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- PDB-5e9p: Spirochaeta thermophila X module - CBM64 - wildtype -

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Basic information

Entry
Database: PDB / ID: 5e9p
TitleSpirochaeta thermophila X module - CBM64 - wildtype
ComponentsCellulase, glycosyl hydrolase family 5, TPS linker, domain X
KeywordsHYDROLASE / Carbohydrate-binding module 64 / CBM64 / Cellulose and Xylan binding / Type A CBM / Jelly roll
Function / homology
Function and homology information


cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Carbohydrate-binding module 64 / Carbohydrate-binding module 64 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
MALONATE ION / cellulase
Similarity search - Component
Biological speciesSpirochaeta thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Proteins / Year: 2016
Title: Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila.
Authors: Schiefner, A. / Angelov, A. / Liebl, W. / Skerra, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1282
Polymers10,0261
Non-polymers1021
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint2 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.517, 58.517, 33.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cellulase, glycosyl hydrolase family 5, TPS linker, domain X


Mass: 10025.756 Da / Num. of mol.: 1 / Fragment: UNP residues 456-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Gene: STHERM_c20620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0RQU0
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 1.5 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 34847 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 15.377 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.962 / Net I/σ(I): 28.7 / Num. measured all: 253480
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.2-1.36.50.9330.3455.3745329753469660.37592.5
1.3-1.40.9770.2358.6840653555654620.25298.3
1.4-1.60.9940.12415.7154512736572980.13499.1
1.6-1.80.9980.06328.9933292445444340.06799.6
1.8-20.9990.03944.0521525286928610.04199.7
2-30.9990.02863.1340816546254590.0399.9
3-410.0284.6410048134913490.021100
4-610.01986.3251467077070.021100
6-810.01884.9112631741740.02100
8-1010.01684.4947069690.018100
100.9990.01882.8542673680.0293.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e9o

5e9o


Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / WRfactor Rfree: 0.125 / WRfactor Rwork: 0.1052 / FOM work R set: 0.9418 / SU B: 0.703 / SU ML: 0.014 / SU R Cruickshank DPI: 0.0252 / SU Rfree: 0.0258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1249 1739 5 %RANDOM
Rwork0.1056 ---
obs0.1066 33108 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.42 Å2 / Biso mean: 14.336 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 14 148 877
Biso mean--29.55 31.4 -
Num. residues----86
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02818
X-RAY DIFFRACTIONr_bond_other_d0.0030.02653
X-RAY DIFFRACTIONr_angle_refined_deg2.131.8941131
X-RAY DIFFRACTIONr_angle_other_deg1.09831516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3662544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.72715108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg38.088151
X-RAY DIFFRACTIONr_chiral_restr0.1320.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021005
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02214
X-RAY DIFFRACTIONr_mcbond_it1.9711.042383
X-RAY DIFFRACTIONr_mcbond_other1.9351.04382
X-RAY DIFFRACTIONr_mcangle_it2.5821.58491
X-RAY DIFFRACTIONr_rigid_bond_restr6.57331471
X-RAY DIFFRACTIONr_sphericity_free33.83531
X-RAY DIFFRACTIONr_sphericity_bonded16.00451554
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 101 -
Rwork0.15 2060 -
all-2161 -
obs--83.4 %

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