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- PDB-2r7h: CRYSTAL STRUCTURE OF A putative acetyltransferase of the GNAT fam... -

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Basic information

Entry
Database: PDB / ID: 2r7h
TitleCRYSTAL STRUCTURE OF A putative acetyltransferase of the GNAT family (DDE_3044) FROM DESULFOVIBRIO DESULFURICANS SUBSP. AT 1.85 A RESOLUTION
ComponentsPutative D-alanine N-acetyltransferase of GNAT family
KeywordsTRANSFERASE / PUTATIVE ACETYLTRANSFERASE OF THE GNAT FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


peptide-alanine-alpha-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
2-ETHOXYETHANOL / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative D-alanine N-acetyltransferase of GNAT family (YP_389533.1) from Desulfovibrio desulfuricans G20 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 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 1.4Jan 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative D-alanine N-acetyltransferase of GNAT family
B: Putative D-alanine N-acetyltransferase of GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3234
Polymers39,1432
Non-polymers1802
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.750, 47.350, 108.120
Angle α, β, γ (deg.)90.000, 97.040, 90.000
Int Tables number5
Space group name H-MC121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative D-alanine N-acetyltransferase of GNAT family


Mass: 19571.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
Species: Desulfovibrio desulfuricans / Strain: G20 / Gene: YP_389533.1, Dde_3044 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q30WV8
#2: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 35.0% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97951, 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979511
30.979261
ReflectionResolution: 1.85→28.116 Å / Num. obs: 30713 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.03 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
1.85-1.920.6111.2461364666194.9
1.92-1.990.3532.357204328178
1.99-2.080.263364274938182
2.08-2.190.1774.267915260187.1
2.19-2.330.1215.970975557190.1
2.33-2.510.0858.272485660193
2.51-2.760.05611.472625684195.1
2.76-3.160.03218.374395847196.7
3.16-28.1160.01830.276055960198

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.116 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 9.478 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.138
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. TWO 2-ETHOXYETHANOL MOLECULES ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1545 5 %RANDOM
Rwork0.209 ---
all0.211 ---
obs0.211 30712 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.02 Å2
2--2.66 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 12 128 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222493
X-RAY DIFFRACTIONr_bond_other_d0.0040.021631
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9483390
X-RAY DIFFRACTIONr_angle_other_deg1.41833933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.655319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.75522.264106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.43415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0651518
X-RAY DIFFRACTIONr_chiral_restr0.1180.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
X-RAY DIFFRACTIONr_nbd_refined0.1840.3452
X-RAY DIFFRACTIONr_nbd_other0.1550.31639
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51208
X-RAY DIFFRACTIONr_nbtor_other0.0860.51195
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.5195
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.316
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.56
X-RAY DIFFRACTIONr_mcbond_it2.25731659
X-RAY DIFFRACTIONr_mcbond_other0.5643649
X-RAY DIFFRACTIONr_mcangle_it3.20252500
X-RAY DIFFRACTIONr_scbond_it4.93881011
X-RAY DIFFRACTIONr_scangle_it6.12611890
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 119 -
Rwork0.314 2138 -
obs-2257 97.71 %
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)
14.61581.45150.69282.0318-0.23023.396-0.0859-0.54810.6298-0.1002-0.22560.0163-0.23080.16240.3115-0.0491-0.11580.01380.1049-0.08050.040644.71448.068442.2759
21.0868-0.1812-0.36310.2970.22373.26670.0691-0.314-0.0154-0.061-0.03460.02230.11330.1753-0.0344-0.00060.00710.0183-0.01870.03350.001936.556733.974237.9957
35.227-1.8612-0.86211.1975-0.78342.3654-0.13510.02120.59640.03860.0455-0.1499-0.1623-0.10570.0897-0.03150.08150.00050.01060.01870.006125.44751.124812.1606
41.1125-0.66590.7560.6488-1.0262.66310.08390.1192-0.0779-0.1363-0.05120.00520.2154-0.2527-0.03270.0255-0.0154-0.01370.0141-0.0224-0.028227.379635.444415.6944
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA18 - 8019 - 81
22AA81 - 17682 - 177
33BB18 - 8219 - 83
44BB83 - 17684 - 177

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