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- PDB-2zkl: Crystal Structure of capsular polysaccharide assembling protein C... -

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Basic information

Entry
Database: PDB / ID: 2zkl
TitleCrystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus
ComponentsCapsular polysaccharide synthesis enzyme Cap5F
KeywordsISOMERASE / Rossmann fold
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / NAD(P)-binding Rossmann-like Domain / Jelly Rolls / NAD(P)-binding domain superfamily / Sandwich / Rossmann fold ...NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / NAD(P)-binding Rossmann-like Domain / Jelly Rolls / NAD(P)-binding domain superfamily / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Capsular polysaccharide synthesis enzyme Cap5F / Capsular polysaccharide synthesis enzyme Cap5F
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsMiyafusa, T. / Tanaka, Y. / Yao, M. / Tanaka, I. / Tsumoto, K.
CitationJournal: to be published
Title: Crystal structure of capsular polysaccharide assembling protein from Staphylococcus aureus
Authors: Miyafusa, T. / Tanaka, Y. / Kuroda, M. / Yao, M. / Watanabe, N. / Ohta, T. / Tanaka, I. / Tsumoto, K.
History
DepositionMar 25, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 Cap5F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4883
Polymers42,3311
Non-polymers1582
Water30617
1
A: Capsular polysaccharide synthesis enzyme Cap5F
hetero molecules

A: Capsular polysaccharide synthesis enzyme Cap5F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9766
Polymers84,6612
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area7360 Å2
ΔGint-121 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.636, 119.636, 129.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Capsular polysaccharide synthesis enzyme Cap5F


Mass: 42330.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: capF / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q99X63, UniProt: A0A0H3JP37*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2

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Sample preparation

CrystalDensity Matthews: 6.317698 Å3/Da / Density % sol: 80.530884 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 300mM sodium chloride, 100mM ammonium sulfate, 100mM MES, 3.9M HCOONa-HCl(pH6.3), 30%(w/v) Glycerol, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A11
SYNCHROTRONPhoton Factory BL-17A21.0000, 0.9792, 0.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 22, 2007
ADSC QUANTUM 42CCDJan 28, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.97961
ReflectionResolution: 2.6→50 Å / Num. all: 33090 / Num. obs: 32990 / % possible obs: 99.7 % / Redundancy: 11 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.503 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ugiuidata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.61→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1859665.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1649 5.1 %RANDOM
Rwork0.238 ---
obs0.238 32095 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9988 Å2 / ksol: 0.446583 e/Å3
Displacement parametersBiso mean: 62.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å27.38 Å20 Å2
2---1.69 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.61→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 7 17 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 264 5.3 %
Rwork0.365 4692 -
obs-4692 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramCwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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