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- PDB-4npr: Crystal Structure of the Family 12 Xyloglucanase from Aspergillus... -

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Basic information

Entry
Database: PDB / ID: 4npr
TitleCrystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus
ComponentsXyloglucan-specific endo-beta-1,4-glucanase GH12
KeywordsHYDROLASE / b-jelly roll / xyloglucan-specific endo-beta-1 / 4-glucanase
Function / homology
Function and homology information


xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
xyloglucan-specific endo-beta-1,4-glucanase
Similarity search - Component
Biological speciesAspergillus niveus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCordeiro, R.L. / Santos, C.R. / Furtado, G.P. / Damasio, A.R.L. / Polizeli, M.L.T.M. / Ward, R.J. / Murakami, M.T.
CitationJournal: To be Published
Title: Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus
Authors: Santos, C.R. / Cordeiro, R.L. / Furtado, G.P. / Damasio, A.R.L. / Polizeli, M.L.T.M. / Ward, R.J. / Murakami, M.T.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xyloglucan-specific endo-beta-1,4-glucanase GH12
B: Xyloglucan-specific endo-beta-1,4-glucanase GH12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2714
Polymers52,0792
Non-polymers1922
Water84747
1
A: Xyloglucan-specific endo-beta-1,4-glucanase GH12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1362
Polymers26,0401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Xyloglucan-specific endo-beta-1,4-glucanase GH12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1362
Polymers26,0401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Xyloglucan-specific endo-beta-1,4-glucanase GH12
hetero molecules

B: Xyloglucan-specific endo-beta-1,4-glucanase GH12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2714
Polymers52,0792
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Buried area1480 Å2
ΔGint-32 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.368, 62.368, 226.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Xyloglucan-specific endo-beta-1,4-glucanase GH12


Mass: 26039.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niveus (mold) / Production host: Escherichia coli (E. coli)
References: UniProt: H6TQN1, xyloglucan-specific endo-beta-1,4-glucanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 20% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15884 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1450 / % possible all: 91.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VL8

3vl8


Resolution: 2.5→48.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.821 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.714 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 801 5 %RANDOM
Rwork0.18574 ---
obs0.18849 15063 97.14 %-
all-15864 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 10 47 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023431
X-RAY DIFFRACTIONr_bond_other_d0.0010.022995
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9154685
X-RAY DIFFRACTIONr_angle_other_deg0.793.0016893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53625.479146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20615489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.48152
X-RAY DIFFRACTIONr_chiral_restr0.10.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_mcbond_it1.1821.7611758
X-RAY DIFFRACTIONr_mcbond_other1.1791.7591757
X-RAY DIFFRACTIONr_mcangle_it1.9752.6332194
X-RAY DIFFRACTIONr_mcangle_other1.9752.6352195
X-RAY DIFFRACTIONr_scbond_it1.6351.8441673
X-RAY DIFFRACTIONr_scbond_other1.5741.8291665
X-RAY DIFFRACTIONr_scangle_other2.5582.6882479
X-RAY DIFFRACTIONr_long_range_B_refined3.5913.7353725
X-RAY DIFFRACTIONr_long_range_B_other3.58713.7333725
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 61 -
Rwork0.275 971 -
obs--89.97 %

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