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- PDB-3dm8: Crystal Structure of Putative Isomerase from Rhodopseudomonas pal... -

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Basic information

Entry
Database: PDB / ID: 3dm8
TitleCrystal Structure of Putative Isomerase from Rhodopseudomonas palustris
Componentsuncharacterized protein RPA4348
Keywordsstructural genomics / unknown function / SIRAS / Putative Isomerase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DODECYL NONA ETHYLENE GLYCOL ETHER / Nuclear transport factor 2 family protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR/SIRAS / Resolution: 1.8 Å
AuthorsCymborowski, M. / Chruszcz, M. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris
Authors: Cymborowski, M. / Minor, W.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein RPA4348
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9442
Polymers16,3611
Non-polymers5831
Water3,135174
1
A: uncharacterized protein RPA4348
hetero molecules

A: uncharacterized protein RPA4348
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8874
Polymers32,7222
Non-polymers1,1662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.593, 84.071, 97.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

21A-224-

HOH

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Components

#1: Protein uncharacterized protein RPA4348


Mass: 16360.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA4348 / Plasmid: P15TV LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6N1Q6
#2: Chemical ChemComp-CE9 / DODECYL NONA ETHYLENE GLYCOL ETHER / POLYDOCANOL / THESIT


Mass: 582.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: PEG400 15%, MgCl2 0.2M, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97912 / Wavelength: 0.97912 Å
DetectorType: APS-1 / Detector: CCD / Date: Feb 8, 2007 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.8→48.62 Å / Num. all: 15870 / Num. obs: 15870 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 35
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.322 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
Cootmodel building
REFMAC5.4.0069refinement
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SIR/SIRAS / Resolution: 1.8→48.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.219 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 790 5 %RANDOM
Rwork0.178 ---
all0.18 15828 --
obs0.18 15828 --
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: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 12 174 1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221129
X-RAY DIFFRACTIONr_bond_other_d0.0010.02782
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.9471528
X-RAY DIFFRACTIONr_angle_other_deg1.42831880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40822.14356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81815192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4541514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02258
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_it1.0011.5682
X-RAY DIFFRACTIONr_mcbond_other0.3331.5277
X-RAY DIFFRACTIONr_mcangle_it1.86821101
X-RAY DIFFRACTIONr_scbond_it3.2373447
X-RAY DIFFRACTIONr_scangle_it5.0834.5423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 51 -
Rwork0.193 1058 -
obs--96.27 %
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)
11.8018-0.20050.13321.24740.1591.843-0.0246-0.0331-0.1430.0738-0.00140.03330.19230.12780.0261-0.0298-0.0007-0.00060.01380.002-0.0122.03130.27536.448
211.5955-5.6667-4.69529.7302000.1793-0.15840.0838-0.11570.2911.50390.2437-0.4958-0.4702-0.0277-0.0115-0.0185-0.0020.03840.1061.96225.87951.643
32.3941-2.2331-0.02522.1782-0.40951.9679-0.22770.0897-0.30020.17830.06060.0210.0952-0.03790.167-0.04670.0006-0.00050.0398-0.01740.10731.83632.60648.604
414.79663.94580.91873.68023.12864.3582-0.0673-0.1274-0.0207-0.0426-0.16780.21-0.0898-0.40410.2352-0.0722-0.0045-0.02340.0361-0.0007-0.0039-7.10737.21536.288
58.2821-2.92565.02726.8972-2.48875.7531-0.15190.3598-0.5160.21430.1323-0.4065-0.12860.49910.0197-0.09860.0096-0.01190.1057-0.07610.052715.98836.61649.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 683 - 68
2X-RAY DIFFRACTION2AA69 - 7469 - 74
3X-RAY DIFFRACTION3AA75 - 10875 - 108
4X-RAY DIFFRACTION4AA109 - 121109 - 121
5X-RAY DIFFRACTION5AA122 - 135122 - 135

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