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- PDB-4eab: X-ray crystal structure of the H141A mutant of GDP-perosamine N-a... -

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Basic information

Entry
Database: PDB / ID: 4eab
TitleX-ray crystal structure of the H141A mutant of GDP-perosamine N-acetyl transferase 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


transferase activity
Similarity search - Function
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 1.35 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)23,2585
Polymers21,8431
Non-polymers1,4144
Water4,125229
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)69,77315
Polymers65,5303
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 area8160 Å2
ΔGint-69 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.968, 114.968, 114.968
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-505-

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: 21843.266 Da / Num. of mol.: 1 / Mutation: H141A
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, 233 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.: 229 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
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: May 18, 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: 1.35→50 Å / Num. all: 53728 / Num. obs: 53728 / % possible obs: 97.25 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 16.4
Reflection shellResolution: 1.35→1.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8988 / Rsym value: 0.391 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EA7

4ea7


Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.881 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2730 5.1 %RANDOM
Rwork0.187 ---
all0.188 53728 --
obs0.188 53728 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.633 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 88 229 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221609
X-RAY DIFFRACTIONr_angle_refined_deg2.12.0432209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51122.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.7821514
X-RAY DIFFRACTIONr_chiral_restr0.1620.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211162
X-RAY DIFFRACTIONr_mcbond_it1.751.51049
X-RAY DIFFRACTIONr_mcangle_it2.77321673
X-RAY DIFFRACTIONr_scbond_it4.6743560
X-RAY DIFFRACTIONr_scangle_it7.1574.5534
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 208 -
Rwork0.301 3535 -
all-3743 -
obs--91.97 %

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