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- PDB-2q7b: Crystal structure of acetyltransferase (NP_689019.1) from Strepto... -

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Basic information

Entry
Database: PDB / ID: 2q7b
TitleCrystal structure of acetyltransferase (NP_689019.1) from Streptococcus agalactiae 2603 at 2.00 A resolution
ComponentsAcetyltransferase, GNAT family
KeywordsTRANSFERASE / NP_689019.1 / acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-acetyltransferase activity
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
CITRATE ANION / Acetyltransferase, GNAT family
Similarity search - Component
Biological speciesStreptococcus agalactiae 2603V/R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of acetyltransferase (NP_689019.1) from Streptococcus agalactiae 2603 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE PROTEIN WAS EXPRESSED AND PURIFIED WITH A TAG MGSDKIHHHHHHENLYFQG FROM CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3063
Polymers22,0821
Non-polymers2252
Water1,65792
1
A: Acetyltransferase, GNAT family
hetero molecules

A: Acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6126
Polymers44,1632
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)67.985, 67.985, 87.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Acetyltransferase, GNAT family /


Mass: 22081.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Species: Streptococcus agalactiae / Strain: 2603 V/R, Serotype V / Gene: NP_689019.1, SAG2033 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8DX25
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 10.0% PEG 6000, 0.1M Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
ReflectionResolution: 2→29.437 Å / Num. obs: 16338 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.059.21.2290.61074111661.229100
2.05-2.119.21.0070.71052511451.007100
2.11-2.179.20.7411054911440.74100
2.17-2.249.20.6761.1984710660.676100
2.24-2.319.20.51.31005310930.5100
2.31-2.399.20.4091.9940510180.409100
2.39-2.489.20.3192.489999800.319100
2.48-2.589.20.2443.190909930.244100
2.58-2.79.20.2053.684279140.205100
2.7-2.839.10.1684.381688950.168100
2.83-2.989.20.145.175678240.14100
2.98-3.169.10.1116.374208130.111100
3.16-3.389.10.082868387530.082100
3.38-3.6590.067963257030.067100
3.65-490.05710.660446700.057100
4-4.478.90.04911.651945820.049100
4.47-5.168.80.05211.147145350.052100
5.16-6.328.70.05710.739434550.057100
6.32-8.948.30.0521230593700.052100
8.94-29.447.40.04314.316162190.04397.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.437 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.222 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ONE CHLORIDE ANION AND A CITRATE ANION (FLC) ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 821 5 %RANDOM
Rwork0.185 ---
obs0.187 16309 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 14 92 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221472
X-RAY DIFFRACTIONr_bond_other_d0.0020.021309
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9591996
X-RAY DIFFRACTIONr_angle_other_deg0.94233035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6475177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83923.79779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37915259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1321511
X-RAY DIFFRACTIONr_chiral_restr0.120.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021676
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
X-RAY DIFFRACTIONr_nbd_refined0.1910.3277
X-RAY DIFFRACTIONr_nbd_other0.1610.31319
X-RAY DIFFRACTIONr_nbtor_refined0.1820.5738
X-RAY DIFFRACTIONr_nbtor_other0.0860.5851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.5116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1260.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.59
X-RAY DIFFRACTIONr_mcbond_it1.6183901
X-RAY DIFFRACTIONr_mcbond_other0.3643347
X-RAY DIFFRACTIONr_mcangle_it2.47751403
X-RAY DIFFRACTIONr_scbond_it4.5398671
X-RAY DIFFRACTIONr_scangle_it5.85811593
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 67 -
Rwork0.265 1107 -
obs-1174 100 %
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)
10.9278-0.7211-0.13212.89680.05472.48740.16240.1779-0.1871-0.2377-0.10940.24350.183-0.1082-0.053-0.07560.0333-0.0416-0.1287-0.0355-0.0734-2.3452.24518.495
25.0935-0.83311.66896.0194-0.61013.1250.51241.1969-0.0784-1.1379-0.4377-0.34160.27810.5622-0.07470.1590.21070.0410.1475-0.0841-0.18031.71957.2584.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 9917 - 118
2X-RAY DIFFRACTION2AA100 - 161119 - 180

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