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- PDB-2xc8: Crystal structure of the gene 22 product of the Bacillus subtilis... -

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Basic information

Entry
Database: PDB / ID: 2xc8
TitleCrystal structure of the gene 22 product of the Bacillus subtilis SPP1 phage
ComponentsGENE 22 PRODUCT
KeywordsVIRAL PROTEIN / SIPHOVIRIDAE / GRAM-POSITIVE PHAGE
Function / homologyImmunoglobulin-like - #2980 / : / : / Gp22 / Immunoglobulin-like / Sandwich / Mainly Beta / Bacteriophage SPP1 complete nucleotide sequence
Function and homology information
Biological speciesBACILLUS PHAGE SPP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsVeesler, D. / Blangy, S. / Tavares, P. / Campanacci, V. / Cambillau, C.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal Structure of Bacillus Subtilis Spp1 Phage Gp22 Shares Fold Similarity with a Domain of Lactococcal Phage P2 Rbp.
Authors: Veesler, D. / Blangy, S. / Spinelli, S. / Tavares, P. / Campanacci, V. / Cambillau, C.
History
DepositionApr 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 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 1.4Nov 13, 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 / _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: GENE 22 PRODUCT
B: GENE 22 PRODUCT
C: GENE 22 PRODUCT


Theoretical massNumber of molelcules
Total (without water)50,4733
Polymers50,4733
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.911, 64.116, 101.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5267, 1.265, -0.1724), (0.5686, -0.5274, 0.01672), (-0.01258, -0.04301, -0.9973)
Vector: -0.6503, 0.3375, -0.3524)

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Components

#1: Protein GENE 22 PRODUCT / BACTERIOPHAGE SPP1 COMPLETE NUCLEOTIDE SEQUENCE


Mass: 16824.293 Da / Num. of mol.: 3
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: O48465
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.24 Å3/Da / Density % sol: 44.74 % / Description: NONE
Crystal growDetails: 0.1 M MES PH 7.2, 0.01 M COCL2, 2.05 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→54.14 Å / Num. obs: 12165 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.3
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 6.3 / % 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: 2.35→39.68 Å / Cor.coef. Fo:Fc: 0.9111 / Cor.coef. Fo:Fc free: 0.8896 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 904 7.5 %RANDOM
Rwork0.2066 ---
obs0.2094 12092 100 %-
Displacement parametersBiso mean: 33.02 Å2
Baniso -1Baniso -2Baniso -3
1-7.7343 Å20 Å20 Å2
2---12.5853 Å20 Å2
3---4.851 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 0 132 2213
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0142133HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.5252903HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d717SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it2133HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.57
X-RAY DIFFRACTIONt_other_torsion17.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion273SEMIHARMONIC5
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_contact2390SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.57 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2759 207 7.27 %
Rwork0.2185 2639 -
all0.2224 2846 -
obs--100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°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)
1refined-24.708911.4145-14.8883
2refined-27.11398.5783-1.48464.66790.14690.51241.26681.0611.3588-0.07010.2091-0.0199-0.1164-0.05230.0076-0.04850.0950.1224-0.02240.0160.0380.126-0.0428-0.1105
3refined-34.953313.5577-19.06451.43521.0365-1.13752.4755-2.16682.38890.0094-0.0792-0.00250.309-0.0079-0.032-0.22420.0566-0.0015-0.0954-0.0017-0.0103-0.004-0.0048-0.0679
4refined-51.5236.216-41.53010.698-1.02140.2862.11422.00940.3966-0.01270.09180.0254-0.030.00060.0707-0.0396-0.06160.01210.0294-0.0901-0.10720.00810.0341-0.0057
5refined-11.17364.368-20.68825.0722-1.4024-2.71761.2066-1.05141.2073-0.01550.05980.02670.02-0.0298-0.0559-0.02060.02730.0453-0.0053-0.0553-0.04150.0088-0.0691-0.0303
6refined-9.82286.104-34.63944.55680.91142.91040.1276-0.10843.0160.0025-0.2614-0.17650.1969-0.02350.15830.0601-0.20130.0211-0.0832-0.04030.03830.055-0.0482-0.0237
7refined-1.57-0.9887-32.70642.07880.77861.30980.0730.29222.1597-0.01090.18230.1094-0.041-0.0765-0.02730.04850.22210.0874-0.0756-0.008-0.0097-0.0337-0.0345-0.0508
8refined-18.33082.5725-27.27171.36611.929-0.43471.12640.597800.0050.06350.0084-0.0189-0.04440.03920.05620.00440.0395-0.0552-0.03620.00540.1487-0.0773-0.1035
9refined-19.49.86440.45581.73731.08050.26020.00970.8322.17640.0148-0.1587-0.1844-0.0489-0.16780.0370.092-0.03690.1531-0.0584-0.01050.00510.0278-0.00050.0343
100.1205-0.48380.55690.0028-0.28810.3750.00230.0028-0.0042-0.0032-0.0055-0.010.00980.00830.00320.01020.06680.03640.0647-0.0327-0.0797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A 20-37)
2X-RAY DIFFRACTION2(CHAIN A 38-113)
3X-RAY DIFFRACTION3(CHAIN A 114-121)
4X-RAY DIFFRACTION4(CHAIN A 126-137)
5X-RAY DIFFRACTION5(CHAIN B 1-36)
6X-RAY DIFFRACTION6(CHAIN B 37-88)
7X-RAY DIFFRACTION7(CHAIN B 89-96)
8X-RAY DIFFRACTION8(CHAIN B 97-120)
9X-RAY DIFFRACTION9(CHAIN B 126-132)

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