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- PDB-3uws: Crystal structure of a clostripain (PARMER_00083) from Parabacter... -

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Basic information

Entry
Database: PDB / ID: 3uws
TitleCrystal structure of a clostripain (PARMER_00083) from Parabacteroides merdae ATCC 43184 at 1.70 A resolution
Components(hypothetical protein) x 2
KeywordsStructural Genomics / Unknown Function / clostripain family protein / Peptidase_C11 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyRossmann fold - #11970 / Peptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Clostripain family
Function and homology information
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.
Authors: McLuskey, K. / Grewal, J.S. / Das, D. / Godzik, A. / Lesley, S.A. / Deacon, A.M. / Coombs, G.H. / Elsliger, M.A. / Wilson, I.A. / Mottram, J.C.
History
DepositionDec 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3May 11, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,43511
Polymers82,0014
Non-polymers4347
Water12,430690
1
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1875
Polymers41,0002
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-34 kcal/mol
Surface area14390 Å2
MethodPISA
2
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2496
Polymers41,0002
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-30 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.112, 108.683, 77.971
Angle α, β, γ (deg.)90.000, 94.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein /


Mass: 14162.332 Da / Num. of mol.: 2 / Fragment: UNP residues 23-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_00083 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7A9N3
#2: Protein hypothetical protein /


Mass: 26838.033 Da / Num. of mol.: 2 / Fragment: UNP residues 148-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_00083 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7A9N3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 147 AND 148. CLEAVAGE AT THIS SITE WAS CONFIRMED BY ...THERE IS A BREAK IN THE CHAIN BETWEEN RESIDUES 147 AND 148. CLEAVAGE AT THIS SITE WAS CONFIRMED BY INTACT MASS SPECTROMETRY AND IS BELIEVED TO BE THE RESULT OF AUTOPROTEOLYSIS
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2M NH4Cl, 20.0% PEG-3350, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→28.734 Å / Num. obs: 70913 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.869 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.5013.2518611380499.7
1.76-1.830.3784.1525561397199.8
1.83-1.910.2665.4510901358099.8
1.91-2.020.187.7575671532799.8
2.02-2.140.1349.7497761329699.6
2.14-2.310.10411.8539981446699.5
2.31-2.540.08713.7510111376899.5
2.54-2.90.07215.7501861371599
2.9-3.660.05519.6493181395997.8
3.660.04322.9505671372496.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.734 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.587 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 6.THE PROTEIN IS CLEAVED AFTER RESIDUE 147, WHICH RESULTS IN RESIDUE 148 BEING LOCATED FAR FROM RESIDUE 147.
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 3577 5 %RANDOM
Rwork0.1428 ---
obs0.1445 70883 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.01 Å2 / Biso mean: 19.9673 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.35 Å2
2--0.09 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 28 690 6330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.025979
X-RAY DIFFRACTIONr_bond_other_d0.0030.024011
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9698169
X-RAY DIFFRACTIONr_angle_other_deg1.30339864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1785763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94225.125281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.896151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5041519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216712
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021191
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 249 -
Rwork0.186 4822 -
all-5071 -
obs--99.65 %
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)
10.9983-0.88470.53832.5031-1.26351.21490.05250.0072-0.1794-0.19420.02560.15530.1996-0.0826-0.07810.0368-0.0131-0.00040.0365-0.00130.04667.444547.299732.8828
21.2383-0.14980.03321.5654-0.33181.0343-0.01340.0805-0.0529-0.08070.01790.02910.0504-0.004-0.00450.006-0.004700.0236-0.00760.003810.478667.451423.3374
31.542-0.4530.23522.023-0.34620.83320.0481-0.0248-0.2253-0.02350.01450.12450.0874-0.0319-0.06260.0236-0.0103-0.00360.0347-0.00260.038223.366447.629968.2635
41.7247-0.32640.19721.4188-0.56911.40380.0710.10250.1265-0.0436-0.06490.0079-0.12580.0183-0.00610.0501-0.01340.01280.039-0.00860.017726.601168.728262.8247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 147
2X-RAY DIFFRACTION2B148 - 375
3X-RAY DIFFRACTION3C28 - 147
4X-RAY DIFFRACTION4D148 - 375

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