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- PDB-4fmv: Crystal Structure Analysis of a GH30 Endoxylanase from Clostridiu... -

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Basic information

Entry
Database: PDB / ID: 4fmv
TitleCrystal Structure Analysis of a GH30 Endoxylanase from Clostridium papyrosolvens C71
ComponentsGlucuronoarabinoxylan endo-1,4-beta-xylanase
KeywordsHYDROLASE / ALPHA BETA BARREL / (BETA/ALPHA)8 BARREL
Function / homology
Function and homology information


galactosylceramide catabolic process / galactosylceramidase activity / glucosylceramidase activity / cellulase / cellulase activity / xylan catabolic process / carbohydrate binding
Similarity search - Function
Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / Glycoside hydrolase family 30 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain / Dockerin domain profile. ...Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / Glycoside hydrolase family 30 / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium papyrosolvens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsBales, E.B. / Smith, J.K. / St John, F.J. / Hurlbert, J.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A novel member of glycoside hydrolase family 30 subfamily 8 with altered substrate specificity.
Authors: St John, F.J. / Dietrich, D. / Crooks, C. / Pozharski, E. / Gonzalez, J.M. / Bales, E. / Smith, K. / Hurlbert, J.C.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucuronoarabinoxylan endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)43,9401
Polymers43,9401
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.020, 76.520, 150.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-497-

HOH

21A-607-

HOH

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Components

#1: Protein Glucuronoarabinoxylan endo-1,4-beta-xylanase /


Mass: 43939.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium papyrosolvens (bacteria) / Strain: DSM2782 / Gene: Cpap_2855 / Plasmid: pJExpress / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: F1TBY8, glucuronoarabinoxylan endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Ammonium acetate, 0.1M BIS-TRIS, 17% PEG10,000, pH pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: pH 5.5

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.01→75.275 Å / Num. all: 24541 / Num. obs: 24541 / % possible obs: 95 % / Redundancy: 6.1 % / Rsym value: 0.043 / Net I/σ(I): 27.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.01-2.126.10.1295.40.129184.4
2.12-2.255.80.0967.30.096188
2.25-2.45.40.0769.30.076192.9
2.4-2.595.40.06710.40.067198.8
2.59-2.845.80.05113.30.0511100
2.84-3.186.40.04215.70.0421100
3.18-3.676.80.03319.60.0331100
3.67-4.496.90.03219.80.0321100
4.49-6.356.90.03119.40.0311100
6.35-38.266.60.02614.30.026199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→38.26 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.55 / σ(F): 1.38 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1249 5.1 %
Rwork0.164 --
obs0.166 24468 94.9 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.93 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.4772 Å2-0 Å20 Å2
2---3.6595 Å2-0 Å2
3---2.1823 Å2
Refinement stepCycle: LAST / Resolution: 2.01→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 0 212 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013092
X-RAY DIFFRACTIONf_angle_d1.4164208
X-RAY DIFFRACTIONf_dihedral_angle_d12.9981089
X-RAY DIFFRACTIONf_chiral_restr0.129451
X-RAY DIFFRACTIONf_plane_restr0.01544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.09050.23591260.16422239X-RAY DIFFRACTION84
2.0905-2.18560.19351280.15162275X-RAY DIFFRACTION85
2.1856-2.30090.21341220.15512432X-RAY DIFFRACTION90
2.3009-2.4450.23721440.16832546X-RAY DIFFRACTION95
2.445-2.63370.24331590.16972669X-RAY DIFFRACTION99
2.6337-2.89870.20711570.16382678X-RAY DIFFRACTION100
2.8987-3.31790.22591310.1712764X-RAY DIFFRACTION100
3.3179-4.17940.16261390.15882749X-RAY DIFFRACTION100
4.1794-38.260.1641430.1682867X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.5479 Å / Origin y: -29.274 Å / Origin z: 16.9644 Å
111213212223313233
T0.0502 Å20.0134 Å20.0227 Å2-0.0358 Å20.0026 Å2--0.0181 Å2
L0.8439 °2-0.0511 °20.0474 °2-0.5564 °2-0.0592 °2--0.3676 °2
S0.0038 Å °-0.1039 Å °0.0096 Å °0.05 Å °0.0075 Å °-0.0092 Å °-0.0216 Å °0.029 Å °-0.0002 Å °
Refinement TLS groupSelection details: (chain A and resid 3:387)

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