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- PDB-4g5h: Crystal structure of capsular polysaccharide synthesizing enzyme ... -

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Basic information

Entry
Database: PDB / ID: 4g5h
TitleCrystal structure of capsular polysaccharide synthesizing enzyme CapE from Staphylococcus aureus in complex with by-product
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
FORMIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-UD7 / UDP-glucose 4-epimerase / Galactowaldenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsMiyafusa, T. / Caaveiro, J.M.M. / Tanaka, Y. / Tsumoto, K.
CitationJournal: Febs Lett. / Year: 2013
Title: Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus.
Authors: Miyafusa, T. / Caaveiro, J.M. / Tanaka, Y. / Tsumoto, K.
History
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references / Structure summary
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,54619
Polymers40,9571
Non-polymers2,58918
Water2,450136
1
A: Capsular polysaccharide synthesis enzyme Cap8E
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)261,276114
Polymers245,7396
Non-polymers15,537108
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_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area51780 Å2
ΔGint-175 kcal/mol
Surface area66900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.030, 124.030, 103.161
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Capsular polysaccharide synthesis enzyme Cap8E


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)

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Non-polymers , 5 types, 154 molecules

#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-UD7 / [(2R,3R,4R,6R)-3-acetamido-6-methyl-4-oxidanyl-5-oxidanylidene-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 589.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N3O16P2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#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.: 136 / 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: 2.9 Å3/Da / Density % sol: 57.64 % / Mosaicity: 0.33 °
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: 1.88→35.804 Å / Num. all: 38463 / Num. obs: 38463 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.11 / Net I/σ(I): 12.5
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
1.88-1.987.71.0070.8870.84255254930.3531.0070.8872.4100
1.98-2.17.70.6390.5621.34063352500.2250.6390.5623.7100
2.1-2.257.70.3870.3392.23820849380.1360.3870.3395.9100
2.25-2.437.70.2540.2233.33548146010.090.2540.2238.3100
2.43-2.667.70.1860.1624.63267242630.0660.1860.16210.8100
2.66-2.977.60.1210.1056.82946238780.0430.1210.10514.6100
2.97-3.437.50.0770.067102590434500.0280.0770.06719.7100
3.43-4.27.30.0650.05710.52139829340.0240.0650.05724.599.9
4.2-5.957.10.0750.0658.41640323250.0280.0750.06534.199.7
5.95-35.8047.10.0440.03814.9943113310.0160.0440.03843.697.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å35.8 Å
Translation2 Å35.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→35.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2099 / WRfactor Rwork: 0.1757 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.877 / SU B: 5.416 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1189 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1546 4 %RANDOM
Rwork0.1751 ---
all0.1765 38538 --
obs0.1765 38453 99.78 %-
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 max: 135.26 Å2 / Biso mean: 38.5645 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.88→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 167 136 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023014
X-RAY DIFFRACTIONr_angle_refined_deg2.4642.024078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52124.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52815534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6011517
X-RAY DIFFRACTIONr_chiral_restr0.2110.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022206
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 115 -
Rwork0.262 2423 -
all-2538 -
obs-2538 99.96 %
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)
10.1150.0648-0.1010.17590.10320.30180.0025-0.0084-0.0038-0.02940.0449-0.01460.03110.0591-0.04740.21070.0183-0.03050.116-0.02430.1619-49.290718.478912.9501
20.84640.08850.63380.23170.26811.1092-0.03750.0244-0.0060.00840.0255-0.0330.38540.1270.0120.38850.108-0.00310.0571-0.02060.1386-44.1478-3.059223.9994
30.6791-0.0658-0.29140.04140.01680.6594-0.00630.01030.0491-0.0616-0.01490.01770.39340.03050.02120.36870.0579-0.02230.0166-0.02730.1159-51.725-2.153215.4362
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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