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- PDB-4mbu: Crystal structure of N-acetyltransferase from Staphylococcus aure... -

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Basic information

Entry
Database: PDB / ID: 4mbu
TitleCrystal structure of N-acetyltransferase from Staphylococcus aureus Mu50
ComponentsSimilar to N-acetyltransferase
KeywordsTRANSFERASE / N-acetyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Similar to N-acetyltransferase / Similar to N-acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSrivastava, P. / Khandokar, Y. / Forwood, J.K.
CitationJournal: Plos One / Year: 2014
Title: Structural characterization of a Gcn5-related N-acetyltransferase from Staphylococcus aureus.
Authors: Srivastava, P. / Khandokar, Y.B. / Swarbrick, C.M. / Roman, N. / Himiari, Z. / Sarker, S. / Raidal, S.R. / Forwood, J.K.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Similar to N-acetyltransferase
B: Similar to N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,98812
Polymers37,8992
Non-polymers1,08910
Water4,792266
1
A: Similar to N-acetyltransferase
B: Similar to N-acetyltransferase
hetero molecules

A: Similar to N-acetyltransferase
B: Similar to N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,97624
Polymers75,7984
Non-polymers2,17820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_856-x+3,y,-z+11
Buried area7960 Å2
ΔGint-113 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.490, 78.860, 66.010
Angle α, β, γ (deg.)90.00, 111.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-206-

PO4

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.712427, -0.011989, 0.701644), (-0.011743, -0.999918, -0.005162), (0.701648, -0.004562, -0.712509)22.44245, 2.42636, -54.87635

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Components

#1: Protein Similar to N-acetyltransferase


Mass: 18949.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: N-acetyltransferase, SAV2529 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q99RA6, UniProt: A0A0H3JXG2*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.047 M cadmium sulfate hydrate, 0.094 M HEPES pH 7.5,0.94 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationMonochromator: Silicon Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→31.52 Å / Num. all: 82832 / Num. obs: 23855 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
CCP4model building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
Blu-Ice(McPhillipsdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→33.15 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.884 / SU ML: 0.21 / σ(F): 1.94 / Phase error: 21.22 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2226 1299 5.17 %
Rwork0.1854 --
obs0.1873 23855 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 18 266 2931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072721
X-RAY DIFFRACTIONf_angle_d1.0213686
X-RAY DIFFRACTIONf_dihedral_angle_d12.891970
X-RAY DIFFRACTIONf_chiral_restr0.076397
X-RAY DIFFRACTIONf_plane_restr0.004466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.23620.26231610.19352623X-RAY DIFFRACTION99
2.2362-2.33790.28191360.21012643X-RAY DIFFRACTION100
2.3379-2.46110.22511410.19292641X-RAY DIFFRACTION100
2.4611-2.61530.24881250.20242666X-RAY DIFFRACTION100
2.6153-2.81710.2491600.20382638X-RAY DIFFRACTION100
2.8171-3.10040.24641470.19782647X-RAY DIFFRACTION100
3.1004-3.54860.21321270.17912676X-RAY DIFFRACTION100
3.5486-4.46910.1821680.15752643X-RAY DIFFRACTION99
4.4691-33.15410.1951340.17842664X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.06180.045-0.00640.04290.01020.04370.07750.00510.05210.01230.04080.02960.0138-0.08210.10560.044-0.05010.08440.0830.01460.2137106.1975-3.625432.9245
20.05250.0313-0.01990.0235-0.01430.00820.00680.02970.04940.0277-0.02170.07850.0246-0.0339-0.0203-0.0206-0.13570.00690.13640.0050.0826105.4702-9.997627.392
30.00920.0074-0.00150.0151-0.00020.0005-0.0037-0.00570.02330.0086-0.02830.04260.0074-0.0262-0.01440.0291-0.052-0.0210.0464-0.03290.0303117.1397-7.010324.8085
40.0094-0.00060.00120.0031-0.00110.0005-0.0180.00930.01660.00470.0023-0.00680.0676-0.0153-00.0949-0.02710.00680.0555-0.01310.0598119.7226-12.663327.6404
50.00170.0010.00180.00220.00040.00350.0031-0.01370.00380.0067-0.0035-0.0085-0.0053-0.00960.00110.0453-0.0234-0.06490.0259-0.01120.0517127.7439-6.410631.6924
60.0342-0.0049-0.02820.02940.00850.02250.02180.0160.01090.01830.0267-0.00280.0006-0.00520.00570.06740.0244-0.00520.0434-0.00110.0529123.55723.642926.9025
7-0.00180.00060.00240.00620.0050.00580.0017-0.0012-0.0066-0.018-0.00080.01550.0329-0.02860.00850.18260.0263-0.11080.00150.0639-0.0466120.66393.3839-3.3011
80.02010.0056-0.01860.0068-0.01010.02150.0529-0.0138-0.0076-0.085-0.01790.02760.0287-0.04540.01420.08820.0309-0.04570.10670.08720.0792116.984511.0173-0.4239
90.0330.01140.02510.00940.00790.01940.0729-0.0167-0.008-0.0587-0.02170.00120.0234-0.03370.00320.070.01540.00520.04140.0130.0563123.49767.91299.4565
100.00520.0020.00570.00720.00280.01020.02790.01180.02210.02280.02110.00760.0047-0.00570.01210.10320.03960.02490.05210.02370.0682127.424413.50939.3358
110.00530.0079-0.00530.0118-0.00830.00560.0176-0.00430.0103-0.0079-0.0132-0.0156-0.01180.01850.00130.0276-0.02190.0340.04860.02750.1123135.99047.131212.026
120.0031-0.00010.00580.0009-0.00170.00430.0119-0.00620.0063-0.0245-0.0003-0.00950.0264-0.00100.083-0.0054-0.00090.07660.01080.0517129.4894-2.805712.4318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 162 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 34 )
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 69 )
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 94 )
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 123 )
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 162 )

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