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- PDB-5eba: Crystal structure of aromatic mutant (Y343A) of an alkali thermos... -

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Basic information

Entry
Database: PDB / ID: 5eba
TitleCrystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
ComponentsBeta-xylanase
KeywordsHYDROLASE / glycosyl hydrolase family GH10 / xylanase / (beta/alpha)8-TIM barrel
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. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
CitationJournal: To Be Published
Title: Crystal structure of aromatic mutant (Y343A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
Authors: Mahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
History
DepositionOct 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0693
Polymers41,0211
Non-polymers472
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.860, 80.110, 69.210
Angle α, β, γ (deg.)90.000, 111.190, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

#1: Protein Beta-xylanase / alkali thermostable GH10 xylanase


Mass: 41021.348 Da / Num. of mol.: 1 / Fragment: UNP residues 52-405 / Mutation: Y343A
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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.1M NaCl, 150mM MgCl2, 0.1M Tris-HCl pH 8.5, 15% PEG 6000

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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: Sep 3, 2010
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→64.531 Å / Num. all: 15361 / Num. obs: 15361 / % possible obs: 91.9 % / Redundancy: 3.8 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.069 / Rsym value: 0.059 / Net I/av σ(I): 9.351 / Net I/σ(I): 14.3 / Num. measured all: 58295
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.423.60.2183.5823622710.130.2185.193.8
2.42-2.573.60.1624.7789821730.0970.1626.894.5
2.57-2.753.80.1226.1687018300.0710.1228.684.5
2.75-2.973.80.0918734419190.0520.09111.295.4
2.97-3.253.90.06910.3685817600.040.0691595.4
3.25-3.643.90.05213.4580814820.030.05220.286.9
3.64-4.23.90.04414.6483712390.0250.04424.683.5
4.2-5.143.90.04514.2469412040.0250.04526.996.8
5.14-7.273.90.04812.437199520.0280.04823.397.2
7.27-34.0323.80.04112.920315310.0230.04127.996.5

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2f8q

2f8q


Resolution: 2.3→64.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2349 / WRfactor Rwork: 0.178 / FOM work R set: 0.8525 / SU B: 12.429 / SU ML: 0.164 / SU R Cruickshank DPI: 0.4829 / SU Rfree: 0.2586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 732 4.8 %RANDOM
Rwork0.178 ---
obs0.1807 14620 91.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.71 Å2 / Biso mean: 32.416 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0 Å2-0.91 Å2
2--1.28 Å2-0 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 2.3→64.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 2 163 3053
Biso mean--25.92 30.49 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192967
X-RAY DIFFRACTIONr_bond_other_d0.0010.022684
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9274047
X-RAY DIFFRACTIONr_angle_other_deg0.75336159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76924.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45215463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3021519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_mcbond_it0.7462.2041415
X-RAY DIFFRACTIONr_mcbond_other0.7472.2041414
X-RAY DIFFRACTIONr_mcangle_it1.2973.3041767
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 59 -
Rwork0.195 1097 -
all-1156 -
obs--93.23 %
Refinement TLS params.Method: refined / Origin x: 14 Å / Origin y: -3.006 Å / Origin z: 16.932 Å
111213212223313233
T0.043 Å2-0.0378 Å20.0409 Å2-0.062 Å2-0.0259 Å2--0.0495 Å2
L1.4245 °20.222 °2-0.3879 °2-0.4138 °2-0.2316 °2--1.3988 °2
S0.0296 Å °-0.0606 Å °0.0298 Å °0.0308 Å °-0.0164 Å °-0.0077 Å °0.0518 Å °-0.1627 Å °-0.0132 Å °

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