta/alpha)8-TIM barrel / mutant
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. NG-27 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.23 Å
AuthorsMahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
CitationJournal: To Be Published
Title: Crystal structure of an aromatic mutant (F4A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
Authors: Mahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2057
Polymers82,0752
Non-polymers1305
Water2,108117
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0853
Polymers41,0371
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14450 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1204
Polymers41,0371
Non-polymers833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 67.710, 181.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-xylanase / Xylanase / Alkali thermostable GH10 xylanase


Mass: 41037.344 Da / Num. of mol.: 2 / Fragment: UNP residues 52-405 / Mutation: F4A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. NG-27 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O30700, endo-1,4-beta-xylanase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M NaCl, 0.14M MgCl2, 0.05M Tris HCl pH 8.5, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2013
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.227→90.77 Å / Num. all: 31730 / Num. obs: 31730 / % possible obs: 95.5 % / Redundancy: 9.1 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Rsym value: 0.098 / Net I/av σ(I): 6.56 / Net I/σ(I): 17.4 / Num. measured all: 289522
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.21-2.338.20.1963.73029636850.0650.19610.977.4
2.33-2.478.40.1724.23668443770.0580.1721297.3
2.47-2.658.70.1484.83608241600.050.14813.697.8
2.65-2.869.10.1285.43576139310.0430.12815.399
2.86-3.139.50.1076.63447536290.0360.10717.498.6
3.13-3.59.70.0877.73234633260.0290.08721.399.5
3.5-4.049.90.0748.52931829720.0250.07424.399.6
4.04-4.959.90.0679.32489025140.0220.06726.199.8
4.95-79.70.0698.91964520200.0230.06922.2100
7-18.14690.06881002511160.0240.06822.994.4

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
PHASERphasing
RefinementResolution: 2.23→90.77 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.2401 / WRfactor Rwork: 0.1785 / FOM work R set: 0.8869 / SU B: 13.254 / SU ML: 0.16 / SU R Cruickshank DPI: 0.3872 / SU Rfree: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1555 4.9 %RANDOM
Rwork0.1785 ---
obs0.1815 30125 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.06 Å2 / Biso mean: 12.919 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2--0.08 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 2.23→90.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 5 117 5893
Biso mean--13.76 11.54 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195929
X-RAY DIFFRACTIONr_bond_other_d0.0010.025357
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9278088
X-RAY DIFFRACTIONr_angle_other_deg1.973312294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05724.765340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56515925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.871538
X-RAY DIFFRACTIONr_chiral_restr0.0860.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216901
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021449
X-RAY DIFFRACTIONr_mcbond_it0.9121.0422826
X-RAY DIFFRACTIONr_mcbond_other0.9121.0422825
X-RAY DIFFRACTIONr_mcangle_it1.5831.563529
LS refinement shellResolution: 2.227→2.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 100 -
Rwork0.189 1866 -
all-1966 -
obs--82.61 %
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)
10.14240.04380.08390.28480.0070.23820.0139-0.00040.0045-0.04180.00690.0032-0.0018-0.002-0.02090.0192-0.0033-0.00330.00070.00140.0059-11.5096-10.790645.7346
20.2994-0.08290.22540.1374-0.02460.1826-0.0007-0.0111-0.01280.00820.00460.01510.0015-0.0082-0.0040.0131-0.00220.00430.0036-0.0010.0082-2.4326-0.93387.1359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 354
2X-RAY DIFFRACTION2B2 - 354

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