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- PDB-4eyz: Crystal structure of an uncommon cellulosome-related protein modu... -

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Basic information

Entry
Database: PDB / ID: 4eyz
TitleCrystal structure of an uncommon cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
ComponentsCellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
KeywordsHYDROLASE / Putative protease
Function / homologyCellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
Function and homology information
Biological speciesRuminococcus flavefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.383 Å
AuthorsFrolow, F. / Voronov-Goldman, M. / Bayer, E. / Lamed, R.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of an Uncommon Cellulosome-Related Protein Module from Ruminococcus flavefaciens That Resembles Papain-Like Cysteine Peptidases.
Authors: Levy-Assaraf, M. / Voronov-Goldman, M. / Rozman Grinberg, I. / Weiserman, G. / Shimon, L.J. / Jindou, S. / Borovok, I. / White, B.A. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
B: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0555
Polymers54,8692
Non-polymers1863
Water12,971720
1
A: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4962
Polymers27,4341
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5583
Polymers27,4341
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.811, 60.605, 66.126
Angle α, β, γ (deg.)90.00, 107.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellulosome-related protein module from Ruminococcus flavefaciens that resembles papain-like cysteine peptidases


Mass: 27434.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus flavefaciens (bacteria) / Strain: FD-1 / Gene: NlpC/P60_2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: M9MMP4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M BIS-TRIS and 25% w/v polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2008
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 37.5 / Number: 715274 / Rmerge(I) obs: 0.051 / Χ2: 0.94 / D res high: 1.38 Å / D res low: 50 Å / Num. obs: 97755 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.755096.110.0260.7417.2
2.973.7596.610.031.0157.1
2.62.9798.610.0371.1357.3
2.362.698.410.0431.2027.5
2.192.3697.810.0431.147.5
2.062.1997.910.0471.1067.5
1.962.0697.510.0531.0497.5
1.871.9697.110.0641.0127.6
1.81.8796.910.0760.9427.6
1.741.896.910.0940.97.6
1.681.7496.310.1160.8637.6
1.641.6896.210.1420.8487.6
1.591.649610.1710.8547.6
1.551.5995.910.2080.8397.6
1.521.5595.410.2460.8537.6
1.491.5295.310.2980.8517.4
1.461.4995.110.340.8437.2
1.431.4695.210.3940.8366.9
1.41.4394.610.4150.8366.5
1.381.483.510.4490.8385.6
ReflectionResolution: 1.38→50 Å / Num. obs: 182049 / % possible obs: 95.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.38-1.45.60.449183.5
1.4-1.436.50.415194.6
1.43-1.466.90.394195.2
1.46-1.497.20.34195.1
1.49-1.527.40.298195.3
1.52-1.557.60.246195.4
1.55-1.597.60.208195.9
1.59-1.647.60.171196
1.64-1.687.60.142196.2
1.68-1.747.60.116196.3
1.74-1.87.60.094196.9
1.8-1.877.60.076196.9
1.87-1.967.60.064197.1
1.96-2.067.50.053197.5
2.06-2.197.50.047197.9
2.19-2.367.50.043197.8
2.36-2.67.50.043198.4
2.6-2.977.30.037198.6
2.97-3.757.10.03196.6
3.75-507.20.026196.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
PHENIXdev_1180refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.383→38.935 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.1 / σ(F): 1.37 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1524 2002 2.1 %
Rwork0.1265 --
obs0.1271 182049 91.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.123 Å2
Refinement stepCycle: LAST / Resolution: 1.383→38.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 12 720 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094119
X-RAY DIFFRACTIONf_angle_d1.1955626
X-RAY DIFFRACTIONf_dihedral_angle_d12.7031427
X-RAY DIFFRACTIONf_chiral_restr0.071564
X-RAY DIFFRACTIONf_plane_restr0.006729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3825-1.40.1779910.15693907X-RAY DIFFRACTION54
1.4-1.41850.2105850.15084881X-RAY DIFFRACTION68
1.4185-1.43790.16491090.15455372X-RAY DIFFRACTION74
1.4379-1.45840.1961290.15465745X-RAY DIFFRACTION80
1.4584-1.48020.19061260.14696108X-RAY DIFFRACTION84
1.4802-1.50330.18621450.1436289X-RAY DIFFRACTION87
1.5033-1.5280.14771520.13756501X-RAY DIFFRACTION90
1.528-1.55430.17431420.13386604X-RAY DIFFRACTION92
1.5543-1.58260.17241510.13316759X-RAY DIFFRACTION93
1.5826-1.6130.15631490.13066815X-RAY DIFFRACTION95
1.613-1.6460.18281470.12766905X-RAY DIFFRACTION95
1.646-1.68180.14661550.12776892X-RAY DIFFRACTION96
1.6818-1.72090.16221410.12216975X-RAY DIFFRACTION96
1.7209-1.76390.15731500.12226920X-RAY DIFFRACTION97
1.7639-1.81160.13831550.11726971X-RAY DIFFRACTION97
1.8116-1.86490.15731550.1137132X-RAY DIFFRACTION97
1.8649-1.92510.13781440.1126920X-RAY DIFFRACTION97
1.9251-1.99390.12961580.11037117X-RAY DIFFRACTION97
1.9939-2.07370.16581440.11147019X-RAY DIFFRACTION98
2.0737-2.16810.1381520.11197087X-RAY DIFFRACTION98
2.1681-2.28240.15731500.11277078X-RAY DIFFRACTION98
2.2824-2.42540.13251580.11587163X-RAY DIFFRACTION99
2.4254-2.61260.13311400.12727061X-RAY DIFFRACTION98
2.6126-2.87550.15021620.12897130X-RAY DIFFRACTION98
2.8755-3.29140.161490.12597074X-RAY DIFFRACTION98
3.2914-4.1460.13991420.11826905X-RAY DIFFRACTION96
4.146-38.950.16541440.15846894X-RAY DIFFRACTION95

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