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- PDB-2psw: Human MAK3 homolog in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 2psw
TitleHuman MAK3 homolog in complex with CoA
ComponentsN-acetyltransferase 13
KeywordsTRANSFERASE / ACETYLTRANSFERASE / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) family / 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
COENZYME A / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Schuetz, A. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...Walker, J.R. / Schuetz, A. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human MAK3 homolog.
Authors: Schuetz, A. / Walker, J.R. / Antoshenko, T. / Wu, H. / Bernstein, G. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMay 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Atomic model
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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase 13
B: N-acetyltransferase 13
C: N-acetyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9056
Polymers58,6023
Non-polymers2,3033
Water2,720151
1
A: N-acetyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3022
Polymers19,5341
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3022
Polymers19,5341
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3022
Polymers19,5341
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.643, 102.913, 67.157
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-acetyltransferase 13 / / hNAT5 / hSAN


Mass: 19534.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAT13, MAK3, NAT5 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZZ1, EC: 2.3.1.88
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 ...Details: Reservoir: 0.1 M Sodium acetate pH 5.0, 16% PEG3350, 10 mM DTT, 0.1% Dioxane. Protein: 11.8 mg/mL + 3-fold molar excess of CoA in 20 mM HEPES pH 7.5, 0.1 M NaCl, 2.5% 1,2-Propanediol, and 10 mM DTT. Cryo: 75% Reservoir + 25% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2006
Details: 1-M LONG, CYLINDRICALLY BENT ULE GLASS MIRROR WITH PT AND PD COATINGS
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40.26 Å / Num. all: 36244 / Num. obs: 36244 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.1 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3597 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OB0

2ob0


Resolution: 2.1→40.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.158 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26463 1833 5.1 %RANDOM
Rwork0.19709 ---
obs0.2006 34021 98.61 %-
all-35854 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.01 Å2
2---0.16 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 144 151 3962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223923
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9985331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66624.247186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44615658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6521522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022918
X-RAY DIFFRACTIONr_nbd_refined0.2080.21654
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22707
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.25
X-RAY DIFFRACTIONr_mcbond_it1.81832367
X-RAY DIFFRACTIONr_mcangle_it2.61643709
X-RAY DIFFRACTIONr_scbond_it3.46251748
X-RAY DIFFRACTIONr_scangle_it4.75671621
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 133 -
Rwork0.286 2515 -
obs--98.55 %
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)
19.85567.2706-3.04678.66710.4043.07010.01440.13730.0276-0.15160.0795-0.1541-0.6456-0.3794-0.09380.107-0.03620.03320.05740.04550.074744.6733356.7083-95.0568
20.59120.50840.15657.60390.61922.81410.05580.11070.04710.6157-0.03560.8179-0.0224-0.3397-0.0202-0.0122-0.00480.11520.0924-0.01230.137531.4348347.0242-82.5139
33.74411.1876-1.70433.83650.37137.7159-0.1389-0.0196-0.44470.6503-0.06280.35960.6147-0.19880.20170.0529-0.0050.1209-0.01470.04760.116733.0631337.4739-80.1302
40.8273-0.18890.32611.80830.6130.3962-0.13480.04370.08370.2338-0.02930.04430.0279-0.01080.16410.0358-0.00190.05820.1076-0.00070.070338.7218349.8333-85.3738
513.8701-7.375712.24976.8914-8.003911.56620.2296-0.0917-0.38540.5341-0.22160.40340.3159-0.107-0.0080.18280.00330.04220.11430.0444-0.079248.0932334.8826-75.7833
61.3747-1.50710.9852.6775-0.14241.5627-0.22080.0253-0.03090.16360.13970.0907-0.1506-0.04920.0811-0.0346-0.01150.03420.12730.01710.075143.1363341.8128-90.3438
710.3005-9.800812.640912.801-9.424317.463-0.30480.07220.64470.5822-0.339-0.6222-0.29670.07580.64380.0793-0.0844-0.08730.082-0.03770.01353.3472345.4849-80.4494
86.99843.63227.43155.43384.51278.0125-0.2677-0.1126-0.27990.10280.11230.1910.00390.2410.15540.01040.04970.04580.12310.02580.000750.1294333.4415-81.436
91.42710.9547-0.62263.4862-1.62980.78860.14880.33040.06060.0781-0.21930.30910.16060.00480.0705-0.01270.03560.01720.1463-0.06560.077646.6851332.0644-95.2782
105.02612.9819-2.12798.4975-1.60314.2818-0.13070.0046-0.1830.45770.0865-0.41370.29410.40170.04420.0130.06770.02390.0981-0.029-0.028651.2103328.3745-88.9907
1131.39892.4233-0.010728.712-24.567621.15790.5144-1.81530.64051.08691.35492.32330.25520.6889-1.86930.1230.12020.27780.114-0.13790.509334.9868322.5072-87.2
126.39878.31562.524911.67234.7823.5981-0.04050.0289-0.34750.2054-0.1263-0.10230.36930.45310.16680.0050.03250.00960.07510.00850.091851.0069329.374-86.0298
132.51421.71751.9018.3711.40081.4387-0.32980.47870.1576-0.93960.00330.5237-0.31650.11420.32660.23030.0427-0.14110.11240.1217-0.10618.4009347.0703-127.1777
149.5077-2.57833.450812.7654-11.333216.3639-0.4384-0.20740.8989-0.0601-0.20390.60520.0719-0.5580.64230.02970.0388-0.09410.0449-0.03580.086514.8901349.8725-115.3962
1510.31251.993-3.17357.33340.012919.9979-0.392-0.52451.3851-1.3644-0.00140.5114-2.35870.04210.39340.45370.0776-0.2146-0.38630.1766-0.011318.9521359.0324-120.225
160.74571.78310.9436.17830.26443.2617-0.35310.22080.0431-0.57470.0620.09920.00230.17970.29110.1347-0.0573-0.07120.1070.05820.015221.3543344.6475-123.7949
1721.87128.97387.16877.9544.36347.4478-0.2062-0.46461.3329-0.3829-0.0688-0.3174-1.1901-0.19090.2750.4281-0.2392-0.1432-0.22230.15290.175835.1324364.9236-117.64
181.26381.52470.16151.84310.10972.0472-0.09650.13070.0549-0.0287-0.03440.104-0.1898-0.1030.13090.0551-0.0085-0.05250.05970.04760.064825.711347.4103-115.0445
197.8263.21465.69524.72752.20374.15-0.87230.69550.0741-0.88020.45410.2679-0.11350.59340.41820.1473-0.12730.01830.14790.0551-0.041730.9909345.3553-121.0622
205.75021.9831-1.65051.5784-2.41357.2332-0.72840.22860.4589-0.49530.24840.0824-0.21030.21350.480.1826-0.19380.0178-0.02080.06630.053435.3879355.326-117.1099
219.35211.13465.25092.19593.63937.32750.2354-0.3985-0.01990.0304-0.3253-0.09480.2109-0.22090.08990.0075-0.0337-0.02040.08940.01790.046532.0223345.6856-106.8594
224.4878-1.53730.748612.69323.50878.0915-0.37930.39480.0154-0.19280.385-0.0804-0.73230.8225-0.0057-0.0839-0.0939-0.04970.09590.04930.095938.0647351.0195-108.6592
2314.48490.8731.628910.37041.0427.54881.1284-0.07090.2709-0.1962-0.99411.0957-1.2267-0.594-0.1342-0.01280.2564-0.08050.0694-0.13520.121924.0376359.0724-100.3681
245.4383-2.139-6.54783.79123.619913.17530.0185-0.17670.095-0.1656-0.2382-0.4454-0.83880.03510.2197-0.0049-0.0285-0.07150.01980.06390.116335.9913355.7057-108.4738
258.8031-3.8905-2.16028.4921-10.643220.3908-0.03090.3633-0.136-0.65070.21510.25040.5116-0.7009-0.18420.0331-0.0394-0.02750.0778-0.03190.052847.5096366.354-97.6402
262.45314.1548-3.243121.36294.334111.0286-0.5123-0.70170.0346-0.52150.3241-1.13520.47891.03670.1882-0.14320.0988-0.03630.1410.01130.146958.4089364.6246-85.2384
272.0472-2.9003-0.26339.6983-2.75976.1632-0.2603-0.68670.29640.29590.4768-0.92370.23320.7314-0.2165-0.09290.112-0.19210.1414-0.05330.129255.7149369.1877-76.7831
280.7743-0.2704-0.42850.33990.5721.3818-0.1257-0.0791-0.1220.00130.0828-0.24890.07840.20850.04290.00260.00190.02130.08560.03080.114650.7282364.8585-89.8397
293.34821.1766-2.71551.9860.63074.6-0.3234-0.24830.09050.36930.3379-0.11880.6490.1715-0.01450.1280.1496-0.02160.06320.07460.033241.6403365.0749-72.2469
301.30620.5625-2.38082.5795-1.26894.3649-0.0511-0.08560.11680.02870.0669-0.19570.09520.0638-0.0157-0.04330.0199-0.01630.08790.03650.097945.5946373.0501-84.7242
315.32844.0551-3.27954.8244-3.99243.307-0.28980.1047-0.0578-0.13650.069-0.02730.1995-0.01250.2209-0.00340.00810.00340.1351-0.03270.083539.2615366.3854-87.3754
321.86582.86480.78049.01261.28591.3797-0.1584-0.1529-0.06950.28770.0376-0.02790.0120.01540.1207-0.02110.0160.02760.07660.01310.064437.1446366.3955-76.8458
332.9534-0.81760.35255.20084.32153.96780.04070.02270.24530.03980.0673-0.1280.071-0.0095-0.1080.0240.0189-0.00760.1075-0.01380.065641.1038382.2169-81.5778
341.1126-2.26442.01568.123-2.633914.6520.05240.26260.0380.2746-0.08110.42420.3138-0.45890.0287-0.08310.0121-0.00340.14370.00770.038333.4737377.5254-80.9445
3526.57960.9518-4.5153.50713.99939.9273-0.418-1.65710.44480.50950.8893-0.4198-0.04671.0179-0.47130.04750.0691-0.20990.1014-0.19610.021346.5416381.9876-68.4218
369.47084.8389-0.03512.77960.77833.3109-0.3917-0.68920.0032-0.15430.00630.1124-0.1726-0.27020.38540.03480.0231-0.01610.0915-0.0210.008336.6143375.4116-73.8171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 72 - 8
2X-RAY DIFFRACTION2AA8 - 249 - 25
3X-RAY DIFFRACTION3AA25 - 4026 - 41
4X-RAY DIFFRACTION4AA41 - 5642 - 57
5X-RAY DIFFRACTION5AA57 - 7058 - 71
6X-RAY DIFFRACTION6AA71 - 9472 - 95
7X-RAY DIFFRACTION7AA95 - 10396 - 104
8X-RAY DIFFRACTION8AA104 - 114105 - 115
9X-RAY DIFFRACTION9AA115 - 125116 - 126
10X-RAY DIFFRACTION10AA126 - 136127 - 137
11X-RAY DIFFRACTION11AA137 - 144138 - 145
12X-RAY DIFFRACTION12AA145 - 155146 - 156
13X-RAY DIFFRACTION13BB4 - 195 - 20
14X-RAY DIFFRACTION14BB20 - 2721 - 28
15X-RAY DIFFRACTION15BB28 - 4429 - 45
16X-RAY DIFFRACTION16BB45 - 6046 - 61
17X-RAY DIFFRACTION17BB61 - 7062 - 71
18X-RAY DIFFRACTION18BB71 - 8772 - 88
19X-RAY DIFFRACTION19BB88 - 9689 - 97
20X-RAY DIFFRACTION20BB97 - 11698 - 117
21X-RAY DIFFRACTION21BB117 - 125118 - 126
22X-RAY DIFFRACTION22BB126 - 133127 - 134
23X-RAY DIFFRACTION23BB134 - 144135 - 145
24X-RAY DIFFRACTION24BB145 - 155146 - 156
25X-RAY DIFFRACTION25CC4 - 95 - 10
26X-RAY DIFFRACTION26CC10 - 2311 - 24
27X-RAY DIFFRACTION27CC24 - 4025 - 41
28X-RAY DIFFRACTION28CC41 - 5642 - 57
29X-RAY DIFFRACTION29CC57 - 6958 - 70
30X-RAY DIFFRACTION30CC70 - 8871 - 89
31X-RAY DIFFRACTION31CC89 - 9890 - 99
32X-RAY DIFFRACTION32CC99 - 114100 - 115
33X-RAY DIFFRACTION33CC115 - 124116 - 125
34X-RAY DIFFRACTION34CC125 - 131126 - 132
35X-RAY DIFFRACTION35CC132 - 144133 - 145
36X-RAY DIFFRACTION36CC145 - 155146 - 156

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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