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- PDB-3w1v: Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme ... -

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Basic information

Entry
Database: PDB / ID: 3w1v
TitleCrystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE from Staphylococcus aureus in complex with inihibitor
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
Chem-UDZ / UDP-glucose 4-epimerase / Galactowaldenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionNov 21, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Capsular polysaccharide synthesis enzyme Cap8E
B: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,78620
Polymers81,9132
Non-polymers2,87318
Water6,936385
1
A: Capsular polysaccharide synthesis enzyme Cap8E
B: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules

A: Capsular polysaccharide synthesis enzyme Cap8E
B: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules

A: Capsular polysaccharide synthesis enzyme Cap8E
B: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,35860
Polymers245,7396
Non-polymers8,61954
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area38000 Å2
ΔGint-713 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.780, 123.780, 104.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Capsular polysaccharide synthesis enzyme Cap8E


Mass: 40956.520 Da / Num. of mol.: 2
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)

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Non-polymers , 5 types, 403 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-UDZ / [(2R,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxan-2-yl]methylimino-azanylidene-azanium


Mass: 633.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N6O16P2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES/NaOH, 1.5M Li2SO4, pH 7.5, VAPOR DIFFUSION, 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 / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→34.82 Å / Num. all: 54166 / Num. obs: 54166 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 0.11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.1 / Num. unique all: 7818 / Rsym value: 0.338 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.455 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20732 2755 5.1 %RANDOM
Rwork0.16396 ---
all0.1662 51491 --
obs0.1662 51409 99.84 %-
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: 30.126 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 168 385 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.025812
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.9967867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1355714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47224.662266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.455151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5481538
X-RAY DIFFRACTIONr_chiral_restr0.1730.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214268
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 188 -
Rwork0.197 3543 -
obs--99.95 %
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)
10.4385-0.2467-0.09810.4314-0.11010.30810.02380.04330.0578-0.0279-0.0158-0.0991-0.01080.0817-0.00790.00990.0070.00920.088-0.02980.0503-31.7864-36.8067-36.2892
20.6956-0.0367-0.18960.1596-0.1520.4994-0.0539-0.0767-0.09920.00110.034-0.01830.13890.03840.01980.06950.0397-0.01460.0374-0.00540.0451-45.1739-60.7802-16.0666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 337
2X-RAY DIFFRACTION2B-8 - 337

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