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- PDB-3vvc: Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme ... -

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Basic information

Entry
Database: PDB / ID: 3vvc
TitleCrystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE , K126E, in apo form
ComponentsCapsular polysaccharide synthesis enzyme Cap8E
KeywordsLYASE / Rossmann fold / Short-chain dehydrogenase/reductase / capsular polysaccharide synthesis / oxidase / epimerase
Function / homology
Function and homology information


UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / lipopolysaccharide biosynthetic process / nucleotide binding
Similarity search - Function
UDP-glucose 4-epimerase CapD, C-terminal domain / Polysaccharide biosynthesis protein C-terminal / Polysaccharide biosynthesis protein, CapD-like domain / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex ...UDP-glucose 4-epimerase CapD, C-terminal domain / Polysaccharide biosynthesis protein C-terminal / Polysaccharide biosynthesis protein, CapD-like domain / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / UDP-glucose 4-epimerase / Galactowaldenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMiyafusa, T. / Caaveiro, J.M. / Tanaka, Y. / Tsumoto, K.
CitationJournal: Biosci.Rep. / Year: 2013
Title: Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus.
Authors: Miyafusa, T. / Caaveiro, J.M. / Tanaka, Y. / Tanner, M.E. / Tsumoto, K.
History
DepositionJul 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1807
Polymers40,9561
Non-polymers1,2246
Water1,47782
1
A: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)253,08142
Polymers245,7396
Non-polymers7,34236
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area29080 Å2
ΔGint-555 kcal/mol
Surface area73000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.540, 160.540, 80.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-406-

SO4

21A-406-

SO4

31A-561-

HOH

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Components

#1: Protein Capsular polysaccharide synthesis enzyme Cap8E


Mass: 40956.453 Da / Num. of mol.: 1 / Fragment: 4.2.1.115 / Mutation: K126E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: capE / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A2Y4, UniProt: A0A0H3JPH0*PLUS
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES-NaOH, PEG 400, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→80.27 Å / Num. all: 20104 / Num. obs: 20104 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.096 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.2-2.324.40.5411.40.5411100
2.32-2.464.70.3732.10.3731100
2.46-2.634.70.2972.60.2971100
2.63-2.844.70.2213.40.2211100
2.84-3.114.70.145.10.141100
3.11-3.484.70.09570.0951100
3.48-4.024.70.0698.90.0691100
4.02-4.924.70.05410.60.0541100
4.92-6.964.60.05910.70.0591100
6.96-34.744.20.05510.80.055196.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.4 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.74 Å
Translation2.5 Å34.74 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0 / SU B: 13.742 / SU ML: 0.175 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26524 1022 5.1 %RANDOM
Rwork0.19236 ---
obs0.19592 19080 99.83 %-
all-20136 --
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: 50.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 73 82 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022633
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9983566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86924.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1915474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9231515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021936
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 72 -
Rwork0.296 1317 -
obs--100 %
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)
12.3516-0.2543-0.32031.8796-0.01491.96880.0750.2373-0.1727-0.3089-0.0405-0.02640.16650.0823-0.03450.19360.0268-0.00740.1107-0.0370.0192.2983-21.5105-12.9764
24.1344-2.97441.60225.8463-2.20532.8358-0.2802-0.3751-0.44610.22890.23840.47460.274-0.23790.04170.4175-0.04320.02580.16890.0130.2943-2.4793-44.6195-4.2123
34.9698-3.82610.50557.7729-1.22373.1051-0.05580.0486-0.4702-0.6259-0.10610.31560.70250.23410.16190.5357-0.044-0.04040.1850.00690.2430.8111-46.8847-10.686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 163
2X-RAY DIFFRACTION1A201 - 225
3X-RAY DIFFRACTION2A166 - 199
4X-RAY DIFFRACTION2A227 - 282
5X-RAY DIFFRACTION3A283 - 337

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