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- PDB-3sma: A new N-acetyltransferase fold in the structure and mechanism of ... -

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Basic information

Entry
Database: PDB / ID: 3sma
TitleA new N-acetyltransferase fold in the structure and mechanism of the phosphonate biosynthetic enzyme FrbF
ComponentsFrbF
KeywordsTRANSFERASE / N-acetyl transferase / acetyl CoA binding
Function / homologyaminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ACETYL COENZYME *A / CMP-5'-(N-hydroxy-3-aminopropyl)phosphonate acetyltransferase
Function and homology information
Biological speciesStreptomyces rubellomurinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBae, B. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF.
Authors: Bae, B. / Cobb, R.E. / Desieno, M.A. / Zhao, H. / Nair, S.K.
History
DepositionJun 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: FrbF
B: FrbF
C: FrbF
D: FrbF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5848
Polymers126,3464
Non-polymers3,2384
Water9,206511
1
A: FrbF
B: FrbF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7924
Polymers63,1732
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-18 kcal/mol
Surface area21600 Å2
MethodPISA
2
C: FrbF
hetero molecules

D: FrbF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7924
Polymers63,1732
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5170 Å2
ΔGint-16 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.832, 35.692, 136.087
Angle α, β, γ (deg.)90.00, 117.60, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
FrbF


Mass: 31586.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubellomurinus (bacteria) / Gene: frbF / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ZQ43
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.2M magnesium chloride, 0.1 Tris, 20%-25% peg 4000, 20% glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→45.34 Å / Num. all: 93253 / Num. obs: 74767 / Biso Wilson estimate: 26.44 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.34 Å / Cor.coef. Fo:Fc: 0.8846 / Cor.coef. Fo:Fc free: 0.8466 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 3757 5.03 %RANDOM
Rwork0.1928 ---
obs0.1954 74765 --
Displacement parametersBiso mean: 35.93 Å2
Baniso -1Baniso -2Baniso -3
1-5.177 Å20 Å2-0.1135 Å2
2---24.8038 Å20 Å2
3---19.6268 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: LAST / Resolution: 2→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8139 0 204 511 8854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018560HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1111679HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2797SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes211HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1294HARMONIC5
X-RAY DIFFRACTIONt_it8560HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion19.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1045SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10033SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2974 284 5.41 %
Rwork0.2391 4965 -
all0.2423 5249 -

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