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- PDB-3f3b: Structure of the phage-like element PBSX protein xkdH from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3f3b
TitleStructure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.
ComponentsPhage-like element PBSX protein xkdH
Keywordsstructural genomics / unknown function / NESG X-Ray SR362 P54328 Structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyProtein of unknown function DUF3599 / Protein of unknown function DUF3599 / XkdH-like superfamily / Domain of unknown function (DUF3599) / Thrombin, subunit H / Beta Barrel / Mainly Beta / PHOSPHATE ION / Phage-like element PBSX protein XkdH
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Neely, H. / Seetharaman, J. / Clayton, G. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Neely, H. / Seetharaman, J. / Clayton, G. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Structure of the phage-like element PBSX protein xkdH from Bacillus Subtilus. Northeast Structural Genomics Consortium target SR352.
Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Clayton, G. / Ho, C.K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Phage-like element PBSX protein xkdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3553
Polymers15,1651
Non-polymers1902
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.661, 42.661, 283.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Phage-like element PBSX protein xkdH


Mass: 15164.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xkdH, BSU12620 / References: UniProt: P54328
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.55M NaH2PO4, 0.5M KH2PO4, 0.08M Hepes-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 9878 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 49.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 16.9 / Num. unique all: 922 / % possible all: 96.4

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Processing

Software
NameVersionClassification
APEXdata collection
SnBphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 268301.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 518 5.5 %RANDOM
Rwork0.23 ---
obs0.23 9410 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2987 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--3.01 Å20 Å2
3----6.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 10 60 1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 82 5.6 %
Rwork0.288 1376 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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