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- PDB-2vfc: The structure of Mycobacterium marinum arylamine N-acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 2vfc
TitleThe structure of Mycobacterium marinum arylamine N-acetyltransferase in complex with CoA
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


acetyltransferase activity
Similarity search - Function
Arylamine N-acetyltransferase / Cysteine proteinases / Arylamine N-acetyltransferase fold / Arylamine N-acetyltransferase / N-acetyltransferase / Papain-like cysteine peptidase superfamily / Lipocalin / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMYCOBACTERIUM MARINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFullam, E. / Westwood, I.M. / Anderton, M.C. / Lowe, E.D. / Sim, E. / Noble, M.E.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Divergence of Cofactor Recognition Across Evolution: Coenzyme a Binding in a Prokaryotic Arylamine N-Acetyltransferase.
Authors: Fullam, E. / Westwood, I.M. / Anderton, M.C. / Lowe, E.D. / Sim, E. / Noble, M.E.M.
History
DepositionNov 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARYLAMINE N-ACETYLTRANSFERASE
B: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8734
Polymers61,3382
Non-polymers1,5352
Water4,017223
1
A: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4362
Polymers30,6691
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4362
Polymers30,6691
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.950, 98.000, 123.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.08485, 0.97981, 0.18104), (0.98143, -0.11355, 0.15457), (0.17201, 0.16457, -0.97125)
Vector: 34.19567, -31.73386, -33.22157)

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Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30668.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM MARINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: B2HIZ6*PLUS, arylamine N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS TAG ADDED

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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: 1.86 Å3/Da / Density % sol: 33.9 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1M NA CITRATE PH5.6, 10% W/V 2-PROPANOL AND 22% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→24.88 Å / Num. obs: 16557 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 5.27 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.27
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VFB

2vfb


Resolution: 2.7→30.23 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 24.74 / SU ML: 0.268 / TLS residual ADP flag: UNVERIFIED / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 844 5.1 %RANDOM
Rwork0.181 ---
obs0.185 16517 97.1 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 5.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.404 Å20 Å20 Å2
2--0.993 Å20 Å2
3----1.396 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4179 0 96 223 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9915965
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4215540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42522.487197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63815655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0211547
X-RAY DIFFRACTIONr_chiral_restr0.1720.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023333
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.22005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22926
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.52736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08424309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64231821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8694.51656
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 11.25→30.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 8
Rwork0.219 242
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.02060.8543-0.08552.32640.0113.05070.0493-0.17480.10360.2479-0.0566-0.0153-0.3623-0.08960.0074-0.08830.04540.0047-0.11830.0064-0.092415.5011-0.1749-1.0037
22.98120.422-0.31912.41950.18812.895-0.12380.2166-0.02-0.28040.0962-0.09280.0666-0.08240.0277-0.1783-0.00750.0264-0.1829-0.0132-0.134635.0554-16.5745-29.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 275
2X-RAY DIFFRACTION2B4 - 275

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