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

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Basic information

Entry
Database: PDB / ID: 3vvb
TitleCrystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE from Staphylococcus aureus in apo form
ComponentsCapE
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / 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 / Resolution: 2.8 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: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CapE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7002
Polymers40,9571
Non-polymers7431
Water543
1
A: CapE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)250,20012
Polymers245,7396
Non-polymers4,4606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area23240 Å2
ΔGint-89 kcal/mol
Surface area65680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.180, 125.180, 101.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein CapE


Mass: 40956.520 Da / Num. of mol.: 1
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, UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.81 Å3/Da / Density % sol: 56.24 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium succinate, Potassium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→108.409 Å / Num. all: 12014 / Num. obs: 12014 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rsym value: 0.12 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.958.30.8550.8010.91425317160.2960.8550.8012.9100
2.95-3.138.20.5320.4981.51346516350.1850.5320.4984.5100
3.13-3.358.20.3320.3112.41259615270.1150.3320.3116.699.9
3.35-3.618.20.1920.184.21174714410.0670.1920.1810.199.9
3.61-3.968.10.1280.1261073613210.0450.1280.1214.299.7
3.96-4.4380.0980.0917.8966512110.0340.0980.09118.499.7
4.43-5.117.90.0890.0838845210760.0310.0890.08320.999.7
5.11-6.267.50.1050.0986.769379300.0380.1050.09819.699.6
6.26-8.857.40.0560.05211.553857270.020.0560.05226.399.1
8.85-34.05470.050.04711.430284300.0180.050.04732.896.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å34.05 Å
Translation2.8 Å34.05 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementStarting model: 4G5H

4g5h


Resolution: 2.8→34.05 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.894 / SU B: 27.991 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 575 4.8 %RANDOM
Rwork0.23583 ---
obs0.23777 11439 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 48 3 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9873025
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50924.757103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73915410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2111513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021636
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: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 33 -
Rwork0.272 719 -
obs--99.87 %
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)
12.10770.53530.72625.1269-1.06313.94440.2757-0.6358-0.20530.7062-0.1341-0.80190.32260.4972-0.14170.1813-0.0306-0.12790.4478-0.0950.2541-41.103833.8221-12.6939
27.52390.6710.12196.8117-1.84132.8970.06530.0174-0.1267-0.6803-0.2033-1.28470.18491.03020.1380.3599-0.1769-0.07210.8245-0.14390.8051-22.591345.1598-16.5607
39.0011-4.67670.308211.8278-2.09654.05610.4455-0.38360.2553-0.513-0.6948-2.24650.83861.34730.24920.5753-0.0716-0.12031.1343-0.12350.9448-17.215637.8624-15.9896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 163
2X-RAY DIFFRACTION1A201 - 225
3X-RAY DIFFRACTION2A166 - 199
4X-RAY DIFFRACTION2A227 - 282
5X-RAY DIFFRACTION3A283 - 334

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