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- PDB-3k63: X-ray structure of the PF04200 domain from Q9PRA0_UREPA protein o... -

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Basic information

Entry
Database: PDB / ID: 3k63
TitleX-ray structure of the PF04200 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. NESG target UuR17a.
ComponentsConserved hypothetical membrane lipoprotein
KeywordsLIPID BINDING PROTEIN / LIPOPROTEIN-17 / Q9PRA0 / PF04200 / DUF1976 / UUR17A / NESG. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Lipoprotein
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #270 / Lipoprotein-associated domain / Lipoprotein associated domain / Uncharacterised protein family MG067 / Mycoplasma peptidase DUF31 / Mycoplasma peptidase (DUF31) / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Membrane-associated lipoprotein
Similarity search - Component
Biological speciesUreaplasma parvum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.494 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray structure of the PF04200 domain from Q9PRA0_UREPA protein of Ureaplasma parvum.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,8761
Polymers14,8761
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.557, 60.557, 64.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsmonomer according to gel-filtration

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Components

#1: Protein Conserved hypothetical membrane lipoprotein


Mass: 14876.400 Da / Num. of mol.: 1 / Fragment: Lipoprotein_17 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma parvum (bacteria) / Strain: ATCC 700970 / SEROVAR 3 / Gene: UU045 / Plasmid: PET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) +MAGIC / References: UniProt: Q9PRA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7.5
Details: 40% PEG 8000, 0.1M KBr, 0.1M HEPES pH 7.5, MICROBATCH UNDER PARAFFIN OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.494→50 Å / Num. all: 9299 / Num. obs: 9252 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 36.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 3.65 / Num. unique all: 933 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXD/Emodel building
RESOLVEmodel building
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXD/Ephasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.494→27.538 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 426 4.61 %RANDOM
Rwork0.2131 ---
obs0.2147 9232 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.652 Å2 / ksol: 0.289 e/Å3
Refinement stepCycle: LAST / Resolution: 2.494→27.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 14 999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081006
X-RAY DIFFRACTIONf_angle_d1.6391357
X-RAY DIFFRACTIONf_dihedral_angle_d21.267374
X-RAY DIFFRACTIONf_chiral_restr0.112143
X-RAY DIFFRACTIONf_plane_restr0.009178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4944-2.8550.36521410.28512955X-RAY DIFFRACTION99
2.855-3.59580.30741520.23222912X-RAY DIFFRACTION100
3.5958-27.53970.19961330.18522939X-RAY DIFFRACTION99

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