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- PDB-2euc: Crystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324 -

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Basic information

Entry
Database: PDB / ID: 2euc
TitleCrystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324
ComponentsHypothetical protein yfmB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG
Function / homologyHypothetical protein YfmB / Protein of unknown function DUF3212 / YfmB domain superfamily / Protein of unknown function (DUF3212) / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YfmB
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBenach, J. / Abashidze, M. / Jayaraman, S. / Janjua, H. / Cooper, B. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of YfmB from bacillus subtilis NESG TARGET SR324.
Authors: Benach, J. / Abashidze, M. / Jayaraman, S. / Rong, X. / Acton, T.B. / Montelione, G.T. / Tong, L.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yfmB
B: Hypothetical protein yfmB


Theoretical massNumber of molelcules
Total (without water)30,6192
Polymers30,6192
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-25 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.543, 67.637, 78.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein yfmB


Mass: 15309.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yfmB / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / References: UniProt: O34626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789, 0.9795, 0.96804
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97951
30.968041
ReflectionResolution: 2.5→30 Å / Num. obs: 22474 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 35.107
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 1.76 / % possible all: 83.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→24.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 843866.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1599 9.1 %RANDOM
Rwork0.274 ---
obs0.274 17606 74 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7618 Å2 / ksol: 0.298453 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--9.69 Å20 Å20 Å2
2---9.15 Å20 Å2
3---18.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 216 1960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.436 119 9.1 %
Rwork0.431 1190 -
obs--33.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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