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- PDB-5ir2: Crystal structure of novel cellulases from microbes associated wi... -

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Basic information

Entry
Database: PDB / ID: 5ir2
TitleCrystal structure of novel cellulases from microbes associated with the gut ecosystem
ComponentsCellulase
KeywordsHYDROLASE / Structural Genomics / Midwest Center for Structural Genomics / MCSG / novel cellulases
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase activity / metal ion binding
Similarity search - Function
Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / Regulator of ribonuclease activity homolog
Similarity search - Component
Biological speciesParabacteroides johnsonii DSM 18315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.079 Å
AuthorsChang, C. / Mack, J. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: Crystal structure of novel cellulases from microbes associated with the gut ecosystem
Authors: Chang, C. / Mack, J. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2265
Polymers25,7451
Non-polymers4824
Water3,567198
1
A: Cellulase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)157,35730
Polymers154,4686
Non-polymers2,88924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area27800 Å2
ΔGint-65 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.240, 100.240, 129.698
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-595-

HOH

31A-597-

HOH

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Components

#1: Protein Cellulase


Mass: 25744.621 Da / Num. of mol.: 1 / Mutation: P191S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides johnsonii DSM 18315 (bacteria)
Gene: PRABACTJOHN_04122 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B7BGD3
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: Lithium sulfate, CHESS, Sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2014
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.079→50 Å / Num. obs: 23828 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 23.92 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.02 / Rrim(I) all: 0.108 / Χ2: 1.019 / Net I/av σ(I): 39.063 / Net I/σ(I): 10.4 / Num. measured all: 634423
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.08-2.1213.50.98211450.9270.2760.847100
2.12-2.1515.70.85311670.9660.2160.8531000.881
2.15-2.219.90.89211740.9840.2010.8691000.916
2.2-2.24220.81911580.9640.1760.891000.838
2.24-2.2924.20.74411710.980.1530.9011000.76
2.29-2.3425.90.6911660.9850.1370.9071000.703
2.34-2.4270.67211570.9860.1310.8961000.685
2.4-2.4728.10.6211770.9860.1190.9071000.631
2.47-2.5428.70.49611610.990.0940.9231000.504
2.54-2.6229.30.42811790.9930.080.951000.435
2.62-2.7129.50.33911940.9940.0630.9681000.345
2.71-2.82300.2711710.9970.050.9821000.274
2.82-2.95300.20511960.9970.0381.0091000.209
2.95-3.1130.40.15311790.9980.0281.0381000.156
3.11-3.330.70.12911770.9970.0241.1231000.131
3.3-3.5630.40.09812190.9980.0181.1911000.1
3.56-3.9130.10.08212070.9990.0151.2261000.084
3.91-4.4829.30.06812250.9990.0131.21000.069
4.48-5.6429.10.06212520.9990.0121.1111000.063
5.64-5027.40.0713530.9970.0141.20999.50.071

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.079→41.161 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.187 2177 5.21 %
Rwork0.142 39647 -
obs0.1444 22660 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.08 Å2 / Biso mean: 35.6628 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 2.079→41.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 31 198 1996
Biso mean--42.61 45.19 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021880
X-RAY DIFFRACTIONf_angle_d0.4732535
X-RAY DIFFRACTIONf_chiral_restr0.045280
X-RAY DIFFRACTIONf_plane_restr0.003328
X-RAY DIFFRACTIONf_dihedral_angle_d16.3591151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0786-2.12380.2316850.19231538162359
2.1238-2.17320.26481400.19441952209276
2.1732-2.22750.24161500.19262466261696
2.2275-2.28780.22011540.18692533268798
2.2878-2.35510.25821200.17532586270699
2.3551-2.43110.22821520.16672566271899
2.4311-2.5180.18751610.156525972758100
2.518-2.61880.21781510.14892568271999
2.6188-2.73790.25421350.14832593272899
2.7379-2.88220.2181410.141525882729100
2.8822-3.06280.18871260.136326072733100
3.0628-3.29910.16631290.125725812710100
3.2991-3.6310.14371420.112126182760100
3.631-4.15590.13641300.111626182748100
4.1559-5.23440.14851310.115326082739100
5.2344-41.16940.17681300.166726282758100

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