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- PDB-4eaa: X-ray crystal structure of the H141N mutant of perosamine N-acety... -

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Basic information

Entry
Database: PDB / ID: 4eaa
TitleX-ray crystal structure of the H141N mutant of perosamine N-acetyltransferase from Caulobacter crescentus in complex with CoA and GDP-perosamine
ComponentsPerosamine N-acetyltransferase
KeywordsTRANSFERASE / beta helix / acetyltransferase / acetyl coenzyme A / GDP-perosamine
Function / homology
Function and homology information


Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COENZYME A / GDP-perosamine / Putative acetyltransferase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.45 Å
AuthorsThoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2012
Title: Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses.
Authors: Thoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / Holden, H.M.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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

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Assembly

Deposited unit
A: Perosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3015
Polymers21,8861
Non-polymers1,4144
Water3,603200
1
A: Perosamine N-acetyltransferase
hetero molecules

A: Perosamine N-acetyltransferase
hetero molecules

A: Perosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,90215
Polymers65,6593
Non-polymers4,24312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area9150 Å2
ΔGint-127 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.007, 115.007, 115.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21A-489-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Perosamine N-acetyltransferase / PerB / Hexapeptide transferase family protein


Mass: 21886.289 Da / Num. of mol.: 1 / Mutation: H141N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_1011, wbqR / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: O85353, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 204 molecules

#2: Chemical ChemComp-JB2 / GDP-perosamine


Mass: 588.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N6O14P2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% PEG5000 MME, 100 mM HEPES, pH 7.5, 5 mM CoA, 5 mM GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 17, 2010 / Details: montel
RadiationMonochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.45→81.322 Å / Num. all: 44567 / Num. obs: 44567 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.5
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8131 / Rsym value: 0.364 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementStarting model: PDB ENTRY 4EA7

4ea7


Resolution: 1.45→40.661 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.186 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 2200 5.1 %RANDOM
Rwork0.17958 ---
obs0.18112 41237 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.081 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 88 200 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1052.0372229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30122.74551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2815237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7491514
X-RAY DIFFRACTIONr_chiral_restr0.1740.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211176
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_it1.8681.51046
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84121670
X-RAY DIFFRACTIONr_scbond_it4.9083574
X-RAY DIFFRACTIONr_scangle_it7.6324.5552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 145 -
Rwork0.299 2810 -
obs--88.87 %

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