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- PDB-2xf6: Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putat... -

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Basic information

Entry
Database: PDB / ID: 2xf6
TitleCrystal structure of Bacillus subtilis SPP1 phage gp23.1, a putative chaperone.
ComponentsGP23.1
KeywordsVIRAL PROTEIN / CHAPERONE
Function / homologyArc Repressor Mutant, subunit A - #1530 / : / SPP1 phage GP23.1 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Bacteriophage SPP1 complete nucleotide sequence
Function and homology information
Biological speciesBACILLUS PHAGE SPP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsVeesler, D. / Blangy, S. / Lichiere, J. / Ortiz-Lombardia, M. / Tavares, P. / Campanacci, V. / Cambillau, C.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal Structure of Bacillus Subtilis Spp1 Phage Gp23.1, A Putative Chaperone.
Authors: Veesler, D. / Blangy, S. / Lichiere, J. / Ortizlombardia, M. / Tavares, P. / Campanacci, V. / Cambillau, C.
History
DepositionMay 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP23.1


Theoretical massNumber of molelcules
Total (without water)5,7611
Polymers5,7611
Non-polymers00
Water48627
1
A: GP23.1
x 6


Theoretical massNumber of molelcules
Total (without water)34,5686
Polymers34,5686
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555y,-x+y,z1
Buried area5820 Å2
ΔGint-43 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 52.400, 30.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

#1: Protein GP23.1


Mass: 5761.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SPP1 (virus) / Plasmid: PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS IQ PLYSS / References: UniProt: O48468
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.95 Å3/Da / Density % sol: 36.38 % / Description: NONE
Crystal growDetails: 0.1 M NA HEPES PH7.5 20 PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.12→45.38 Å / Num. obs: 2826 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 21.89 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.7
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER-TNT2.9.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→45.38 Å / Cor.coef. Fo:Fc: 0.9091 / Cor.coef. Fo:Fc free: 0.8498 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 931 33.03 %RANDOM
Rwork0.1912 ---
obs0.2056 2819 --
Displacement parametersBiso mean: 29.59 Å2
Baniso -1Baniso -2Baniso -3
1-8.6389 Å20 Å20 Å2
2--8.6389 Å20 Å2
3----17.2778 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.12→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms397 0 0 27 424
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015432HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.06594HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d143SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes15HARMONIC2
X-RAY DIFFRACTIONt_gen_planes63HARMONIC5
X-RAY DIFFRACTIONt_it432HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.3
X-RAY DIFFRACTIONt_other_torsion17.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion52SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact594SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.37 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.253 227 28.95 %
Rwork0.1975 557 -
all0.213 784 -
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)
11.7124-0.2515-1.13286.001-1.0831.2402-0.0765-0.0215-0.00540.11340.1580.00310.02720.012-0.0815-0.09760.02680.0208-0.05190.01770.043-12.1824-6.23770.2915
20.75710.743-1.10751.95962.61811.18340.0214-0.0238-0.21780.0109-0.0787-0.027-0.0575-0.0220.0572-0.1924-0.01120.0026-0.19630.02990.304-15.4422-16.8231.2556
37.3656-0.30812.16661.00010.9520.01690.12660.0146-0.3477-0.2116-0.0810.1486-0.1056-0.1794-0.0456-0.02170.03320.0125-0.08890.00230.0135-19.3499-5.9574-0.6602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A:2-18)
2X-RAY DIFFRACTION2(CHAIN A:19-32)
3X-RAY DIFFRACTION3(CHAIN A:33-50)

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