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- PDB-3i86: Crystal structure of the P60 Domain from M. avium subspecies para... -

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Basic information

Entry
Database: PDB / ID: 3i86
TitleCrystal structure of the P60 Domain from M. avium subspecies paratuberculosis antigen MAP1204
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / ALPHA AND BETA PROTEIN / HYPOTHETICAL CYSTEINE PROTEASE
Function / homology
Function and homology information


cysteine-type peptidase activity
Similarity search - Function
: / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / NlpC/P60 domain-containing protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRamyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V.
CitationJournal: To be Published
Title: Atypical structural features of two P60 family members from Mycobacterium avium subspecies paratuberculosis
Authors: Ramyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8063
Polymers29,7462
Non-polymers601
Water81145
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,8731
Polymers14,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9332
Polymers14,8731
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.107, 97.107, 97.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Putative uncharacterized protein


Mass: 14872.784 Da / Num. of mol.: 2 / Fragment: P60 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: MAP1204, MAP_1204 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q740Y8, gamma-D-glutamyl-meso-diaminopimelate peptidase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 3350, 18% 2-propanol, 0.1M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43.43 Å / Num. obs: 12254 / % possible obs: 99.6 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 5.6 / Redundancy: 13 % / Biso Wilson estimate: 39.333 Å2 / Rmerge(I) obs: 0.169 / Rsym value: 0.199 / Net I/σ(I): 14.09
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1213 / Rsym value: 0.856 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GT2

3gt2


Resolution: 2.4→43.428 Å / SU ML: 1.11 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHT / σ(F): 1.34 / σ(I): 3.9 / Stereochemistry target values: ML / Details: USED PHENIX.REFINE
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 585 4.8 %RANDOM
Rwork0.2203 ---
obs0.2232 12189 99.61 %-
all-12236 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.938 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso mean: 30.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 4 45 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082093
X-RAY DIFFRACTIONf_angle_d1.212818
X-RAY DIFFRACTIONf_dihedral_angle_d16.995751
X-RAY DIFFRACTIONf_chiral_restr0.077281
X-RAY DIFFRACTIONf_plane_restr0.006376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.64080.2981460.24832849X-RAY DIFFRACTION99
2.6408-3.02280.33111520.23762873X-RAY DIFFRACTION100
3.0228-3.80810.2921280.21882900X-RAY DIFFRACTION100
3.8081-43.43470.20821590.17692982X-RAY DIFFRACTION100

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