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- PDB-3ect: Crystal Structure of the Hexapeptide-Repeat Containing-Acetyltran... -

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Basic information

Entry
Database: PDB / ID: 3ect
TitleCrystal Structure of the Hexapeptide-Repeat Containing-Acetyltransferase VCA0836 from Vibrio cholerae
ComponentsHexapeptide-repeat containing-acetyltransferase
KeywordsTRANSFERASE / alpha-beta structure / beta-helix / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


O-acyltransferase activity / acetyltransferase activity / metal ion binding / cytosol
Similarity search - Function
Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Hexapeptide-repeat containing-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsKim, Y. / Maltseva, N. / Kwon, K. / Papazisi, L. / Hasseman, J. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Hexapeptide-Repeat Containing-Acetyltransferase VCA0836 from Vibrio cholerae
Authors: Kim, Y. / Maltseva, N. / Kwon, K. / Papazisi, L. / Hasseman, J. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8103
Polymers21,7301
Non-polymers802
Water1,22568
1
A: Hexapeptide-repeat containing-acetyltransferase
hetero molecules

A: Hexapeptide-repeat containing-acetyltransferase
hetero molecules

A: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4309
Polymers65,1893
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7740 Å2
ΔGint-122 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.319, 73.319, 178.515
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-193-

CA

21A-194-

CA

31A-212-

HOH

41A-261-

HOH

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Components

#1: Protein Hexapeptide-repeat containing-acetyltransferase


Mass: 21729.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: N16961 / Gene: VC_A0836 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9KLB0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M Calcium Chloride, 0.1 M Sodium Acetate, 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 10, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→31.26 Å / Num. all: 6617 / Num. obs: 6617 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2.16 / Num. unique all: 327 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→31.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 23.109 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.806 / ESU R Free: 0.305
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 314 4.7 %RANDOM
Rwork0.193 ---
all0.196 6302 --
obs0.196 6302 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.646 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å21.06 Å20 Å2
2--2.12 Å20 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.51→31.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 2 68 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221396
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.621.951891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84723.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.64415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0521511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211052
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_it0.7081.5876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38721415
X-RAY DIFFRACTIONr_scbond_it2.1433520
X-RAY DIFFRACTIONr_scangle_it3.5134.5476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 22 -
Rwork0.224 430 -
obs-452 96.38 %
Refinement TLS params.Method: refined / Origin x: 8.5982 Å / Origin y: -11.5431 Å / Origin z: 47.4319 Å
111213212223313233
T0.0939 Å20.024 Å20.0684 Å2-0.0713 Å2-0.0528 Å2--0.2064 Å2
L3.1344 °20.0005 °21.1263 °2-2.4741 °2-0.4022 °2--1.5367 °2
S-0.007 Å °0.1889 Å °-0.1772 Å °-0.3394 Å °0.0395 Å °-0.2111 Å °0.0421 Å °0.0026 Å °-0.0324 Å °

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