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- PDB-2xf5: Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putat... -

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Basic information

Entry
Database: PDB / ID: 2xf5
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 / SAD / Resolution: 2 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. / Ortiz-Lombardia, 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 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP23.1
B: GP23.1
C: GP23.1
D: GP23.1
E: GP23.1
F: GP23.1


Theoretical massNumber of molelcules
Total (without water)35,1836
Polymers35,1836
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-47.9 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.737, 66.465, 82.933
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
GP23.1


Mass: 5863.895 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-51 / Mutation: YES
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.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 24 TO MSE ...ENGINEERED RESIDUE IN CHAIN A, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN E, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN E, LEU 24 TO MSE ENGINEERED RESIDUE IN CHAIN F, LEU 23 TO MSE ENGINEERED RESIDUE IN CHAIN F, LEU 24 TO MSE
Has protein modificationY
Sequence detailsDOUBLE MUTANT USED FOR PHASING

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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: 2.1 Å3/Da / Density % sol: 40.89 % / Description: NONE
Crystal growDetails: 1.6 M NA-CITRATE PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→51.86 Å / Num. obs: 20318 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER-TNT2.9.2refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→44.5 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9326 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 728 3.58 %RANDOM
Rwork0.1691 ---
obs0.1701 20315 --
Displacement parametersBiso mean: 36.41 Å2
Baniso -1Baniso -2Baniso -3
1-3.8369 Å20 Å20 Å2
2---10.3266 Å20 Å2
3---6.4897 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 2→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 137 2472
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0152399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.43261HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d789SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes338HARMONIC5
X-RAY DIFFRACTIONt_it2399HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion19.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion289SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2893SEMIHARMONIC4
LS refinement shellResolution: 2→2.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.1997 112 3.86 %
Rwork0.1805 2792 -
all0.1813 2904 -
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)
12.5169-0.4093-0.89493.08371.22415.1149-0.0101-0.06020.05010.0103-0.01560.111-0.21890.06690.0257-0.1334-0.00180.01340.269-0.0223-0.148518.534877.6824-16.4756
22.70062.2989-0.21321.729-1.30242.81790.0354-0.1485-0.26870.05880.0943-0.0853-0.00110.1747-0.1297-0.2534-0.02430.00690.3018-0.0238-0.229728.9977.2344-18.3762
32.8255-2.9104-0.46272.0611-2.85953.7537-0.1792-0.4398-0.00330.37910.046-0.0191-0.12790.41380.1332-0.0642-0.05140.00560.2736-0.0281-0.222621.956378.2149-10.4557
41.5264-0.8241-0.77266.38731.74024.92370.006-0.2021-0.02210.0675-0.00010.118-0.2316-0.0682-0.0059-0.1628-0.01780.01370.258-0.02-0.13797.25772.8915-36.9291
52.19580.1002-1.50044.5592-2.20243.0477-0.07750.110.0969-0.08310.08520.12960.0127-0.19-0.0076-0.1857-0.0064-0.04560.279-0.0364-0.1887-0.027271.4739-44.578
60.9836-0.64650.30272.6866-0.4351.124-0.0170.3517-0.18220.00560.0409-0.11350.074-0.0524-0.0238-0.13-0.0477-0.00190.2057-0.0308-0.132610.965770.4463-42.0944
71.6786-0.73860.47940.8058-0.25383.77340.09360.1742-0.135-0.1272-0.1135-0.06-0.1325-0.02320.0199-0.14040.0361-0.00990.2189-0.0008-0.17216.034778.6723-9.7441
81.56151.6026-0.79433.0193-2.85920.0250.0089-0.0212-0.0372-0.2575-0.0127-0.1097-0.1003-0.05470.0038-0.04560.01380.02020.2840.0263-0.181813.42180.3409-1.9652
97.7011-0.433-1.63452.2674-2.91045.49850.0401-0.0845-0.4101-0.02380.0195-0.0403-0.1725-0.3408-0.0596-0.08990.0366-0.00160.2448-0.0084-0.19682.669279.312-3.5541
104.22971.04490.47491.07541.87152.8254-0.04790.202-0.0438-0.0068-0.1393-0.1109-0.04930.28170.1872-0.08330.0383-0.01570.24530.0068-0.1407-5.626976.1057-16.5216
110.27252.8631-0.25081.60842.30973.2704-0.053-0.07960.08310.0523-0.0037-0.0775-0.1121-0.3110.0567-0.09870.0263-0.00280.2376-0.0014-0.1267-9.180878.7536-6.8516
124.37262.36171.26610-0.18975.3357-0.0340.1649-0.03630.0791-0.02840.030.2056-0.48160.0623-0.1430.00740.01660.2418-0.0025-0.1881-12.717775.7909-16.7905
135.2251-2.4309-0.4264.63771.36034.0144-0.10380.1365-0.18730.0971-0.13370.0279-0.1380.08580.2374-0.16720.01790.03440.2298-0.0301-0.1517-4.687673.9177-30.2258
140.5952.8191.74370.46061.21784.6169-0.0216-0.0647-0.43830.17470.0010.1651-0.0597-0.1820.0206-0.30080.0225-0.00040.2779-0.089-0.0267-15.197773.5595-28.1153
151.36682.733-1.23764.1624-0.5913.9867-0.19710.1715-0.4177-0.4274-0.14780.05540.0849-0.39590.3449-0.133-0.0146-0.00390.2698-0.0609-0.1895-8.071171.7241-35.9527
162.03941.3263-0.80114.4872.86635.5071-0.0747-0.14980.1640.07950.14440.0474-0.04770.4017-0.0696-0.186-0.0459-0.00210.2295-0.0463-0.158519.172274.6218-29.7924
172.112-0.39080.86453.6072-0.031.4834-0.0092-0.0342-0.0603-0.36660.2316-0.1804-0.1260.3174-0.2223-0.1515-0.05860.02340.2729-0.0552-0.152722.484672.2667-39.7389
185.57410.636-0.06575.05752.83955.1216-0.04960.07270.06060.11980.4879-0.30030.05270.5442-0.4383-0.304-0.0733-0.01190.2927-0.1508-0.29226.246374.3627-29.602
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)
4X-RAY DIFFRACTION4(CHAIN B:2-18)
5X-RAY DIFFRACTION5(CHAIN B:19-32)
6X-RAY DIFFRACTION6(CHAIN B:33-51)
7X-RAY DIFFRACTION7(CHAIN C:2-18)
8X-RAY DIFFRACTION8(CHAIN C:19-32)
9X-RAY DIFFRACTION9(CHAINC:33-50)
10X-RAY DIFFRACTION10(CHAIN D:3-18)
11X-RAY DIFFRACTION11(CHAIN D:19-32)
12X-RAY DIFFRACTION12(CHAIN D:33-50)
13X-RAY DIFFRACTION13(CHAIN E:2-18)
14X-RAY DIFFRACTION14(CHAIN E:19-32)
15X-RAY DIFFRACTION15(CHAIN E:33-50)
16X-RAY DIFFRACTION16(CHAIN F:2-18)
17X-RAY DIFFRACTION17(CHAIN F:19-32)
18X-RAY DIFFRACTION18(CHAIN F:33-50)

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