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- PDB-4guc: 1.4 Angstrom resolution crystal structure of uncharacterized prot... -

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Basic information

Entry
Database: PDB / ID: 4guc
Title1.4 Angstrom resolution crystal structure of uncharacterized protein BA_2500 from Bacillus anthracis str. Ames
ComponentsProtein BA_2500
KeywordsUNKNOWN FUNCTION / virulence / pathogenesis / vaccine candidate / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


Immunoglobulin-like - #3720 / Protein of unknown function DUF5065 / Domain of unknown function (DUF5065) / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DUF5065 family protein / Uncharacterized protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.4 Angstrom resolution crystal structure of uncharacterized protein BA_2500 from Bacillus anthracis str. Ames
Authors: Halavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein BA_2500
B: Protein BA_2500
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2396
Polymers27,7852
Non-polymers4554
Water5,441302
1
A: Protein BA_2500
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9842
Polymers13,8921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein BA_2500
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2554
Polymers13,8921
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.470, 34.708, 61.928
Angle α, β, γ (deg.)81.33, 79.45, 70.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein BA_2500


Mass: 13892.291 Da / Num. of mol.: 2 / Fragment: UNP residues 40-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_2500, BAS2320, GBAA_2500 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81QC7, UniProt: A0A6L7HJ72*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.96 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystallization condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris pH 5.6. Freezing condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris 7% Glyserol,7% EG, 7% Sucrose. Protein: 3.4 ...Details: Crystallization condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris pH 5.6. Freezing condition: 25% PEG 3350, 0.2M Na Chloride, 0.1M Bis-Tris 7% Glyserol,7% EG, 7% Sucrose. Protein: 3.4 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03316 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2012 / Details: Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 39510 / Num. obs: 39510 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.22
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1892 / % possible all: 92.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.215 / SU ML: 0.041 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18693 1745 4.9 %RANDOM
Rwork0.14737 ---
obs0.14932 33587 85.32 %-
all-33587 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.227 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.24 Å2-0.04 Å2
2--0.5 Å20.02 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 30 302 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212086
X-RAY DIFFRACTIONr_bond_other_d0.0010.021413
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9412825
X-RAY DIFFRACTIONr_angle_other_deg0.8833423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7485250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77623.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.19815336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.246159
X-RAY DIFFRACTIONr_chiral_restr0.1190.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022372
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02469
X-RAY DIFFRACTIONr_mcbond_it1.1941.51196
X-RAY DIFFRACTIONr_mcbond_other0.381.5500
X-RAY DIFFRACTIONr_mcangle_it1.95921937
X-RAY DIFFRACTIONr_scbond_it2.5883890
X-RAY DIFFRACTIONr_scangle_it3.9564.5888
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 79 -
Rwork0.153 1345 -
obs-1345 45.98 %
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)
11.2104-0.01960.22940.66430.26371.7928-0.04060.0217-0.0196-0.03480.0313-0.0240.1032-0.02130.00930.013-0.00760.00410.04130.00930.035238.639622.007538.6341
20.703-0.08720.03691.6729-1.25452.2607-0.00050.03460.0539-0.00550.05350.0813-0.0797-0.0188-0.05310.01850.00470.00750.0243-0.00270.05434.011330.532948.7841
30.7216-0.1859-0.52980.93210.12612.22660.0280.08120.0132-0.0940.0036-0.0285-0.13510.1307-0.03160.0173-0.01230.00020.05370.00480.043543.60427.308836.7584
40.6031-0.0008-0.39470.542-0.44161.47490.0162-0.01080.07850.0464-0.0423-0.0073-0.16260.13550.02610.0205-0.0186-0.00520.03430.00750.030238.272731.074148.767
51.5165-0.99070.57114.6281-1.29512.97090.01410.04720.0778-0.1044-0.0041-0.0577-0.0101-0.0349-0.00990.0091-0.00850.01410.0582-0.00120.035235.30627.882539.6226
61.8956-0.2974-0.21260.90160.51131.7671-0.031-0.1453-0.03480.08130.00420.05150.0680.01190.02680.02960.00210.00480.01250.00660.031245.923920.292377.173
71.1234-0.5141-0.06761.61170.95822.0030.05530.07720.01290.0105-0.11280.1075-0.00470.0530.05750.0043-0.00040.00060.0185-0.00480.070251.100723.978162.7193
80.9670.1468-0.07860.42480.1242.87130.0385-0.03220.0469-0.0043-0.0047-0.0304-0.0861-0.1197-0.03380.00840.0061-0.00050.0101-0.00230.031242.533624.99871.7172
90.69740.10540.13972.0276-0.26491.64410.00850.06060.073-0.07660.04750.0352-0.07320.0029-0.0560.00920.0003-0.00640.00650.00120.082147.078927.522963.9229
102.15360.18430.53231.3502-0.48362.07890.046-0.0181-0.10040.0354-0.068-0.21150.0534-0.00150.02210.0193-0.00380.00560.01260.00520.050948.664922.348871.6609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 67
2X-RAY DIFFRACTION2A68 - 86
3X-RAY DIFFRACTION3A87 - 111
4X-RAY DIFFRACTION4A112 - 143
5X-RAY DIFFRACTION5A144 - 156
6X-RAY DIFFRACTION6B42 - 64
7X-RAY DIFFRACTION7B65 - 87
8X-RAY DIFFRACTION8B88 - 117
9X-RAY DIFFRACTION9B118 - 139
10X-RAY DIFFRACTION10B140 - 156

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