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- PDB-4lgn: The structure of Acidothermus cellulolyticus family 74 glycoside ... -

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Basic information

Entry
Database: PDB / ID: 4lgn
TitleThe structure of Acidothermus cellulolyticus family 74 glycoside hydrolase
ComponentsCellulose-binding, family II
KeywordsCELLULOSE BINDING PROTEIN / GH74 / xyloglucanase
Function / homology
Function and homology information


cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...: / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / : / Cellulose-binding, family II
Similarity search - Component
Biological speciesAcidothermus cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 angstrom resolution.
Authors: Alahuhta, M. / Adney, W.S. / Himmel, M.E. / Lunin, V.V.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose-binding, family II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45637
Polymers79,4781
Non-polymers1,97836
Water20,1951121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.761, 78.686, 143.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellulose-binding, family II


Mass: 79478.406 Da / Num. of mol.: 1 / Fragment: UNP residues 47-786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidothermus cellulolyticus (bacteria) / Strain: ATCC 43068 / 11B / Gene: Acel_0618 / Production host: Escherichia coli (E. coli) / References: UniProt: A0LSI1

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Non-polymers , 7 types, 1157 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M tri-Sodium citrate Dihydrate pH 5.0, 1.5 M Na Formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 5, 2010 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→40.41 Å / Num. all: 76875 / Num. obs: 76875 / % possible obs: 100 % / Redundancy: 5.66 % / Rsym value: 0.1557 / Net I/σ(I): 8.52
Reflection shellResolution: 1.82→1.91 Å / Redundancy: 4.34 % / Mean I/σ(I) obs: 1.98 / Num. unique all: 10202 / Rsym value: 0.5343 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.7.0032refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CN3

2cn3


Resolution: 1.82→40.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.491 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 3861 5 %RANDOM
Rwork0.15019 ---
obs0.1525 72650 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.08 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 121 1121 6779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025911
X-RAY DIFFRACTIONr_bond_other_d0.0020.025286
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9278089
X-RAY DIFFRACTIONr_angle_other_deg0.946312173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30923.878245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14615767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2881527
X-RAY DIFFRACTIONr_chiral_restr0.1280.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0050.9553004
X-RAY DIFFRACTIONr_mcbond_other1.0050.9563005
X-RAY DIFFRACTIONr_mcangle_it1.4781.4243762
X-RAY DIFFRACTIONr_mcangle_other1.4831.4263763
X-RAY DIFFRACTIONr_scbond_it1.4021.0752907
X-RAY DIFFRACTIONr_scbond_other1.3821.0722900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1031.5544310
X-RAY DIFFRACTIONr_long_range_B_refined5.9129.8177722
X-RAY DIFFRACTIONr_long_range_B_other5.0718.6337055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 277 -
Rwork0.265 5309 -
obs--99.79 %

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