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- PDB-4npo: Crystal structure of protein with unknown function from Deinococc... -

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Basic information

Entry
Database: PDB / ID: 4npo
TitleCrystal structure of protein with unknown function from Deinococcus radiodurans at P61 spacegroup
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / ACETATE ION / ABM domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsBoyko, K.M. / Gorbacheva, M.A. / Rakitina, T.V. / Korgenevsky, D.A. / Shabalin, I.G. / Shumilin, I.A. / Dorovatovsky, P.V. / Lipkin, A.V. / Popov, V.O.
CitationJournal: To be Published
Title: Crystal structure of protein with unknown function at P61 spacegroup
Authors: Boyko, K.M. / Gorbacheva, M.A. / Rakitina, T.V. / Korgenevsky, D.A. / Shabalin, I.G. / Shumilin, I.A. / Dorovatovsky, P.V. / Lipkin, A.V. / Popov, V.O.
History
DepositionNov 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0459
Polymers27,5912
Non-polymers4537
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-50 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.390, 80.390, 69.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 13795.624 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RSM4

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Non-polymers , 5 types, 248 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.5M Sodium chloride, 10mM HEPES, 0.1M Sodium acetate, 2.6M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.9815 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2011 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9815 Å / Relative weight: 1
ReflectionResolution: 1.47→20 Å / Num. all: 44067 / Num. obs: 43293 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.47→1.55 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E8O

3e8o


Resolution: 1.47→19.37 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.762 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17462 2181 5 %RANDOM
Rwork0.14969 ---
obs0.15094 41305 99.57 %-
all-67760 --
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 mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å20 Å20 Å2
2--3.34 Å20 Å2
3----6.67 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 29 241 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191705
X-RAY DIFFRACTIONr_bond_other_d0.0020.021647
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9372314
X-RAY DIFFRACTIONr_angle_other_deg2.2733780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71224.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41115286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.718155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5191.669835
X-RAY DIFFRACTIONr_mcbond_other1.5191.67836
X-RAY DIFFRACTIONr_mcangle_it2.1862.4891035
X-RAY DIFFRACTIONr_mcangle_other2.1862.491036
X-RAY DIFFRACTIONr_scbond_it2.8522.021870
X-RAY DIFFRACTIONr_scbond_other2.852.022871
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2162.9141278
X-RAY DIFFRACTIONr_long_range_B_refined6.21315.4222141
X-RAY DIFFRACTIONr_long_range_B_other6.21115.4312142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 149 -
Rwork0.229 2993 -
obs--97.82 %

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