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- PDB-3okx: Crystal structure of YaeB-like protein from Rhodopseudomonas palustris -

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Basic information

Entry
Database: PDB / ID: 3okx
TitleCrystal structure of YaeB-like protein from Rhodopseudomonas palustris
ComponentsYaeB-like protein RPA0152
Keywordsstructural genomics / unknown function / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG
Function / homology
Function and homology information


YaeB-like / TrmO-like, N-terminal domain / YaeB-like superfamily / YaeB, N-terminal domain superfamily / YaeB-like / tRNA-methyltransferase O N-terminal domain / TsaA-like domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / S-adenosyl-L-methionine-binding protein RPA0152
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Evdokimova, E. / Liu, F. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of YaeB-like protein from Rhodopseudomonas palustris
Authors: Chang, C. / Evdokimova, E. / Liu, F. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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: YaeB-like protein RPA0152
B: YaeB-like protein RPA0152
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6494
Polymers37,8522
Non-polymers7972
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-24 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.317, 74.317, 116.817
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein YaeB-like protein RPA0152


Mass: 18926.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0152 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q6NDF6
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 0.2M di-sodium tartrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 35236 / Num. obs: 35229 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 44
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 11 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1690 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.746 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 1761 5 %RANDOM
Rwork0.1469 ---
all0.1487 35078 --
obs0.1487 35078 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 133.8 Å2 / Biso mean: 23.1136 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 54 286 2728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212583
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9963528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69921.803122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7381535
X-RAY DIFFRACTIONr_chiral_restr0.1030.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222046
X-RAY DIFFRACTIONr_mcbond_it1.1151.51581
X-RAY DIFFRACTIONr_mcangle_it1.87922554
X-RAY DIFFRACTIONr_scbond_it2.96331002
X-RAY DIFFRACTIONr_scangle_it4.4794.5974
X-RAY DIFFRACTIONr_rigid_bond_restr1.46532583
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 114 -
Rwork0.181 2420 -
all-2534 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2653-0.3758-4.7630.76590.61114.71390.3360.76230.311-0.2843-0.06690.0552-0.3471-0.7295-0.26910.1770.0699-0.04120.14680.03790.044425.2503-3.9224-0.9224
21.24710.3755-0.16471.63520.39711.38010.02320.03550.0751-0.14190.0349-0.0492-0.1569-0.0408-0.05810.07860.01720.01260.07030.00590.077928.99557.228321.0318
31.5346-1.0672-0.9832.07490.67672.87530.06660.04170.1113-0.19930.008-0.1281-0.2996-0.007-0.07460.14120.01070.01420.08320.00980.059932.9099-2.27583.6287
40.82870.22070.03311.28830.36141.14450.061-0.00380.0266-0.07590.0248-0.1007-0.0566-0.0084-0.08580.08050.01750.00470.0836-0.00010.099430.49995.32424.2314
50.8970.9744-0.25442.0717-0.07370.6031-0.0190.01670.1054-0.0193-0.021-0.10720.09260.0090.040.14990.0066-0.02140.16640.02940.169330.3533-19.822130.1615
60.679-0.4226-0.56871.3917-1.83367.5161-0.04880.0555-0.0859-0.02440.15370.23440.1254-1.1553-0.10490.0131-0.0214-0.01030.2571-0.00390.119510.9792-5.328325.0179
71.1620.006-0.50680.9138-0.49141.6361-0.0250.0074-0.1077-0.14260.01420.03130.1697-0.10790.01080.0877-0.0168-0.01640.0815-0.01160.073129.037-18.682412.9357
80.12980.0790.10240.9154-0.02222.7160.0241-0.0012-0.03950.0763-0.04590.07840.0134-0.1940.02180.06-0.0141-0.00110.13420.00030.109818.8019-8.844328.2074
91.5981-0.3654-0.57090.3782-0.37661.26080.00080.0215-0.039-0.0812-0.0040.02570.1496-0.03360.00320.10360.0032-0.00880.0857-0.00960.088332.9998-17.784912.4805
1020.6252-7.9147-3.080421.4658-13.057711.4661-0.4811-0.83091.01421.1508-0.1883-1.499-0.68950.52230.66940.1017-0.0729-0.06860.2093-0.09470.297145.0465-6.972614.1544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 77
3X-RAY DIFFRACTION3A78 - 112
4X-RAY DIFFRACTION4A113 - 146
5X-RAY DIFFRACTION5A147 - 167
6X-RAY DIFFRACTION6B1 - 25
7X-RAY DIFFRACTION7B26 - 77
8X-RAY DIFFRACTION8B78 - 112
9X-RAY DIFFRACTION9B113 - 146
10X-RAY DIFFRACTION10B147 - 167

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