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- PDB-3ltw: The structure of mycobacterium marinum arylamine n-acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3ltw
TitleThe structure of mycobacterium marinum arylamine n-acetyltransferase in complex with hydralazine
ComponentsArylamine N-acetyltransferase Nat
KeywordsTRANSFERASE / Mycobacterium marinum / aryalmine N-acetyl transferase / MMNAT / hydralazine / Mycobacterium tuberculosis
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 / Lipocalin / Papain-like cysteine peptidase superfamily / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 1-hydrazinophthalazine / Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsAbuhammad, A.M. / Lowe, E.D. / Fullam, E. / Noble, M. / Garman, E.F. / Sim, E.
CitationJournal: Protein Cell / Year: 2010
Title: Probing the architecture of the Mycobacterium marinum arylamine N-acetyltransferase active site
Authors: Abuhammad, A.M. / Lowe, E.D. / Fullam, E. / Noble, M. / Garman, E.F. / Sim, E.
History
DepositionFeb 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Arylamine N-acetyltransferase Nat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1276
Polymers30,6691
Non-polymers4585
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Arylamine N-acetyltransferase Nat
hetero molecules

A: Arylamine N-acetyltransferase Nat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,25412
Polymers61,3382
Non-polymers91710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 51.940, 176.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

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Components

#1: Protein Arylamine N-acetyltransferase Nat


Mass: 30668.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: nat, MMAR_5055 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: B2HIZ6, arylamine N-acetyltransferase
#2: Chemical ChemComp-HLZ / 1-hydrazinophthalazine / Hydralazine / phthalazin-1-ylhydrazine / Hydralazine


Mass: 160.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8N4 / Comment: medication*YM
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.94 Å3/Da / Density % sol: 36.67 % / Mosaicity: 0.42 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 0.1M sodium chloride 0.1M MES pH 6.7, 1.65M ammonium sulphate, vapour diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.1→38.952 Å / Num. all: 15018 / Num. obs: 15018 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.125 / Rsym value: 0.125
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2110 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.07 Å38.95 Å
Translation2.07 Å38.95 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.95 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.844 / SU B: 12.594 / SU ML: 0.152 / SU R Cruickshank DPI: 0.292 / SU Rfree: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.292 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 761 5.1 %RANDOM
Rwork0.216 ---
all0.2165 15018 --
obs0.219 14947 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.74 Å2 / Biso mean: 28.511 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 33 95 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212132
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.9832915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.265275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35723.06888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51815294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0131517
X-RAY DIFFRACTIONr_chiral_restr0.0570.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211654
X-RAY DIFFRACTIONr_mcbond_it0.1561.51364
X-RAY DIFFRACTIONr_mcangle_it0.2922168
X-RAY DIFFRACTIONr_scbond_it0.2963768
X-RAY DIFFRACTIONr_scangle_it0.4964.5747
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 77 -
Rwork0.258 1003 -
all-1080 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -24.458 Å / Origin y: -3.567 Å / Origin z: -12.022 Å
111213212223313233
T0.0198 Å20.0121 Å20.004 Å2-0.0381 Å20.0034 Å2--0.0069 Å2
L1.6981 °20.2013 °20.1404 °2-1.3912 °2-0.2284 °2--1.6061 °2
S-0.0082 Å °0.1001 Å °0.067 Å °-0.0692 Å °0.0129 Å °0.0418 Å °-0.0379 Å °-0.0919 Å °-0.0048 Å °

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