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- PDB-3d3s: Crystal structure of L-2,4-diaminobutyric acid acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 3d3s
TitleCrystal structure of L-2,4-diaminobutyric acid acetyltransferase from Bordetella parapertussis
ComponentsL-2,4-diaminobutyric acid acetyltransferase
KeywordsTRANSFERASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Acyltransferase
Function / homology
Function and homology information


diaminobutyrate acetyltransferase / diaminobutyrate acetyltransferase activity / ectoine biosynthetic process
Similarity search - Function
L-2,4-diaminobutyric acid 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
2,4-DIAMINOBUTYRIC ACID / L-2,4-diaminobutyric acid acetyltransferase
Similarity search - Component
Biological speciesBordetella parapertussis 12822 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsKim, Y. / Volkart, L. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of L-2,4-diaminobutyric acid acetyltransferase from Bordetella parapertussis.
Authors: Kim, Y. / Volkart, L. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-2,4-diaminobutyric acid acetyltransferase
B: L-2,4-diaminobutyric acid acetyltransferase
C: L-2,4-diaminobutyric acid acetyltransferase
D: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,46322
Polymers84,7054
Non-polymers1,75718
Water6,792377
1
A: L-2,4-diaminobutyric acid acetyltransferase
B: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,30112
Polymers42,3532
Non-polymers94910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-13.3 kcal/mol
Surface area14900 Å2
MethodPISA
2
C: L-2,4-diaminobutyric acid acetyltransferase
D: L-2,4-diaminobutyric acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,16110
Polymers42,3532
Non-polymers8098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-12.2 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.160, 63.145, 77.331
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-2,4-diaminobutyric acid acetyltransferase / DABA acetyltransferase


Mass: 21176.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis 12822 (bacteria)
Strain: 12822 / NCTC 13253 / Gene: ectA, BPP1888 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7W980, diaminobutyrate acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DAB / 2,4-DIAMINOBUTYRIC ACID


Type: L-peptide linking / Mass: 118.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 1.26 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 22, 2008 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.87→48.8 Å / Num. all: 55224 / Num. obs: 55224 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 29.14 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2 / Num. unique all: 2729 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.87→48.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.982 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2802 5.1 %RANDOM
Rwork0.165 ---
all0.167 52345 --
obs0.167 52345 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0.23 Å2
2--1.85 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.87→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 100 377 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.957388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26820.903288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07415838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2041581
X-RAY DIFFRACTIONr_chiral_restr0.1320.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024351
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22457
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23570
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2821.53341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00725239
X-RAY DIFFRACTIONr_scbond_it3.05632283
X-RAY DIFFRACTIONr_scangle_it4.6184.52149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 202 -
Rwork0.215 3711 -
obs-3913 94.95 %
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)
11.64850.62340.50181.28850.06981.39810.0963-0.0768-0.08620.0715-0.1202-0.10110.21730.02060.0239-0.0445-0.0010.0097-0.08880.0148-0.07747.8927-6.743355.8754
21.3758-0.16480.32461.38320.27422.53640.06920.15570.0676-0.1246-0.1007-0.0843-0.10820.18020.0315-0.0934-0.00420.0363-0.05920.0346-0.050512.202811.188939.9321
31.56410.0106-0.66791.14040.08451.77360.0173-0.12650.12460.051-0.0178-0.0491-0.0590.02040.0005-0.06480.013-0.0134-0.0293-0.0008-0.0723-11.126820.836864.9404
43.2236-0.25110.45660.774-0.3660.75210.029-0.0896-0.27570.0063-0.00080.08180.0756-0.1209-0.0283-0.0999-0.0159-0.0047-0.01580.0132-0.0708-27.19190.931864.7842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 15926 - 184
2X-RAY DIFFRACTION2BB1 - 15926 - 184
3X-RAY DIFFRACTION3CC0 - 15925 - 184
4X-RAY DIFFRACTION4DD1 - 16126 - 186

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