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- PDB-3ipf: Crystal structure of the Q251Q8_DESHY protein from Desulfitobacte... -

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Basic information

Entry
Database: PDB / ID: 3ipf
TitleCrystal structure of the Q251Q8_DESHY protein from Desulfitobacterium hafniense. Northeast Structural Genomics Consortium Target DhR8c.
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Q251Q8_DESHY / NESG / DhR8c / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore
Similarity search - Function
Immunoglobulin-like - #2000 / Spore protein YabP / Spore protein YabP/YqfC / YabP superfamily / YabP family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sporulation protein YabP
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Andre, I. / Rossi, P. / Kennedy, M. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q251Q8_DESHY protein from Desulfitobacterium hafniense.
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Andre, I. / Rossi, P. / Kennedy, M. / ...Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Andre, I. / Rossi, P. / Kennedy, M. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,0042
Polymers16,0042
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,0021
Polymers8,0021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,0021
Polymers8,0021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.796, 69.796, 132.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailsbiological unit is dimer according to gel-filtration and aggregation screening

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Components

#1: Protein uncharacterized protein


Mass: 8002.207 Da / Num. of mol.: 2 / Fragment: residues 20-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: DSY0195 / Plasmid: pET 21-23c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) +magic / References: UniProt: Q251Q8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293 K / Method: microbatch under paraffin oil
Details: 20% PEG 3350, 0.2M tri-lithium citrate, microbatch under paraffin oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97839 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97839 Å / Relative weight: 1
ReflectionResolution: 1.988→50 Å / Num. all: 24725 / Num. obs: 24675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 26.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: calculated CS Rosetta structure

Resolution: 1.988→33.741 Å / SU ML: 0.13 / σ(F): 1.89 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1217 4.95 %
Rwork0.1967 --
obs0.1984 24574 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.465 Å2 / ksol: 0.397 e/Å3
Refinement stepCycle: LAST / Resolution: 1.988→33.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 0 57 1103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081065
X-RAY DIFFRACTIONf_angle_d1.5651437
X-RAY DIFFRACTIONf_dihedral_angle_d19.146393
X-RAY DIFFRACTIONf_chiral_restr0.109170
X-RAY DIFFRACTIONf_plane_restr0.006182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9885-2.06810.33161270.25762506X-RAY DIFFRACTION96
2.0681-2.16220.23291460.22452592X-RAY DIFFRACTION99
2.1622-2.27620.2941500.20282581X-RAY DIFFRACTION100
2.2762-2.41880.26811450.20772627X-RAY DIFFRACTION100
2.4188-2.60540.23151480.20952594X-RAY DIFFRACTION100
2.6054-2.86750.23681460.2132598X-RAY DIFFRACTION100
2.8675-3.28220.251460.20172602X-RAY DIFFRACTION100
3.2822-4.1340.17781110.16752649X-RAY DIFFRACTION100
4.134-33.74630.2141980.18142608X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.7564-0.68530.50723.2557-0.43992.39870.03960.008-0.05380.1269-0.0187-0.05850.04-0.1536-0.00740.1705-0.0111-0.01630.17620.05360.161510.262456.144945.1119
21.3115-0.11120.50862.3886-1.55030.85420.0556-0.0065-0.0023-0.01110.0637-0.0230.0147-0.1187-0.12770.2033-0.0145-0.01830.20960.05770.195
Refinement TLS groupSelection details: chain B

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