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- PDB-4mge: 1.85 Angstrom Resolution Crystal Structure of PTS System Cellobio... -

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Basic information

Entry
Database: PDB / ID: 4mge
Title1.85 Angstrom Resolution Crystal Structure of PTS System Cellobiose-specific Transporter Subunit IIB from Bacillus anthracis.
ComponentsPTS system, cellobiose-specific IIB component
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / PTS system IIB component-like / cellobiose-specific transporter
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity
Similarity search - Function
: / Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system, cellobiose-specific IIB component / PTS system, cellobiose-specific IIB component
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Shuvalova, L. / Halavaty, A. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.85 Angstrom Resolution Crystal Structure of PTS System Cellobiose-specific Transporter Subunit IIB from Bacillus anthracis.
Authors: Minasov, G. / Shuvalova, L. / Halavaty, A. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system, cellobiose-specific IIB component
B: PTS system, cellobiose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4154
Polymers25,3172
Non-polymers982
Water1,06359
1
A: PTS system, cellobiose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7563
Polymers12,6591
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PTS system, cellobiose-specific IIB component


Theoretical massNumber of molelcules
Total (without water)12,6591
Polymers12,6591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PTS system, cellobiose-specific IIB component
hetero molecules

B: PTS system, cellobiose-specific IIB component


Theoretical massNumber of molelcules
Total (without water)25,4154
Polymers25,3172
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area1290 Å2
ΔGint-15 kcal/mol
Surface area11180 Å2
MethodPISA
4
A: PTS system, cellobiose-specific IIB component
hetero molecules

A: PTS system, cellobiose-specific IIB component
hetero molecules

B: PTS system, cellobiose-specific IIB component

B: PTS system, cellobiose-specific IIB component


Theoretical massNumber of molelcules
Total (without water)50,8308
Polymers50,6354
Non-polymers1954
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area4770 Å2
ΔGint-39 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.788, 70.802, 84.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 12658.675 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: celA2, BA_5444, BAS5059, GBAA_5444 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q81X06, UniProt: A0A6H3A658*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.77 Å3/Da / Density % sol: 30.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.5 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (B7), 0.056 M Sodium phosphate, 1.344 M Potasium phosphate; Cryo: 4.0 M Sodium formate., VAPOR ...Details: Protein: 7.5 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (B7), 0.056 M Sodium phosphate, 1.344 M Potasium phosphate; Cryo: 4.0 M Sodium formate., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 15627 / Num. obs: 15627 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 33.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.2 / Num. unique all: 736 / % possible all: 98.1

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IIB

1iib


Resolution: 1.85→29.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.34 / SU ML: 0.121
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 777 5 %RANDOM
Rwork0.17608 ---
all0.17841 14797 --
obs0.17841 14797 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.509 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å2-0 Å20 Å2
2---0.41 Å2-0 Å2
3---3.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 5 59 1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191665
X-RAY DIFFRACTIONr_bond_other_d0.0010.021666
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9812245
X-RAY DIFFRACTIONr_angle_other_deg0.7613.0023830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9715219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.725.4161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.66157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_mcbond_it2.873.32873
X-RAY DIFFRACTIONr_mcbond_other2.8653.316872
X-RAY DIFFRACTIONr_mcangle_it3.9064.9521093
X-RAY DIFFRACTIONr_mcangle_other3.9044.9581094
X-RAY DIFFRACTIONr_scbond_it4.2423.955792
X-RAY DIFFRACTIONr_scbond_other4.2233.954792
X-RAY DIFFRACTIONr_scangle_other6.1675.6981153
X-RAY DIFFRACTIONr_long_range_B_refined9.14928.2581984
X-RAY DIFFRACTIONr_long_range_B_other9.15928.1311969
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 48 -
Rwork0.257 1038 -
obs-1038 98.64 %
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)
15.2637-0.53120.50531.5890.48492.74430.0035-0.6994-0.25890.1064-0.07180.01410.1894-0.21870.06830.0555-0.0321-0.00940.1580.00270.05064.881820.336247.5522
26.0819-4.98081.52056.10880.06396.11430.24390.3662-0.0412-0.4742-0.2241-0.16180.25280.1342-0.01980.111-0.0213-0.00370.0801-0.02780.11116.62718.048234.7852
35.43221.0004-0.13623.559-1.1852.81090.035-0.2441-0.7176-0.1711-0.05620.20590.4156-0.12590.02120.0893-0.0487-0.02550.13760.00440.1687-3.751713.796840.5246
43.9219-0.5655-2.45432.0560.88495.90910.04140.6553-0.0762-0.2235-0.2439-0.2328-0.5385-0.34170.20250.15020.01050.03420.1881-0.00980.0628-16.72988.349328.457
511.7826-2.26775.04729.9049-3.982911.0935-0.16440.4938-0.9008-0.407-0.44640.11281.4469-0.20820.61080.3645-0.07590.19560.3201-0.16720.2401-18.0452-5.265225.4174
65.18841.2218-0.15963.99630.46633.8595-0.06320.7485-0.0081-0.5682-0.3153-0.2126-0.02040.29850.37850.22250.0130.10490.28890.00850.1312-10.44994.197820.9441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 47
2X-RAY DIFFRACTION2A48 - 75
3X-RAY DIFFRACTION3A76 - 108
4X-RAY DIFFRACTION4B1 - 55
5X-RAY DIFFRACTION5B56 - 74
6X-RAY DIFFRACTION6B75 - 107

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