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- PDB-3pp9: 1.6 Angstrom resolution crystal structure of putative streptothri... -

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Basic information

Entry
Database: PDB / ID: 3pp9
Title1.6 Angstrom resolution crystal structure of putative streptothricin acetyltransferase from Bacillus anthracis str. Ames in complex with acetyl coenzyme A
ComponentsPutative streptothricin acetyltransferase
KeywordsTRANSFERASE / Putative Streptothricin Acetyltransferase / Toxin Production and Resistance / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases (CSGID)
Function / homology
Function and homology information


N-acetyltransferase activity / response to antibiotic
Similarity search - Function
Streptothricin acetyltransferase / 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
ACETYL COENZYME *A / : / PHOSPHATE ION / N-acetyltransferase / Putative streptothricin acetyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.6 Angstrom resolution crystal structure of putative streptothricin acetyltransferase from Bacillus anthracis str. Ames in complex with acetyl coenzyme A
Authors: Halavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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: Putative streptothricin acetyltransferase
B: Putative streptothricin acetyltransferase
C: Putative streptothricin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,08513
Polymers66,1033
Non-polymers2,98210
Water6,395355
1
A: Putative streptothricin acetyltransferase
hetero molecules

A: Putative streptothricin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9568
Polymers44,0692
Non-polymers1,8876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area17900 Å2
MethodPISA
2
B: Putative streptothricin acetyltransferase
C: Putative streptothricin acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1079
Polymers44,0692
Non-polymers2,0387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-50 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.097, 68.009, 174.168
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative streptothricin acetyltransferase


Mass: 22034.252 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS2961, BA_3185, GBAA3185, GBAA_3185 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81NK7, UniProt: A0A6L7H2K5*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 2.41 mg/mL. Crystallization conditions: PEG8K 20% KdihidrogenPO4 0.05M. Cryoprotectant - Paratone-N , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.9787
SYNCHROTRONAPS 21-ID-D21.04
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDAug 16, 2010Be-Lenses/Diamond Laue Mono
MARMOSAIC 300 mm CCD2CCDAug 23, 2010Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond[111]SINGLE WAVELENGTHMx-ray1
2Si(111) ChannelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
21.041
ReflectionResolution: 1.6→30 Å / Num. all: 70883 / Num. obs: 70883 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.96 / Num. unique all: 2912 / % possible all: 82

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: SAD model of the data set collected on 21-ID-F

Resolution: 1.6→29.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.794 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22203 3571 5 %RANDOM
Rwork0.18863 ---
obs0.1903 67311 98.44 %-
all-67311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-1.19 Å2
2---0.19 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 180 355 4843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225013
X-RAY DIFFRACTIONr_bond_other_d0.0010.023293
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9926854
X-RAY DIFFRACTIONr_angle_other_deg0.90438080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3065597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.72725.301249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.07115874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2931517
X-RAY DIFFRACTIONr_chiral_restr0.1030.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025606
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021023
X-RAY DIFFRACTIONr_mcbond_it0.7961.52862
X-RAY DIFFRACTIONr_mcbond_other0.2021.51146
X-RAY DIFFRACTIONr_mcangle_it1.46924673
X-RAY DIFFRACTIONr_scbond_it2.36632151
X-RAY DIFFRACTIONr_scangle_it3.694.52181
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 218 -
Rwork0.229 4139 -
obs-4139 82.88 %
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)
10.8233-0.43610.1021.34510.49330.60870.0465-0.0039-0.03210.0052-0.0007-0.0389-0.02240.0427-0.04590.07790.01040.04510.1110.0240.115835.275125.292711.1887
21.4107-0.40720.32981.86060.26511.19620.005-0.07760.03930.13010.00180.122-0.0086-0.0311-0.00680.02130.00520.03170.03520.00260.054929.731229.791716.3385
32.28150.1063-0.57221.869-0.15883.25090.03710.0762-0.01950.0674-0.0383-0.05940.18460.11150.00120.01690.01060.00930.0440.00990.130728.980218.76194.7137
40.6447-0.2846-0.41451.77451.282.71130.0515-0.02030.0106-0.14460.1062-0.2062-0.18960.0325-0.15770.09180.0274-0.00230.1383-0.00830.1584.935323.951838.6786
50.94040.0250.80191.18430.32523.6970.0878-0.0907-0.01290.129-0.0026-0.08110.26580.0054-0.08530.10470.0138-0.01420.0799-0.02350.06844.061419.663742.1504
61.5361-0.61940.75360.7610.11884.35810.0313-0.05220.0917-0.0577-0.13930.0133-0.148-0.3230.1080.08170.0130.01110.1481-0.02360.02881.837627.190952.8796
72.7350.2124-0.51181.8838-0.16341.83930.01190.1629-0.3240.14150.1309-0.4010.220.0976-0.14280.25290.0156-0.06680.1149-0.10440.222717.0414.392272.2021
81.9250.1693-0.01161.78670.41891.86330.05440.1375-0.08470.15770.1798-0.35950.17370.2609-0.23430.09790.0298-0.03680.0952-0.07150.107621.241220.329672.4885
91.88680.59920.80492.746-0.29263.777-0.00540.0566-0.1189-0.04960.1097-0.0420.321-0.2111-0.10430.0753-0.01540.01670.0726-0.01830.02857.44922.509367.6287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 67
2X-RAY DIFFRACTION2A68 - 148
3X-RAY DIFFRACTION3A149 - 182
4X-RAY DIFFRACTION4B-1 - 36
5X-RAY DIFFRACTION5B37 - 137
6X-RAY DIFFRACTION6B138 - 183
7X-RAY DIFFRACTION7C1 - 72
8X-RAY DIFFRACTION8C73 - 148
9X-RAY DIFFRACTION9C149 - 183

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