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- PDB-5efd: Crystal structure of a surface pocket creating mutant (W6A) of an... -

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Basic information

Entry
Database: PDB / ID: 5efd
TitleCrystal structure of a surface pocket creating mutant (W6A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27
ComponentsBeta-xylanase
KeywordsHYDROLASE / glycosyl hydrolase family 10 (GH10) / xylanase / mutant / (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 / SYNCHROTRON / Resolution: 1.674 Å
AuthorsMahanta, P. / Bhardwaj, A. / Reddy, V.S. / 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
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _citation_author.identifier_ORCID / _citation_author.name / _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
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)82,56114
Polymers81,9972
Non-polymers56512
Water7,963442
1
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2677
Polymers40,9981
Non-polymers2696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14540 Å2
MethodPISA
2
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2947
Polymers40,9981
Non-polymers2966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.990, 76.600, 176.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-xylanase / Alkali 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

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Non-polymers , 5 types, 454 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.82656 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.674→88.245 Å / Num. all: 86625 / Num. obs: 86625 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Rsym value: 0.077 / Net I/av σ(I): 6.081 / Net I/σ(I): 14.7 / Num. measured all: 496202
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
1.67-1.765.30.4211.766169124280.1980.421499.3
1.76-1.875.50.2622.865091118020.1210.2626.399.6
1.87-25.50.1664.461663111400.0770.1669.299.8
2-2.165.60.1076.657728103740.050.10713.199.9
2.16-2.375.70.0857.95448796070.0390.08516.299.8
2.37-2.655.90.0679.95175287320.030.06719.4100
2.65-3.066.20.0639.54842677680.0280.06322.5100
3.06-3.746.30.0747.54131265820.0320.07426.4100
3.74-5.296.20.05210.43209751850.0230.05228.9100
5.29-32.0975.80.02618.31747730070.0120.02627.999.6

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
PHASERphasing
RefinementResolution: 1.674→88.245 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1873 / WRfactor Rwork: 0.1576 / FOM work R set: 0.8979 / SU B: 2.992 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0895 / SU Rfree: 0.0885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 4338 5 %RANDOM
Rwork0.1576 ---
obs0.1591 82205 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.31 Å2 / Biso mean: 16.887 Å2 / Biso min: 6.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å2-0 Å20 Å2
2---0.77 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.674→88.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 33 442 6247
Biso mean--21.63 25.94 -
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196033
X-RAY DIFFRACTIONr_bond_other_d0.0030.025448
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9288230
X-RAY DIFFRACTIONr_angle_other_deg0.87312501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22224.74346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57515933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1381538
X-RAY DIFFRACTIONr_chiral_restr0.1050.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021480
X-RAY DIFFRACTIONr_mcbond_it0.9750.9432857
X-RAY DIFFRACTIONr_mcbond_other0.9750.9422856
X-RAY DIFFRACTIONr_mcangle_it1.5591.4113577
LS refinement shellResolution: 1.674→1.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 313 -
Rwork0.206 5982 -
all-6295 -
obs--99.02 %
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)
10.24570.0330.29150.2307-0.17530.55350.02530.0006-0.00970.0216-0.00320.00580.00790.0136-0.02220.01250.00330.0030.1349-0.00580.005510.662-16.087-44.09
20.538-0.02520.20250.1467-0.02420.5149-0.0060.0111-0.0337-0.00750.0251-0.00070.009-0.0096-0.0190.0032-0.00110.00030.1266-0.01180.00635.144-0.525-4.872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 354
2X-RAY DIFFRACTION2B1 - 354

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