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- PDB-2ao9: Structural Genomics, The crystal structure of a Phage protein (ph... -

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Basic information

Entry
Database: PDB / ID: 2ao9
TitleStructural Genomics, The crystal structure of a Phage protein (phBC6A51) from Bacillus cereus ATCC 14579
ComponentsPhage protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nine-fold NCS. / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHomeodomain, phBC6A51-type / Helix-turn-helix of insertion element transposase / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Phage protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Joachimiak, G. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a Phage protein (phBC6A51) from Bacillus cereus ATCC 14579
Authors: Zhang, R. / Joachimiak, G. / Collart, F. / Joachimiak, A.
History
DepositionAug 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage protein
B: Phage protein
C: Phage protein
D: Phage protein
E: Phage protein
F: Phage protein
G: Phage protein
H: Phage protein
I: Phage protein


Theoretical massNumber of molelcules
Total (without water)160,8449
Polymers160,8449
Non-polymers00
Water17,493971
1
A: Phage protein
B: Phage protein
C: Phage protein
D: Phage protein
E: Phage protein
F: Phage protein
G: Phage protein
H: Phage protein
I: Phage protein

A: Phage protein
B: Phage protein
C: Phage protein
D: Phage protein
E: Phage protein
F: Phage protein
G: Phage protein
H: Phage protein
I: Phage protein


Theoretical massNumber of molelcules
Total (without water)321,68718
Polymers321,68718
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area78210 Å2
ΔGint-473 kcal/mol
Surface area83550 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.016, 150.481, 99.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe deposited structure represents the nonamer in the asymmetric unit. The biological assembly is two nonamers. The second nonamer is genarated by the two fold acis: -x,-y,z

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Components

#1: Protein
Phage protein / Bacteriophage phBC6A51


Mass: 17871.504 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81ES4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.67 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.26M (NH)4SO4, 0.1M CHES. 0.2M NaCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 28, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 135664 / Num. obs: 134863 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.76
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2 / Num. unique all: 25899 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→39.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.433 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23581 6772 5 %RANDOM
Rwork0.20494 ---
all0.2065 128540 --
obs0.2065 128090 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.437 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8172 0 0 971 9143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228274
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.98111079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.125980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96925.746402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.683151727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7581545
X-RAY DIFFRACTIONr_chiral_restr0.0730.21240
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025985
X-RAY DIFFRACTIONr_nbd_refined0.1990.24366
X-RAY DIFFRACTIONr_nbtor_refined0.2940.25737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2800
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.228
X-RAY DIFFRACTIONr_mcbond_it0.8261.55166
X-RAY DIFFRACTIONr_mcangle_it1.32627952
X-RAY DIFFRACTIONr_scbond_it2.14433581
X-RAY DIFFRACTIONr_scangle_it3.224.53127
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 451 -
Rwork0.252 9257 -
obs--98.28 %
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)
10.33080.1193-0.12091.43650.32620.79450.0673-0.0753-0.02720.2665-0.0716-0.0910.00090.17120.00430.014-0.0498-0.07250.0148-0.0016-0.084375.2773.24549.341
20.31520.0620.02360.430.12381.3504-0.0060.02740.0155-0.07440.0592-0.0859-0.19580.1159-0.0532-0.021-0.06410.0355-0.0243-0.0036-0.02776.06719.156.002
30.5514-0.24060.00821.35470.33330.2676-0.0205-0.0059-0.1189-0.0552-0.02290.07260.02130.0840.0434-0.0290.02830.0412-0.0347-0.0229-0.001874.08-13.944-0.18
40.16480.03760.06711.19040.66111.3750.00110.01050.0187-0.17080.0019-0.0852-0.06070.083-0.003-0.0399-0.02060.0412-0.0107-0.0185-0.05374.0333.745-2.127
50.32870.0469-0.13561.1685-0.68020.89190.0168-0.02950.0486-0.00230.0309-0.0907-0.08950.0609-0.0477-0.0075-0.07690.0212-0.0687-0.0143-0.0176.23325.40122.602
60.60430.3126-0.22720.5643-0.35551.31710.04630.0384-0.17040.07050.0167-0.10650.2040.1023-0.0630.0120.0884-0.0637-0.08370.0182-0.006273.354-25.47232.166
70.35870.1803-0.07870.64850.38871.55820.0882-0.0049-0.08660.1845-0.0718-0.12570.08530.0819-0.01640.02240.0215-0.0823-0.03590.0315-0.061972.795-13.92844.769
80.49680.2050.05750.62420.24430.4215-0.0389-0.08950.0769-0.00870.01920.0543-0.12780.15670.01970.0469-0.0818-0.054-0.0083-0.0392-0.038475.76219.65743.049
90.84350.6329-0.11971.3670.11260.0811-0.0811-0.0748-0.24780.3170.0095-0.16190.04730.09430.07160.05140.07390.0319-0.02120.00670.066973.042-23.94412.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 6313 - 63
2X-RAY DIFFRACTION1AA64 - 13264 - 132
3X-RAY DIFFRACTION2BB14 - 6314 - 63
4X-RAY DIFFRACTION2BB64 - 13164 - 131
5X-RAY DIFFRACTION3CC14 - 6314 - 63
6X-RAY DIFFRACTION3CC64 - 13264 - 132
7X-RAY DIFFRACTION4DD23 - 6323 - 63
8X-RAY DIFFRACTION4DD64 - 13264 - 132
9X-RAY DIFFRACTION5EE14 - 6314 - 63
10X-RAY DIFFRACTION5EE64 - 13264 - 132
11X-RAY DIFFRACTION6FF16 - 6316 - 63
12X-RAY DIFFRACTION6FF64 - 13164 - 131
13X-RAY DIFFRACTION7GG24 - 6324 - 63
14X-RAY DIFFRACTION7GG64 - 13264 - 132
15X-RAY DIFFRACTION8HH15 - 6315 - 63
16X-RAY DIFFRACTION8HH64 - 13064 - 130
17X-RAY DIFFRACTION9II23 - 6323 - 63
18X-RAY DIFFRACTION9II64 - 13364 - 133

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