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- PDB-3k1s: Crystal Structure of the PTS Cellobiose Specific Enzyme IIA from ... -

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Basic information

Entry
Database: PDB / ID: 3k1s
TitleCrystal Structure of the PTS Cellobiose Specific Enzyme IIA from Bacillus anthracis
ComponentsPTS system, cellobiose-specific IIA component
KeywordsTRANSFERASE / all alpha protein / spectrin repeat-like / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / metal ion binding
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Lichenan-specific phosphotransferase enzyme IIA component / PTS system, cellobiose-specific IIA component
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the PTS Cellobiose Specific Enzyme IIA from Bacillus anthracis
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system, cellobiose-specific IIA component
B: PTS system, cellobiose-specific IIA component
C: PTS system, cellobiose-specific IIA component
D: PTS system, cellobiose-specific IIA component
E: PTS system, cellobiose-specific IIA component
F: PTS system, cellobiose-specific IIA component
G: PTS system, cellobiose-specific IIA component
H: PTS system, cellobiose-specific IIA component
I: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,97729
Polymers111,4769
Non-polymers50120
Water11,115617
1
A: PTS system, cellobiose-specific IIA component
B: PTS system, cellobiose-specific IIA component
C: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,36911
Polymers37,1593
Non-polymers2108
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-41 kcal/mol
Surface area15010 Å2
MethodPISA
2
D: PTS system, cellobiose-specific IIA component
E: PTS system, cellobiose-specific IIA component
F: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2989
Polymers37,1593
Non-polymers1396
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-37 kcal/mol
Surface area15080 Å2
MethodPISA
3
G: PTS system, cellobiose-specific IIA component
H: PTS system, cellobiose-specific IIA component
I: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3109
Polymers37,1593
Non-polymers1526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-39 kcal/mol
Surface area15170 Å2
MethodPISA
4
A: PTS system, cellobiose-specific IIA component
B: PTS system, cellobiose-specific IIA component
C: PTS system, cellobiose-specific IIA component
hetero molecules

A: PTS system, cellobiose-specific IIA component
B: PTS system, cellobiose-specific IIA component
C: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,73822
Polymers74,3176
Non-polymers42016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area15650 Å2
ΔGint-90 kcal/mol
Surface area26410 Å2
MethodPISA
5
D: PTS system, cellobiose-specific IIA component
E: PTS system, cellobiose-specific IIA component
F: PTS system, cellobiose-specific IIA component
hetero molecules

G: PTS system, cellobiose-specific IIA component
H: PTS system, cellobiose-specific IIA component
I: PTS system, cellobiose-specific IIA component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60818
Polymers74,3176
Non-polymers29112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area15280 Å2
ΔGint-87 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.887, 92.887, 260.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
PTS system, cellobiose-specific IIA component


Mass: 12386.215 Da / Num. of mol.: 9 / Mutation: N-terminal Ser-Asn-Ala expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: celC-2, celC2, BAS5057, BA_5442, GBAA5442, GBAA_5442 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81X08, UniProt: A0A6H3A5D1*PLUS
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / pH: 7
Details: 30% PEG3350, 200mM sodium formate, 10mM fructose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 51800 / Num. obs: 48951 / % possible obs: 94.5 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.5 / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.6 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→43.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.601 / SU ML: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.226 2506 5.1 %
Rwork0.185 --
obs0.187 48925 94.6 %
all-51800 -
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 37.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å2-0 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 20 621 8229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7491.95610368
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.695995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98326.478372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.816151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5151520
X-RAY DIFFRACTIONr_chiral_restr0.0540.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5941.54825
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7727692
X-RAY DIFFRACTIONr_scbond_it4.88332880
X-RAY DIFFRACTIONr_scangle_it7.1374.52656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.284 173 -
Rwork0.216 3414 -
obs--95.73 %
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)
11.10090.3965-0.11421.25860.02431.1621-0.03350.0983-0.0468-0.10630.1003-0.1557-0.0852-0.0177-0.06680.2808-0.0419-0.00050.28960.00850.005426.341-12.95956.618
21.5145-0.155-0.27431.58240.51521.5352-0.06090.0067-0.0468-0.02060.0023-0.2272-0.04780.16740.05860.2927-0.0368-0.02750.27010.03020.040743.082-5.61862.795
31.70930.2267-0.17310.7793-0.15591.17550.01760.0425-0.1802-0.0038-0.0477-0.12630.10640.11210.03010.2894-0.0319-0.04750.25580.02160.049135.243-20.62972.328
41.40940.65150.20482.56111.2192.2180.0182-0.0711-0.11660.0514-0.0603-0.05310.0632-0.09370.0420.29010.00060.04350.28980.01720.043840.6164.23242.535
50.8455-0.1106-0.68781.51430.30823.1514-0.0580.19170.0820.0590.04760.2149-0.0542-0.47150.01040.33370.02560.04620.36240.05210.064824.86211.6349.86
61.1242-0.15550.25230.90350.38991.47160.15880.1115-0.1176-0.1804-0.0088-0.1129-0.079-0.1885-0.15010.36360.02820.04550.35260.04320.057732.76219.88334.693
71.4070.81940.10142.10730.19371.8222-0.07120.14190.097-0.32210.1921-0.0633-0.10290.2185-0.12090.34160.0092-0.02860.3278-0.02580.046258.942-16.90178.698
81.05730.899-0.23132.08990.39311.0762-0.11160.0399-0.0929-0.09790.186-0.1917-0.00750.1674-0.07450.28860.0162-0.03760.3436-0.06480.070666.716-8.36793.976
91.00530.02280.50541.59830.26071.181-0.036-0.02560.0846-0.1020.0052-0.0294-0.18160.1430.03080.34230.0026-0.03740.2997-0.05240.064150.631-1.20286.118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 105
2X-RAY DIFFRACTION2B5 - 105
3X-RAY DIFFRACTION3C5 - 105
4X-RAY DIFFRACTION4D5 - 105
5X-RAY DIFFRACTION5E5 - 105
6X-RAY DIFFRACTION6F5 - 105
7X-RAY DIFFRACTION7G5 - 105
8X-RAY DIFFRACTION8H5 - 105
9X-RAY DIFFRACTION9I5 - 105

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