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- PDB-5eb8: Crystal structure of aromatic mutant (F4W) of an alkali thermosta... -

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Basic information

Entry
Database: PDB / ID: 5eb8
TitleCrystal structure of aromatic mutant (F4W) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / glycosyl hydrolase famility 10 / xylanase / (beta/alpha)8-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. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
CitationJournal: To Be Published
Title: Crystal structure of aromatic mutant (F4W) 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,4006
Polymers82,3052
Non-polymers954
Water7,512417
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2003
Polymers41,1521
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2003
Polymers41,1521
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.270, 77.320, 176.750
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 endoxylanase


Mass: 41152.477 Da / Num. of mol.: 2 / Fragment: UNP residues 52-405 / Mutation: F4W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. NG-27 (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.3 Å3/Da / Density % sol: 46.56 % / Description: Plate shaped
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.1M NaCl, 120mM MgCl2, 0.1M Tris-HCl pH 8.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54179 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.219→88.375 Å / Num. all: 38071 / Num. obs: 38071 / % possible obs: 98.4 % / Redundancy: 7.1 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Rsym value: 0.083 / Net I/av σ(I): 6.565 / Net I/σ(I): 15.1 / Num. measured all: 270609
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
2.21-2.336.70.23.73318849560.0810.26.989.8
2.33-2.477.10.1584.63742552730.0630.1588.9100
2.47-2.657.10.1265.73580050080.050.12610.7100
2.65-2.867.20.1086.33320746050.0430.10812.8100
2.86-3.137.20.0927.33093542700.0360.09215.5100
3.13-3.57.30.0778.52839239080.030.07719.7100
3.5-4.047.30.0679.52508934540.0260.06723.4100
4.04-4.957.20.0639.52144429670.0250.06325.2100
4.95-77.10.0698.11657723330.0280.06922.4100
7-18.976.60.0657.8855212970.0270.06523.995.2

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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: 2.22→88.375 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2111 / WRfactor Rwork: 0.166 / FOM work R set: 0.8672 / SU B: 9.65 / SU ML: 0.131 / SU R Cruickshank DPI: 0.2827 / SU Rfree: 0.2007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1841 4.8 %RANDOM
Rwork0.1684 ---
obs0.1706 36158 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.4 Å2 / Biso mean: 27.172 Å2 / Biso min: 10.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-0 Å2
2--1.43 Å20 Å2
3----4.17 Å2
Refinement stepCycle: final / Resolution: 2.22→88.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 4 417 6217
Biso mean--20.28 28.86 -
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195958
X-RAY DIFFRACTIONr_bond_other_d0.0060.025376
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9258130
X-RAY DIFFRACTIONr_angle_other_deg0.783312336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0324.737342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30115928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2951538
X-RAY DIFFRACTIONr_chiral_restr0.0720.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021462
X-RAY DIFFRACTIONr_mcbond_it0.9111.8562830
X-RAY DIFFRACTIONr_mcbond_other0.9111.8562829
X-RAY DIFFRACTIONr_mcangle_it1.5032.783534
LS refinement shellResolution: 2.219→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 111 -
Rwork0.201 2393 -
all-2504 -
obs--90.4 %
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)
10.6979-0.0195-0.41310.1358-0.02611.29920.0608-0.05190.0473-0.0087-0.01940.0101-0.10620.0248-0.04150.0107-0.00330.00340.0164-0.01130.10694.9030.245181.877
20.55950.1681-0.44250.1698-0.5182.06830.02340.0180.01830.00330.0314-0.0025-0.1095-0.0111-0.05480.0275-0.01610.00310.021-0.01980.07910.60415.342220.995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 354
2X-RAY DIFFRACTION2B1 - 354

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