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- PDB-2pfr: Human N-acetyltransferase 2 -

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Basic information

Entry
Database: PDB / ID: 2pfr
TitleHuman N-acetyltransferase 2
ComponentsArylamine N-acetyltransferase 2
KeywordsTRANSFERASE / Arylamine N-acetyltransferase 2 / Arylamide acetylase 2 / structural genomics consortium / SGC
Function / homology
Function and homology information


Acetylation / arylamine N-acetyltransferase / arylamine N-acetyltransferase activity / xenobiotic metabolic process / cytosol
Similarity search - Function
Arylamine N-acetyltransferase fold - #20 / Arylamine N-acetyltransferase fold / Arylamine N-acetyltransferase / N-acetyltransferase / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Arylamine N-acetyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsTempel, W. / Wu, H. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Grant, D.M. / Bochkarev, A. ...Tempel, W. / Wu, H. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Grant, D.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: The Crystal Structure of Human N-acetyltransferase 2 in complex with CoA
Authors: Wu, H. / Tempel, W. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Grant, D.M. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arylamine N-acetyltransferase 2
B: Arylamine N-acetyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78938
Polymers67,5812
Non-polymers2,20836
Water5,008278
1
A: Arylamine N-acetyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,94224
Polymers33,7911
Non-polymers1,15223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Arylamine N-acetyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,84614
Polymers33,7911
Non-polymers1,05613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Arylamine N-acetyltransferase 2
hetero molecules

B: Arylamine N-acetyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78938
Polymers67,5812
Non-polymers2,20836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456x-1/2,-y+1/2,-z+5/41
Buried area5570 Å2
ΔGint-114 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.063, 130.063, 111.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Arylamine N-acetyltransferase 2 / Arylamide acetylase 2 / Polymorphic arylamine N-acetyltransferase / PNAT / N- acetyltransferase type 2 / NAT-2


Mass: 33790.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAT2, AAC2 / Plasmid: pET28a-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P11245, arylamine N-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 27 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.564.7
2
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.5 M Ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E11.5418
2
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 7, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 139603 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.133 / Χ2: 1.731 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
1.92-1.991006.90.997139461.4691,2
1.99-2.0710070.749139721.5061,2
2.07-2.161007.10.572139201.5581,2
2.16-2.281007.20.475139871.591,2
2.28-2.421007.40.355139501.6191,2
2.42-2.611007.50.275139501.641,2
2.61-2.871007.60.199139581.7381,2
2.87-3.281007.70.115139761.9171,2
3.28-4.131007.70.067139422.2291,2
4.13-301007.80.044140021.9531,2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.55 Å
Translation2.5 Å29.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
MolProbitymodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IJA

2ija


Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.188 / SU B: 2.923 / SU ML: 0.087 / ESU R: 0.13 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 2659 3.646 %thin shells
Rwork0.2094 ---
all0.211 ---
obs-72932 99.821 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å20 Å20 Å2
2--0.061 Å20 Å2
3----0.122 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4580 0 158 278 5016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224896
X-RAY DIFFRACTIONr_bond_other_d0.0020.023206
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.996700
X-RAY DIFFRACTIONr_angle_other_deg1.03937864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59424.34212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62615807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5791521
X-RAY DIFFRACTIONr_chiral_restr0.0870.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
X-RAY DIFFRACTIONr_nbd_refined0.1980.2821
X-RAY DIFFRACTIONr_nbd_other0.1980.23275
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22330
X-RAY DIFFRACTIONr_nbtor_other0.0780.22412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.2150.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.214
X-RAY DIFFRACTIONr_mcbond_it2.45823037
X-RAY DIFFRACTIONr_mcbond_other0.61221182
X-RAY DIFFRACTIONr_mcangle_it3.29734756
X-RAY DIFFRACTIONr_scbond_it2.5922180
X-RAY DIFFRACTIONr_scangle_it3.50531928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.92-1.970.36820.25646250.261531399.887
1.97-2.02300.22951560.229517099.729
2.023-2.08200.21450060.214501599.821
2.082-2.1460.2841480.21747580.219491699.797
2.146-2.2160.2573850.21343730.217476399.895
2.216-2.29300.21145770.211459499.63
2.293-2.37900.21144490.211445999.776
2.379-2.4750.2544440.21138160.215427699.626
2.475-2.58500.21741200.217412699.855
2.585-2.7100.22139580.221396199.924
2.71-2.8550.2533420.2234130.223376399.787
2.855-3.02700.22135730.221357699.916
3.027-3.2330.2652260.21731350.221336499.911
3.233-3.48900.20731450.207315299.778
3.489-3.8170.2161880.20727150.207290599.931
3.817-4.25900.17626500.176265699.774
4.259-4.9010.1921180.17222420.173236499.831
4.901-5.96300.220400.2204299.902
5.963-8.2710.242760.24515460.2451622100
8.271-300.208500.2119760.2111026100

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