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- PDB-5i2u: Crystal structure of a novel Halo-Tolerant Cellulase from Soil Me... -

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Basic information

Entry
Database: PDB / ID: 5i2u
TitleCrystal structure of a novel Halo-Tolerant Cellulase from Soil Metagenome
ComponentsCellulase
KeywordsHYDROLASE / CELLULASE / HALO-TOLERANT / TIM BARREL / GH5 FAMILY
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarg, R. / Brahma, V. / Srivastava, R. / Verma, L. / Karthikeyan, S. / Sahni, G.
CitationJournal: Sci Rep / Year: 2016
Title: Biochemical and structural characterization of a novel halotolerant cellulase from soil metagenome
Authors: Garg, R. / Srivastava, R. / Brahma, V. / Verma, L. / Karthikeyan, S. / Sahni, G.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,31615
Polymers76,2492
Non-polymers1,06713
Water2,414134
1
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7999
Polymers38,1241
Non-polymers6758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5176
Polymers38,1241
Non-polymers3935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.766, 88.128, 146.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 11 - 305 / Label seq-ID: 31 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cellulase


Mass: 38124.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUniProt sequence of this protein is not yet available. The first 21 amino acids in the sequence ...UniProt sequence of this protein is not yet available. The first 21 amino acids in the sequence "MGSSHHHHHHSSGLVPRGSHM" is from Expression tag.

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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: 2.1 Å3/Da / Density % sol: 36.5 % / Description: RECTANGLULAR
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2014
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→45.77 Å / Num. obs: 30246 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.7 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZT

3pzt


Resolution: 2.2→45.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.296 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25706 1567 5.2 %RANDOM
Rwork0.20895 ---
obs0.21146 28609 98.19 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.151 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2--1.24 Å2-0 Å2
3----3.9 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 66 134 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194982
X-RAY DIFFRACTIONr_bond_other_d0.0040.024540
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9286780
X-RAY DIFFRACTIONr_angle_other_deg1.054310433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69824.524252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3441528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215658
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021182
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_it2.4143.6812377
X-RAY DIFFRACTIONr_mcbond_other2.4083.682376
X-RAY DIFFRACTIONr_mcangle_it3.5415.5132970
X-RAY DIFFRACTIONr_mcangle_other3.5415.5142971
X-RAY DIFFRACTIONr_scbond_it2.7973.9642605
X-RAY DIFFRACTIONr_scbond_other2.7413.9532597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1995.8223798
X-RAY DIFFRACTIONr_long_range_B_refined6.67630.1855915
X-RAY DIFFRACTIONr_long_range_B_other6.67630.1855915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 37450 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 95 -
Rwork0.325 1844 -
obs--86.99 %

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