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- PDB-2odk: Putative prevent-host-death protein from Nitrosomonas europaea -

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Basic information

Entry
Database: PDB / ID: 2odk
TitlePutative prevent-host-death protein from Nitrosomonas europaea
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / prevent-host-death protein / APC7367 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyYefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / 3-Layer(aba) Sandwich / Alpha Beta / Antitoxin
Function and homology information
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsOsipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crsytal structure of putative prevent-host-death protein from Nitrosomonas europaea.
Authors: Osipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DIMER IS A PUTATIVE BIOLOGICAL UNIT BASED ON ANALYSIS OF THE PROTEIN INTERFACES.
Remark 999 SEQUENCE AUTHORS STATE THAT THE C-TERMINUS OF THIS PROTEIN IS FLEXIBLE AND THEREFORE THE RESIDUES ... SEQUENCE AUTHORS STATE THAT THE C-TERMINUS OF THIS PROTEIN IS FLEXIBLE AND THEREFORE THE RESIDUES 52-87 ARE MISSING IN COORDINATES DUE TO LACK OF ELECTRON DENSITY.

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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)40,7867
Polymers40,5014
Non-polymers2843
Water5,621312
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3473
Polymers20,2512
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-33 kcal/mol
Surface area5560 Å2
MethodPISA
2
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4394
Polymers20,2512
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-28 kcal/mol
Surface area5590 Å2
MethodPISA
3
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules

C: Hypothetical protein
D: Hypothetical protein
hetero molecules

C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,57114
Polymers81,0038
Non-polymers5686
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area15410 Å2
ΔGint-137 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.146, 78.873, 54.987
Angle α, β, γ (deg.)90.00, 115.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-426-

HOH

21B-464-

HOH

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Components

#1: Protein
Hypothetical protein /


Mass: 10125.341 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NE2111 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82T22
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 1.86 Å3/Da / Density % sol: 33.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 25% PEG 3350, 0.1 M Hepes buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→37.1 Å / Num. all: 56074 / Num. obs: 56074 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 40.9
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.03 / % possible all: 62.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→37.1 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.341 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15379 2838 5.1 %RANDOM
Rwork0.13386 ---
obs0.13487 53222 96.34 %-
all-56060 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.243 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20.02 Å2
2--0.03 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 16 312 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9492607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3225263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.38923.107103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1211525
X-RAY DIFFRACTIONr_chiral_restr0.1210.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021506
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2966
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21289
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4550.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7921.51162
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53521837
X-RAY DIFFRACTIONr_scbond_it3.4523830
X-RAY DIFFRACTIONr_scangle_it4.8454.5737
X-RAY DIFFRACTIONr_rigid_bond_restr2.16831992
X-RAY DIFFRACTIONr_sphericity_free7.0483313
X-RAY DIFFRACTIONr_sphericity_bonded4.82931817
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 141 -
Rwork0.24 2692 -
obs--65.7 %

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