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- PDB-4m1r: Structure of a novel cellulase 5 from a sugarcane soil metagenomi... -

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Basic information

Entry
Database: PDB / ID: 4m1r
TitleStructure of a novel cellulase 5 from a sugarcane soil metagenomic library
ComponentsCellulase 5
KeywordsHYDROLASE / TIM barrel / cellulase
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPaiva, J.H. / Alvarez, T.M. / Cairo, J.P. / Paixao, D.A. / Almeida, R.A. / Tonoli, C.C.C. / Ruiz, D.M. / Ruller, R. / Santos, C.R. / Squina, F.M. / Murakami, M.T.
CitationJournal: Plos One / Year: 2013
Title: Structure and function of a novel cellulase 5 from sugarcane soil metagenome.
Authors: Alvarez, T.M. / Paiva, J.H. / Ruiz, D.M. / Cairo, J.P. / Pereira, I.O. / Paixao, D.A. / de Almeida, R.F. / Tonoli, C.C. / Ruller, R. / Santos, C.R. / Squina, F.M. / Murakami, M.T.
History
DepositionAug 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Cellulase 5
B: Cellulase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7884
Polymers63,5442
Non-polymers2442
Water7,008389
1
A: Cellulase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8942
Polymers31,7721
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8942
Polymers31,7721
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.888, 87.512, 66.630
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellulase 5


Mass: 31772.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Production host: Escherichia coli (E. coli) / References: cellulase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 1.9 Å3/Da / Density % sol: 35.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35% (v/v) isopropanol, 30% (w/v) PEG3350 and 100 mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: Double-crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 41174 / Num. obs: 41174 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
NatXraydata collection
PHASERphasing
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→28.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.703 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17271 2062 5 %RANDOM
Rwork0.13072 ---
obs0.13284 39059 93.27 %-
all-41174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 16 389 4893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0224654
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9046368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5715604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19325.33197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28315689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.748158
X-RAY DIFFRACTIONr_chiral_restr0.1640.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213564
X-RAY DIFFRACTIONr_mcbond_it1.2061.52952
X-RAY DIFFRACTIONr_mcangle_it1.89924740
X-RAY DIFFRACTIONr_scbond_it3.09931702
X-RAY DIFFRACTIONr_scangle_it4.5644.51621
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 132 -
Rwork0.246 2317 -
obs--76.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32-0.09-0.05910.41480.19760.4254-0.0268-0.00220.00910.02720.02550.00780.0050.00390.00140.01460.00280.00370.00210.00210.008-2.3127-0.002432.881
20.40490.1304-0.0170.46250.03660.3560.00040.00490.0027-0.0117-0.0020.0116-0.02090.00540.00170.00490.00520.00320.0090.00340.017112.1567-22.523765.1148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 296
2X-RAY DIFFRACTION2B1 - 296

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