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- PDB-3gt2: Crystal Structure of the P60 Domain from M. avium paratuberculosi... -

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Basic information

Entry
Database: PDB / ID: 3gt2
TitleCrystal Structure of the P60 Domain from M. avium paratuberculosis Antigen MAP1272c
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / P60 Domain / Antigen
Function / homology
Function and homology information


cysteine-type peptidase activity / membrane
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
NlpC/P60 domain-containing protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsRamyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V.
CitationJournal: To be Published
Title: Crystal Structures of Two P60-Family Antigens from Mycobacterium Avium Paratuberculosis
Authors: Ramyar, K.X. / Lingle, C.K. / McWhorter, W.J. / Bouyain, S. / Bannantine, J.P. / Geisbrecht, B.V.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4445
Polymers15,1281
Non-polymers3164
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.715, 53.212, 38.325
Angle α, β, γ (deg.)90.00, 102.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 15128.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: MAP1272c, MAP_1272c / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q740S0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M BisTris-HCl, 1.6 M Ammonium Sulfate, 4% (v/v) PEG 400, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 9.45 / Number: 47147 / Rmerge(I) obs: 0.072 / Χ2: 1.04 / D res high: 1.75 Å / D res low: 500 Å / Num. obs: 13278 / % possible obs: 96.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.7750096.310.050.9713.7
2.993.7799.910.0551.0474
2.612.9999.910.081.0314.1
2.382.6199.910.0951.064.1
2.22.3899.910.1141.0614.1
2.072.299.910.151.0313.9
1.972.0799.210.1640.9783.5
1.891.9796.610.2011.1163
1.811.8990.610.2091.1162.5
1.751.8178.110.2160.9782.2
ReflectionResolution: 1.75→500 Å / Num. obs: 13278 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.446
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.216 / % possible all: 78.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0
Phasing dmFOM : 0.64 / FOM acentric: 0.65 / FOM centric: 0.6 / Reflection: 13001 / Reflection acentric: 12391 / Reflection centric: 610
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5-30.5710.930.940.8757350568
3.1-50.920.930.8118371713124
2.5-3.10.780.790.6323162203113
2.2-2.50.670.670.482294219995
1.9-2.20.490.490.4639783837141
1.8-1.90.430.430.372003193469

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→22.675 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.76 / σ(F): 0.03 / Phase error: 20.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2008 1313 10.09 %
Rwork0.183 --
obs0.1848 13012 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.643 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 23.627 Å2
Baniso -1Baniso -2Baniso -3
1-4.534 Å2-0 Å23.888 Å2
2--3.407 Å20 Å2
3----7.941 Å2
Refinement stepCycle: LAST / Resolution: 1.75→22.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 30 100 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061037
X-RAY DIFFRACTIONf_angle_d0.9711407
X-RAY DIFFRACTIONf_dihedral_angle_d15.002365
X-RAY DIFFRACTIONf_chiral_restr0.064147
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81690.22141130.197971X-RAY DIFFRACTION71
1.8169-1.89960.19471370.19631183X-RAY DIFFRACTION87
1.8996-1.99960.20931490.17641292X-RAY DIFFRACTION94
1.9996-2.12480.21571520.16861364X-RAY DIFFRACTION98
2.1248-2.28880.20011480.16931363X-RAY DIFFRACTION99
2.2888-2.51880.22161530.16881386X-RAY DIFFRACTION99
2.5188-2.88270.21661530.17471372X-RAY DIFFRACTION99
2.8827-3.62950.19621550.1751390X-RAY DIFFRACTION100
3.6295-22.67650.18021530.19611378X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -7.3847 Å / Origin y: 30.8294 Å / Origin z: 34.5798 Å
111213212223313233
T0.1333 Å20.0108 Å2-0.0012 Å2-0.1459 Å20.01 Å2--0.1428 Å2
L0.2744 °20.6927 °20.0993 °2-0.9183 °20.0131 °2--0.6832 °2
S-0.0414 Å °0.0097 Å °-0.0842 Å °0.0266 Å °0.058 Å °0.0064 Å °0.0304 Å °-0.1162 Å °-0.0196 Å °
Refinement TLS groupSelection details: all

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