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- PDB-4fk9: High Resolution Structure of the Catalytic Domain of Mannanase SA... -

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Basic information

Entry
Database: PDB / ID: 4fk9
TitleHigh Resolution Structure of the Catalytic Domain of Mannanase SActE_2347 from Streptomyces sp. SirexAA-E
ComponentsCellulose-binding family II
KeywordsHYDROLASE / GH5 TIM Barrel / glycoside hydrolase / beta-mannanase
Function / homology
Function and homology information


cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
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 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Fibronectin type III domain / Fibronectin type 3 domain ...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 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.06 Å
AuthorsAcheson, J.F. / Takasuka, T.E. / Fox, B.G.
CitationJournal: Plos One / Year: 2014
Title: Biochemical properties and atomic resolution structure of a proteolytically processed beta-mannanase from cellulolytic Streptomyces sp. SirexAA-E.
Authors: Takasuka, T.E. / Acheson, J.F. / Bianchetti, C.M. / Prom, B.M. / Bergeman, L.F. / Book, A.J. / Currie, C.R. / Fox, B.G.
History
DepositionJun 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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)36,4708
Polymers36,2781
Non-polymers1927
Water9,134507
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellulose-binding family II
hetero molecules

A: Cellulose-binding family II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,94016
Polymers72,5552
Non-polymers38514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2660 Å2
ΔGint-113 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.805, 102.360, 45.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-795-

HOH

31A-907-

HOH

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Components

#1: Protein Cellulose-binding family II


Mass: 36277.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: 2347, SACTE_2347 / Plasmid: pVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: G2NHM6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.01 Å3/Da / Density % sol: 38.77 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 18, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. all: 130049 / Num. obs: 130004 / % possible obs: 97.7 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.191 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.06-1.082.80.31562740.799195.3
1.08-1.130.25363940.828197.8
1.1-1.123.40.22164400.905197.9
1.12-1.143.50.18364770.956197.8
1.14-1.173.50.16164440.992197.9
1.17-1.193.50.14564530.992197.8
1.19-1.223.50.13564391.07197.8
1.22-1.263.60.12664591.156198
1.26-1.293.60.11864801.311198
1.29-1.343.60.11665241.488198.3
1.34-1.383.60.10564871.382198.5
1.38-1.443.60.09465371.428198.8
1.44-1.53.70.08265641.458199.1
1.5-1.583.70.08166101.425199.2
1.58-1.683.70.07866131.391199.2
1.68-1.813.70.08366281.241199.2
1.81-1.993.70.06466051.249198.8
1.99-2.283.70.05466251.225198.1
2.28-2.883.80.0565941.173197.1
2.88-503.60.04864021.039190.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.81 Å36.76 Å
Translation5.81 Å36.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1061refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.06→36.765 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9477 / SU ML: 0.06 / σ(F): 1.35 / Phase error: 10.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1315 2000 1.54 %
Rwork0.1185 --
all0.1187 130049 -
obs0.1187 130004 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.33 Å2 / Biso mean: 12.6539 Å2 / Biso min: 4.68 Å2
Refinement stepCycle: LAST / Resolution: 1.06→36.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 7 507 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072527
X-RAY DIFFRACTIONf_angle_d1.2323464
X-RAY DIFFRACTIONf_chiral_restr0.068373
X-RAY DIFFRACTIONf_plane_restr0.006462
X-RAY DIFFRACTIONf_dihedral_angle_d11.86870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0598-1.08630.17531380.1588821895995
1.0863-1.11570.14661410.12449027916898
1.1157-1.14850.13441410.10759061920298
1.1485-1.18560.15271420.10339101924398
1.1856-1.22790.12991430.10369086922998
1.2279-1.27710.12911420.10349078922098
1.2771-1.33520.10881430.1019171931498
1.3352-1.40560.11471420.09849139928199
1.4056-1.49370.11281450.09439238938399
1.4937-1.6090.10261450.09939287943299
1.609-1.7710.11741450.10879288943399
1.771-2.02720.14581460.11459336948299
2.0272-2.5540.12541450.12099296944198
2.554-36.78680.14361420.14289075921792

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