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- PDB-4qcf: Crystal structure of N-terminal mutant (V1A) of an alkali thermos... -

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Basic information

Entry
Database: PDB / ID: 4qcf
TitleCrystal structure of N-terminal mutant (V1A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
ComponentsAlkaline thermostable endoxylanase
KeywordsHYDROLASE / GH10 Xylanase / (beta/alpha)8-barrel / Glycosyl Hydrolase
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: 2.26 Å
AuthorsMahanta, P. / Bhardwaj, A. / Reddy, V.S. / Ramakumar, S.
CitationJournal: Febs J. / Year: 2015
Title: Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (beta/alpha)8-triosephosphate isomerase barrel enzyme
Authors: Mahanta, P. / Bhardwaj, A. / Kumar, K. / Reddy, V.S. / Ramakumar, S.
History
DepositionMay 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Mar 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 / struct_conn / struct_ref_seq_dif / 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_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline thermostable endoxylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2396
Polymers41,0851
Non-polymers1545
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.570, 80.120, 69.900
Angle α, β, γ (deg.)90.000, 110.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

CL

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Components

#1: Protein Alkaline thermostable endoxylanase


Mass: 41085.387 Da / Num. of mol.: 1 / Fragment: UNP residues 52-405 / Mutation: V1A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 1.37 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M NaCl, 0.09M MgCl2, 0.05M Tris HCl pH 8.5, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Oct 13, 2012 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→65.34 Å / Num. all: 17095 / Num. obs: 17095 / % possible obs: 96.3 % / Redundancy: 5.2 % / Rsym value: 0.039 / Net I/σ(I): 25.5
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
2.26-2.385.10.1534.91245624190.0810.1531094.5
2.38-2.535.10.116.71195823220.0590.1113.295.2
2.53-2.75.20.0848.81139922070.0440.08416.195.9
2.7-2.925.20.0612.11066520590.0320.062196.1
2.92-3.25.20.04216.1996319200.0220.04226.896.3
3.2-3.575.20.03220.8894517290.0170.03235.297.4
3.57-4.135.20.02623.9796915390.0140.02641.297.1
4.13-5.055.20.02920.9676413090.0150.02945.198
5.05-7.155.10.02722.3524610200.0150.02740.698.2
7.15-26.76250.02423.528425710.0140.02446.897.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→26.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.1697 / FOM work R set: 0.8813 / SU B: 9.859 / SU ML: 0.133 / SU R Cruickshank DPI: 0.37 / SU Rfree: 0.2297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 877 5.1 %RANDOM
Rwork0.1745 ---
obs0.177 17094 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.06 Å2 / Biso mean: 26.355 Å2 / Biso min: 4.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å2-1.22 Å2
2--0.06 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.26→26.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 5 202 3100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192987
X-RAY DIFFRACTIONr_bond_other_d0.0050.022693
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.9274077
X-RAY DIFFRACTIONr_angle_other_deg0.71836185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8924.798173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98615467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6771519
X-RAY DIFFRACTIONr_chiral_restr0.0550.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_mcbond_it0.3261.4331419
X-RAY DIFFRACTIONr_mcbond_other0.3261.4331418
X-RAY DIFFRACTIONr_mcangle_it0.582.1491773
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 63 -
Rwork0.199 1129 -
all-1192 -
obs--93.64 %
Refinement TLS params.Method: refined / Origin x: -26.398 Å / Origin y: -5.715 Å / Origin z: 15.649 Å
111213212223313233
T0.0173 Å20.0313 Å20.0031 Å2-0.1347 Å20.0048 Å2--0.0104 Å2
L1.5771 °2-0.2442 °2-0.2897 °2-0.6022 °20.1525 °2--1.5011 °2
S0.0492 Å °0.1038 Å °-0.0402 Å °-0.0553 Å °-0.0191 Å °-0.0181 Å °0.0925 Å °0.2026 Å °-0.0301 Å °

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