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- PDB-4jg2: Structure of phage-related protein from Bacillus cereus ATCC 10987 -

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Basic information

Entry
Database: PDB / ID: 4jg2
TitleStructure of phage-related protein from Bacillus cereus ATCC 10987
ComponentsPhage-related protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / phage-related protein
Function / homologyEnterobacter phage Enc34, ssDNA-binding protein / Enterobacter phage Enc34, ssDNA-binding protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Phage-related protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. ...Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Structure of phage-related protein from Bacillus cereus ATCC 10987
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural ...Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage-related protein


Theoretical massNumber of molelcules
Total (without water)22,9621
Polymers22,9621
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.532, 51.476, 73.345
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 Phage-related protein


Mass: 22962.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_0376 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q73EI2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 1.83 Å3/Da / Density % sol: 32.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MMT buffer, 25% PEG 1500, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2013 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 42130 / Num. obs: 42130 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 41.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.89 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.329 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16349 2127 5.1 %RANDOM
Rwork0.12434 ---
obs0.12631 39942 99.77 %-
all-39942 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.3→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 0 312 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191571
X-RAY DIFFRACTIONr_bond_other_d0.0010.021436
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9452154
X-RAY DIFFRACTIONr_angle_other_deg0.86833318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23925.32577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.64215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.808159
X-RAY DIFFRACTIONr_chiral_restr0.130.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211940
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02369
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_it1.9980.967821
X-RAY DIFFRACTIONr_mcbond_other1.9820.963820
X-RAY DIFFRACTIONr_mcangle_it2.3121.4581049
X-RAY DIFFRACTIONr_scbond_it4.1161.291750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.9533007
X-RAY DIFFRACTIONr_sphericity_free35.811574
X-RAY DIFFRACTIONr_sphericity_bonded11.39553213
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 155 -
Rwork0.219 2850 -
obs--98.11 %
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)
10.6853-0.1107-0.07880.97850.13330.4760.011-0.00070.02680.0025-0.0168-0.0003-0.03960.00350.00590.0125-0.00150.00210.01790.00010.001914.6483-2.30890.4202
21.0961-0.5988-0.4590.60550.47240.71240.0830.10740.1244-0.0974-0.0219-0.1045-0.09430.0193-0.0610.032-0.00260.0260.02650.01650.043724.18355.4713-8.5197
30.3020.1135-0.02360.2007-0.01950.15040.0305-0.02-0.00080.0183-0.0246-0.0053-0.01760.0073-0.00590.01460.00370.0050.01210.00230.007211.1558-6.858-0.0435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 49
2X-RAY DIFFRACTION2A50 - 90
3X-RAY DIFFRACTION3A91 - 176

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