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- PDB-1xhd: X-ray crystal structure of putative acetyltransferase, product of... -

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Basic information

Entry
Database: PDB / ID: 1xhd
TitleX-ray crystal structure of putative acetyltransferase, product of BC4754 gene [Bacillus cereus]
Componentsputative acetyltransferase/acyltransferase
KeywordsTRANSFERASE / structural genomics / protein structure initiative / Medwest Center for Structural Genomics / MCSG / Macyltransferase / PSI / Midwest Center for Structural Genomics
Function / homologyHexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / acyltransferase activity / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta / Putative acetyltransferase/acyltransferase
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative acetyltransferase, product of BC4754 gene from Bacillus cereus.
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative acetyltransferase/acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3742
Polymers19,2781
Non-polymers961
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: putative acetyltransferase/acyltransferase
hetero molecules

A: putative acetyltransferase/acyltransferase
hetero molecules

A: putative acetyltransferase/acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1216
Polymers57,8333
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area7010 Å2
ΔGint-86 kcal/mol
Surface area18210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.093, 142.093, 142.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-208-

HOH

Detailsthe biological assembly unknown

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Components

#1: Protein putative acetyltransferase/acyltransferase


Mass: 19277.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC4754 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]pMAGIC / References: UniProt: Q816R4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 6.3 Å3/Da / Density % sol: 80.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: SODIUM/POTASSIUM PHOSPHATE, PHOSPHATE CITRATE, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979295 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 16, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979295 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 37577 / Num. obs: 37525 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 48.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.49 / Num. unique all: 2401 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 1.098 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1632 1873 -random
Rwork0.15243 ---
obs0.15298 37517 99.82 %-
all-37517 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.555 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 5 130 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221410
X-RAY DIFFRACTIONr_bond_other_d0.0020.021290
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9621910
X-RAY DIFFRACTIONr_angle_other_deg0.80133027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021539
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02259
X-RAY DIFFRACTIONr_nbd_refined0.2330.2286
X-RAY DIFFRACTIONr_nbd_other0.2530.21534
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.2836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.5874
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47121427
X-RAY DIFFRACTIONr_scbond_it2.8083536
X-RAY DIFFRACTIONr_scangle_it4.8524.5483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.1632 127
Rwork0.15243 2694
obs-2694
Refinement TLS params.Method: refined / Origin x: -8.5637 Å / Origin y: 26.0727 Å / Origin z: 98.1143 Å
111213212223313233
T0.0178 Å2-0.0157 Å2-0.0071 Å2-0.0258 Å2-0.0021 Å2--0.0087 Å2
L0.7526 °20.0448 °2-0.0392 °2-0.5402 °2-0.1429 °2--0.3136 °2
S-0.0434 Å °-0.0809 Å °-0.0052 Å °0.0309 Å °-0.0206 Å °-0.0174 Å °-0.0444 Å °0.0451 Å °0.0641 Å °

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