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- PDB-3n7z: Crystal structure of acetyltransferase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3n7z
TitleCrystal structure of acetyltransferase from Bacillus anthracis
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / PSI2 / MCSG / structural genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologySCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / Gcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsChang, C. / Wu, R. / Gornicki, P. / Zhang, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2015
Title: Biochemical and Structural Analysis of an Eis Family Aminoglycoside Acetyltransferase from Bacillus anthracis.
Authors: Green, K.D. / Biswas, T. / Chang, C. / Wu, R. / Chen, W. / Janes, B.K. / Chalupska, D. / Gornicki, P. / Hanna, P.C. / Tsodikov, O.V. / Joachimiak, A. / Garneau-Tsodikova, S.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_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.pdbx_leaving_atom_flag / _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_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: Acetyltransferase, GNAT family
B: Acetyltransferase, GNAT family
C: Acetyltransferase, GNAT family
D: Acetyltransferase, GNAT family
E: Acetyltransferase, GNAT family
F: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,90412
Polymers278,7666
Non-polymers1386
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-84 kcal/mol
Surface area98660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.429, 176.859, 109.973
Angle α, β, γ (deg.)90.00, 105.73, 90.00
Int Tables number4
Space group name H-MP1211
Detailshexamer as is

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Components

#1: Protein
Acetyltransferase, GNAT family


Mass: 46460.934 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2743 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q6HXD7
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium HEPES, 20% PEG3350, 0.2M sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2006
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 75598 / Num. obs: 75594 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 19.2
Reflection shellResolution: 2.75→2.77 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 2.26 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 29.489 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.351
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24238 3782 5 %RANDOM
Rwork0.18725 ---
obs0.19005 71443 99.43 %-
all-75225 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.946 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å2-0.87 Å2
2---1.06 Å20 Å2
3---3.44 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18924 0 6 92 19022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02219366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.95326166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20552281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5324.369975
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.131153516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63815101
X-RAY DIFFRACTIONr_chiral_restr0.080.22827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114625
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5541.511422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.069218462
X-RAY DIFFRACTIONr_scbond_it1.63937944
X-RAY DIFFRACTIONr_scangle_it2.6914.57704
X-RAY DIFFRACTIONr_rigid_bond_restr0.811319366
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.751→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 285 -
Rwork0.237 5190 -
obs--98.15 %
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)
15.48662.44112.61965.46153.99846.1257-0.2640.7047-0.0697-0.60430.7104-0.83030.03361.1345-0.44640.17290.0180.03580.3303-0.08160.316830.191496.2068105.3219
21.6993-1.736-0.44853.74132.30893.9171-0.0094-0.1837-0.29640.27150.1880.01890.32190.0459-0.17860.0904-0.0218-0.07090.06530.04950.11621.6885100.6019116.3197
37.9907-0.39234.23840.08-0.58324.59040.1287-0.0865-0.9714-0.07420.0510.00360.4681-0.2726-0.17960.1229-0.0574-0.0060.0330.01140.270611.0838102.051113.2018
44.53250.50550.91852.1667-0.68082.2228-0.01950.2768-0.02130.00490.01460.09340.01030.05640.00490.09520.01410.01150.0707-0.02470.018214.8385125.606899.0075
55.2205-0.3906-0.14052.7578-1.30974.3176-0.04-0.7758-0.19450.58350.13120.1474-0.2847-0.3261-0.09120.18450.01040.00430.20040.10670.10636.688110.1362129.4989
61.0993-0.61091.35466.3453-1.08581.7180.22310.1777-0.18510.02790.09790.01490.3670.0977-0.32110.3385-0.0342-0.13050.51050.03410.375313.4867115.823111.218
77.52150.13191.76098.85680.82743.3476-0.0535-0.23890.44660.4535-0.1214-0.9663-0.54070.33830.1750.1841-0.05550.0190.27060.11040.371130.679389.594460.7948
82.87671.9775-0.98822.44910.40871.6681-0.21630.2749-0.0972-0.26630.1036-0.11210.0229-0.00490.11270.16670.03170.0520.20990.0310.12422.598776.868959.2556
98.1812-3.9698-5.59272.15272.85043.90630.33390.55120.3719-0.4271-0.1930.0477-0.4026-0.3213-0.14090.3919-0.0787-0.16750.0960.11430.312911.883478.994262.2308
103.8037-1.0108-0.52641.79970.33792.24540.0099-0.13350.32670.02340.066-0.0787-0.00410.0139-0.07590.0994-0.03820.00710.02430.00110.08115.379478.925389.7735
114.96230.3527-0.07044.29781.19062.8651-0.20660.185-0.5501-0.11510.10110.11740.4903-0.24220.10550.225-0.04910.06020.0925-0.02650.07728.009660.339860.8141
127.74062.4708-5.12814.5909-3.46874.28170.12610.23420.38440.09360.25770.3894-0.131-0.2569-0.38380.2150.05030.00950.27780.01190.288514.413873.727375.0055
136.99692.3742-2.40973.1829-1.76586.98640.03170.0391-0.25560.3905-0.1664-0.79840.5321.06470.13470.2220.0335-0.10720.38230.05890.28730.3735129.173476.4957
141.88620.39361.28991.8284-1.60134.42350.0108-0.14010.213-0.02090.01630.0425-0.41060.1031-0.02710.168-0.06460.06310.18380.04650.106722.2659137.382966.8472
154.88461.6597-0.01893.601-1.01070.33340.0242-0.76240.14620.7378-0.05090.0142-0.241-0.07380.02670.3485-0.04350.00990.36080.05720.192311.4983133.528166.9176
163.46740.5748-0.47073.0832-0.10231.3562-0.0263-0.1625-0.1175-0.1171-0.1078-0.10590.0072-0.0330.13410.122-0.0210.01170.15950.12150.122815.1673110.54552.5457
174.76-0.9091-0.01015.53130.20183.61320.02950.63750.5427-0.8606-0.12460.3868-0.5779-0.12540.09510.36830.0047-0.08840.17480.15120.18817.8576145.196253.1484
184.25812.5304-1.62154.18552.66495.53320.00490.1391-0.03540.3564-0.00830.07610.30640.00920.00340.3959-0.05650.01110.4070.11080.472514.0199125.941955.6247
195.11891.35780.72857.83751.19192.8506-0.16870.33891.1336-0.143601.2381-0.4266-0.45310.16870.08350.04160.03580.20970.11020.7702-31.31984.980497.0868
202.2807-1.4161-2.44485.91271.28243.0111-0.0462-0.12880.2270.38860.03780.31410.20190.13240.00840.1306-0.06950.06890.12630.10340.384-22.886672.883996.1706
214.84653.4886-3.20795.6234-3.84384.55650.3149-0.4210.51550.81730.00870.2601-0.41390.5702-0.32360.2263-0.007-0.04940.2370.01510.2774-12.116175.768893.4532
224.5520.7788-0.40572.537-1.02642.53120.11220.18280.0708-0.15350.0740.11220.11650.0307-0.18620.08890.0013-0.04580.07670.03940.1021-15.760580.559566.6719
235.0895-1.6291.20464.9778-2.93592.94110.02490.1188-0.3935-0.31160.0960.1310.49370.0581-0.12090.2075-0.025-0.02830.0352-0.0030.0346-8.05757.232291.8132
241.9054-1.124-3.29631.10081.58386.12480.08370.03680.09270.0758-0.2142-0.2282-0.44410.17060.13060.3448-0.1465-0.14350.33740.12770.4773-14.640672.745780.0496
256.90681.0637-2.23634.13440.28895.5949-0.21330.6757-0.3026-0.45780.1430.49180.2838-0.90770.07030.0856-0.0205-0.07820.3301-0.08150.2191-31.4837128.824888.8772
262.2834-0.89522.82272.29610.55224.9869-0.06680.04780.0267-0.06110.01970.1831-0.19840.10610.04710.07640.02880.04610.1545-0.04740.3013-23.3564134.342599.8648
273.529-1.9057-0.37475.66873.25162.04390.14440.83580.1714-0.7291-0.0219-0.2407-0.44120.1986-0.12250.1606-0.02280.0440.2933-0.04790.1389-12.714130.567399.0526
283.9325-1.1917-0.39953.51160.02591.38750.07170.0992-0.40720.1279-0.16380.263-0.0048-0.00360.09210.1109-0.030.01590.11020.00240.2578-16.439105.0857108.7261
294.63961.36420.45066.60121.9271.92090.1304-0.6020.22270.6443-0.19680.01120.00520.01480.06640.1803-0.03950.02440.0839-0.02860.0246-8.951138.9792115.1508
303.25341.43942.47154.6698-2.14164.474-0.04360.1843-0.6654-0.24130.3806-0.47680.1225-0.0977-0.3370.23060.07510.03270.4358-0.09090.4246-15.2969120.6543108.5276
315.2024-2.5039-0.49955.8584-2.37853.4413-0.0707-0.3151-0.050.29290.17560.91180.0943-0.4163-0.10490.1402-0.12350.02290.3010.04110.3372-31.2079100.360655.3667
322.63771.56530.16071.1847-0.73133.4489-0.06710.07340.0709-0.266-0.02270.08880.4250.1220.08980.30280.0723-0.13980.34890.0590.1162-22.9572106.832844.705
338.39520.77824.84970.10070.33493.28160.27170.4274-0.9611-0.0210.0257-0.1640.38880.2094-0.29730.30720.01020.01460.28930.06990.371-12.386108.064748.1236
343.7716-0.1320.69681.86380.78093.2526-0.0045-0.24140.20830.0076-0.0269-0.0696-0.17830.00870.03140.1129-0.00050.01180.14420.07180.1309-16.2008128.877265.8604
356.23750.5151-1.36913.78410.83496.58180.01650.85840.3304-0.6409-0.0443-0.2649-0.3163-0.07530.02780.2090.00290.01140.2350.12820.0963-8.6386118.449633.0821
361.0481-0.72522.08522.50910.84916.7989-0.02870.0469-0.0684-0.12580.08070.125-0.34770.2741-0.0520.2446-0.0704-0.0690.40280.06440.3475-14.9605121.212152.1625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 64
2X-RAY DIFFRACTION2A65 - 113
3X-RAY DIFFRACTION3A115 - 136
4X-RAY DIFFRACTION4A137 - 278
5X-RAY DIFFRACTION5A279 - 380
6X-RAY DIFFRACTION6A381 - 390
7X-RAY DIFFRACTION7B6 - 64
8X-RAY DIFFRACTION8B65 - 113
9X-RAY DIFFRACTION9B115 - 136
10X-RAY DIFFRACTION10B137 - 278
11X-RAY DIFFRACTION11B279 - 380
12X-RAY DIFFRACTION12B381 - 390
13X-RAY DIFFRACTION13C6 - 64
14X-RAY DIFFRACTION14C65 - 113
15X-RAY DIFFRACTION15C115 - 136
16X-RAY DIFFRACTION16C137 - 278
17X-RAY DIFFRACTION17C279 - 380
18X-RAY DIFFRACTION18C381 - 390
19X-RAY DIFFRACTION19D6 - 64
20X-RAY DIFFRACTION20D65 - 113
21X-RAY DIFFRACTION21D115 - 136
22X-RAY DIFFRACTION22D137 - 278
23X-RAY DIFFRACTION23D279 - 380
24X-RAY DIFFRACTION24D381 - 390
25X-RAY DIFFRACTION25E6 - 64
26X-RAY DIFFRACTION26E65 - 113
27X-RAY DIFFRACTION27E115 - 136
28X-RAY DIFFRACTION28E137 - 278
29X-RAY DIFFRACTION29E279 - 380
30X-RAY DIFFRACTION30E381 - 390
31X-RAY DIFFRACTION31F6 - 64
32X-RAY DIFFRACTION32F65 - 113
33X-RAY DIFFRACTION33F115 - 136
34X-RAY DIFFRACTION34F137 - 278
35X-RAY DIFFRACTION35F279 - 380
36X-RAY DIFFRACTION36F381 - 390

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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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