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- PDB-4b55: Crystal Structure of the Covalent Adduct Formed between Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 4b55
TitleCrystal Structure of the Covalent Adduct Formed between Mycobacterium marinum Aryalamine N-acetyltransferase and Phenyl vinyl ketone a derivative of Piperidinols
ComponentsARYLAMINE N-ACETYLTRANSFERASE NAT
KeywordsTRANSFERASE / TUBERCULOSIS / COVALENT INHIBITOR
Function / homology
Function and homology information


arylamine N-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
3-hydroxy-1-phenylpropan-1-one / Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMYCOBACTERIUM MARINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAbuhammad, A. / Fullam, E. / Lowe, E.D. / Staunton, D. / Kawamura, A. / Westwood, I.M. / Bhakta, S. / Garner, A.C. / Wilson, D.L. / Seden, P.T. ...Abuhammad, A. / Fullam, E. / Lowe, E.D. / Staunton, D. / Kawamura, A. / Westwood, I.M. / Bhakta, S. / Garner, A.C. / Wilson, D.L. / Seden, P.T. / Davies, S.G. / Russell, A.J. / Garman, E.F. / Sim, E.
CitationJournal: Plos One / Year: 2012
Title: Piperidinols that Show Anti-Tubercular Activity as Inhibitors of Arylamine N-Acetyltransferase: An Essential Enzyme for Mycobacterial Survival Inside Macrophages.
Authors: Abuhammad, A. / Fullam, E. / Lowe, E.D. / Staunton, D. / Kawamura, A. / Westwood, I.M. / Bhakta, S. / Garner, A.C. / Wilson, D.L. / Seden, P.T. / Davies, S.G. / Russell, A.J. / Garman, E.F. / Sim, E.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)31,1012
Polymers30,9511
Non-polymers1501
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.840, 51.840, 176.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE NAT / ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30951.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MODIFIED ACTIVE SITE CYS 70 / Source: (gene. exp.) MYCOBACTERIUM MARINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B2HIZ6, arylamine N-acetyltransferase
#2: Chemical ChemComp-P18 / 3-hydroxy-1-phenylpropan-1-one


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3-HYDROXY-1-PHENYLPROPAN-1-ONE (RESIDUE P18) DERIVES FROM PHENYL VINYL KETONE (1-PHENYLPROP-2-EN-1- ...3-HYDROXY-1-PHENYLPROPAN-1-ONE (RESIDUE P18) DERIVES FROM PHENYL VINYL KETONE (1-PHENYLPROP-2-EN-1-ONE) (PVK). THE ADDED OH LEAVING GROUP IN THE P18 IS NOT PRESENT IN THE COMPOUND USED AS A DOUBLE BOND EXISTS BEFORE REACTION WITH CYS 70.

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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: 1.99 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growDetails: 0.2 M NACL, 0.1 M NA-CACODYLATE PH 6.5 AND 2.0 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.69→19.46 Å / Num. obs: 7020 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 51.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.69→2.84 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 87.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LTW

3ltw


Resolution: 2.7→19.39 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.7932 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.442
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 315 4.54 %RANDOM
Rwork0.2309 ---
obs0.2334 6944 96.78 %-
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.8511 Å20 Å20 Å2
2---6.8511 Å20 Å2
3---13.7022 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 10 39 2079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0062101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822874HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d681SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes332HARMONIC5
X-RAY DIFFRACTIONt_it2101HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion275SEMIHARMONIC5
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_contact2357SEMIHARMONIC4
LS refinement shellResolution: 2.7→3.02 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3098 78 4.39 %
Rwork0.255 1699 -
all0.2574 1777 -
obs--96.78 %
Refinement TLS params.Method: refined / Origin x: 1.2241 Å / Origin y: 22.1945 Å / Origin z: -12.0276 Å
111213212223313233
T-0.0555 Å20.0113 Å2-0.0101 Å2--0.0215 Å20.0002 Å2---0.1062 Å2
L1.2961 °20.0908 °2-0.0379 °2-0.7129 °2-0.1555 °2--1.1535 °2
S0.0119 Å °0.052 Å °0.0499 Å °-0.0693 Å °-0.0132 Å °0.0491 Å °-0.0519 Å °-0.093 Å °0.0012 Å °
Refinement TLS groupSelection details: CHAIN A

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