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- PDB-2p1g: Crystal structure of a putative xylanase from Bacteroides fragilis -

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Basic information

Entry
Database: PDB / ID: 2p1g
TitleCrystal structure of a putative xylanase from Bacteroides fragilis
ComponentsPutative xylanase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / xylan catabolic process
Similarity search - Function
Putative xylanase fold / Putative xylanase like domain / putative xylanase like fold / putative xylanase like domain / N-acetylmuramoyl-L-alanine amidase-like / N-acetylmuramoyl-L-alanine amidase-like / Papain-like cysteine peptidase superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Zhang, F. / Sridhar, V. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative xylanase from Bacteroides fragilis
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Zhang, F. / Sridhar, V. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN SHOWN IN REMARK 350 IS PROBABLE. IT IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative xylanase
B: Putative xylanase


Theoretical massNumber of molelcules
Total (without water)55,9602
Polymers55,9602
Non-polymers00
Water9,350519
1
A: Putative xylanase


Theoretical massNumber of molelcules
Total (without water)27,9801
Polymers27,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative xylanase


Theoretical massNumber of molelcules
Total (without water)27,9801
Polymers27,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.645, 65.830, 74.061
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number4
Space group name H-MP1211
Detailsprobable monomer

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Components

#1: Protein Putative xylanase


Mass: 27979.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: YCH46 / Gene: BF2036 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q64UP6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 28% PEG MME 2000, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.8→22.011 Å / Num. obs: 44349 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6376 / Rsym value: 0.368 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.347 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2229 5 %RANDOM
Rwork0.167 ---
obs0.169 44325 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20.49 Å2
2---0.34 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 0 519 4120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223670
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9784960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37624.843159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27215675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251518
X-RAY DIFFRACTIONr_chiral_restr0.090.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022714
X-RAY DIFFRACTIONr_nbd_refined0.1990.21618
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2400
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.220
X-RAY DIFFRACTIONr_mcbond_it0.9461.52366
X-RAY DIFFRACTIONr_mcangle_it1.4723673
X-RAY DIFFRACTIONr_scbond_it2.63931501
X-RAY DIFFRACTIONr_scangle_it4.0434.51286
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 175 -
Rwork0.187 3051 -
obs-3226 98.17 %

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