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- PDB-5xc0: Crystal structure of an aromatic mutant (W6A) of an alkali thermo... -

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Basic information

Entry
Database: PDB / ID: 5xc0
TitleCrystal structure of an aromatic mutant (W6A) of an alkali thermostable GH10 Xylanase from Bacillus sp. NG-27
ComponentsBeta-xylanase
KeywordsHYDROLASE / TIM barrel / xylanase / cryptic pocket
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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: 2.32 Å
AuthorsBansia, H. / Mahanta, P. / Ramakumar, S.
CitationJournal: J.Chem.Inf.Model. / Year: 2021
Title: Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches.
Authors: Bansia, H. / Mahanta, P. / Yennawar, N.H. / Ramakumar, S.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half ..._reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.2Mar 24, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.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
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)82,0916
Polymers81,9972
Non-polymers954
Water3,765209
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0463
Polymers40,9981
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14310 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0463
Polymers40,9981
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.229, 67.390, 177.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 354 / Label seq-ID: 2 - 355

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta-xylanase / Thermostable GH10 Xylanase


Mass: 40998.309 Da / Num. of mol.: 2 / Fragment: UNP residues 52-405 / Mutation: W6A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M NaCl, 0.16M MgCl2, 0.05M Tris HCl pH 8.5, 20% 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: Apr 6, 2016
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→27.96 Å / Num. obs: 27367 / % possible obs: 97.7 % / Redundancy: 5.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.065 / Rrim(I) all: 0.155 / Net I/σ(I): 9.2 / Num. measured all: 145366 / Scaling rejects: 26
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.452 / CC1/2: 0.775 / Rpim(I) all: 0.207 / Rrim(I) all: 0.499 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALA0.5.27data scaling
PDB_EXTRACT3.22data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F8Q

2f8q


Resolution: 2.32→27.96 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 16.573 / SU ML: 0.212 / SU R Cruickshank DPI: 0.7788 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.779 / ESU R Free: 0.282
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1358 5 %RANDOM
Rwork0.2018 ---
obs0.204 25944 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.64 Å2 / Biso mean: 26.165 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0 Å2
2---0.88 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 2.32→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5710 0 4 209 5923
Biso mean--9.56 17.27 -
Num. residues----707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195864
X-RAY DIFFRACTIONr_bond_other_d0.0020.025109
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9287998
X-RAY DIFFRACTIONr_angle_other_deg2.038311840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90724.801327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62115904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0231534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216684
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021246
Refine LS restraints NCS

Ens-ID: 1 / Number: 24132 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 89 -
Rwork0.254 1801 -
all-1890 -
obs--93.38 %
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)
10.43750.1239-0.23760.0525-0.01920.2790.027-0.00010.03350.0067-0.00190.00870.00390.001-0.02510.0288-0.0014-0.00380.04950.0050.0279-0.9350.945-6.642
20.3070.29840.06460.42640.24890.26750.1410.0233-0.09190.0945-0.0536-0.1398-0.0276-0.1002-0.08750.07690.0343-0.02650.04530.02160.0462-11.50111.34-43.719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 354
2X-RAY DIFFRACTION2B1 - 354

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