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- PDB-3ois: Crystal Structure Xylellain, a cysteine protease from Xylella fas... -

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Basic information

Entry
Database: PDB / ID: 3ois
TitleCrystal Structure Xylellain, a cysteine protease from Xylella fastidiosa
ComponentsCysteine protease
KeywordsHYDROLASE / Alpha and beta
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / nucleotide binding / extracellular space
Similarity search - Function
: / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Cysteine protease
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.65 Å
AuthorsLeite, N.R. / Faro, A.R. / Oliva, M.A.V. / Thiemann, O.H. / Oliva, G.
CitationJournal: Febs Lett. / Year: 2013
Title: The crystal structure of the cysteine protease Xylellain from Xylella fastidiosa reveals an intriguing activation mechanism.
Authors: Leite, N.R. / Faro, A.R. / Dotta, M.A. / Faim, L.M. / Gianotti, A. / Silva, F.H. / Oliva, G. / Thiemann, O.H.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Cysteine protease
B: Cysteine protease
C: Cysteine protease
D: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5258
Polymers131,9094
Non-polymers1,6174
Water25,8521435
1
A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3812
Polymers32,9771
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3812
Polymers32,9771
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3812
Polymers32,9771
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3812
Polymers32,9771
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cysteine protease
B: Cysteine protease
hetero molecules

C: Cysteine protease
D: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5258
Polymers131,9094
Non-polymers1,6174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area12700 Å2
ΔGint-37 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.089, 69.314, 82.368
Angle α, β, γ (deg.)75.860, 75.430, 66.510
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cysteine protease


Mass: 32977.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Gene: XF_0156 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9PGZ0
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1435 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20-22% PEG 4000, 60 mM Sodium citrate, 134 mM Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 4, 2005 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→78.664 Å / Num. all: 117070 / Num. obs: 117070 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.744.40.41.971306163080.486.7
1.74-1.848.70.2842.7136326156570.28488.2
1.84-1.978.70.1824.2130660149710.18289.4
1.97-2.138.70.1186.4122549140380.11890.5
2.13-2.338.70.0819.2114556131270.08191.7
2.33-2.618.70.06211.6104954120250.06292.8
2.61-3.018.70.0521393863107500.05294
3.01-3.698.70.04215.37947491250.04295.1
3.69-5.228.70.03319.16219071770.03396.2
5.22-23.1068.50.0320.63327238920.0395.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.65→23.06 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2095 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8597 / SU B: 2.286 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1122 / SU Rfree: 0.1151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 5859 5 %RANDOM
Rwork0.166 ---
all0.1685 116835 --
obs0.1685 116835 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.77 Å2 / Biso mean: 22.8106 Å2 / Biso min: 4.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å21.31 Å2-0.05 Å2
2---0.82 Å2-0.1 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→23.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8578 0 100 1435 10113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0229402
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.96512920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24651205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16923.665472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.671151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5551568
X-RAY DIFFRACTIONr_chiral_restr0.1460.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217466
X-RAY DIFFRACTIONr_mcbond_it1.3031.55568
X-RAY DIFFRACTIONr_mcangle_it2.02129131
X-RAY DIFFRACTIONr_scbond_it3.09533834
X-RAY DIFFRACTIONr_scangle_it4.4834.53718
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 412 -
Rwork0.343 7818 -
all-8230 -
obs--86.44 %

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