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- PDB-4orf: cAMP-binding acyltransferase from Mycobacterium smegmatis, mutant R95K -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4orf
TitlecAMP-binding acyltransferase from Mycobacterium smegmatis, mutant R95K
ComponentsAcetyltransferase Pat
KeywordsTRANSFERASE / alpha-beta fold / linker peptide / cyclic nucleotide binding domain / acyl-transferase domain
Function / homology
Function and homology information


N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Gcn5-related N-acetyltransferase (GNAT) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Acetyltransferase (GNAT) domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Gcn5-related N-acetyltransferase (GNAT) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Jelly Rolls / Acyl-CoA N-acyltransferase / Aminopeptidase / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acetyltransferase Pat
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPodobnik, M. / Rebolj, K. / Visweswariah, S.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Allostery and Conformational Dynamics in cAMP-binding Acyltransferases.
Authors: Podobnik, M. / Siddiqui, N. / Rebolj, K. / Nambi, S. / Merzel, F. / Visweswariah, S.S.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase Pat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5744
Polymers37,4681
Non-polymers1063
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.295, 82.847, 104.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetyltransferase Pat / GCN5-related N-acetyltransferase / GNAT / Protein acetyltransferase / Pat


Mass: 37468.047 Da / Num. of mol.: 1 / Mutation: R95K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5458, MSMEI_5308 / Plasmid: pPROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0R3F9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, NaCl, Bis-Tris, MgCl2, DAPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2010
Details: CMOS hybrid-pixel technology operating in dingle photon couting mode
RadiationMonochromator: Si(111) double-crystal fixed exit / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23229 / Num. obs: 22549 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.047 / Χ2: 1 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.053.80.64814651.001196.6
2.05-2.14.30.48614811.002197.9
2.1-2.154.40.38414900.997198.9
2.15-2.224.40.29715050.997198.3
2.22-2.294.10.22214991198
2.29-2.374.50.17514961198
2.37-2.474.50.13815021.001198.3
2.47-2.584.40.10715031.001197.3
2.58-2.714.40.08614910.997197
2.71-2.884.60.06814911.001196.9
2.88-3.114.40.05414891.003196.5
3.11-3.424.40.04715220.999196.9
3.42-3.914.40.03915101196.1
3.91-4.934.50.03415091.001194.3
4.93-504.20.0315961193.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
Elettradevelopeddata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.244 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 2280 10.1 %RANDOM
Rwork0.2199 ---
obs0.2257 22516 96.92 %-
all-23229 --
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 max: 122.23 Å2 / Biso mean: 58.028 Å2 / Biso min: 25.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.36 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 3 124 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192536
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.973453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.315316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51522.478113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.50515410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.051528
X-RAY DIFFRACTIONr_chiral_restr0.1320.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211929
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 158 -
Rwork0.292 1310 -
all-1468 -
obs--95.26 %
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)
11.8504-0.0919-0.53511.90860.11273.62340.3036-0.1830.07650.522-0.12640.013-0.2050.0109-0.17720.2079-0.05390.02270.1918-0.01380.183636.5092188.431117.1942
20.25160.3428-0.51884.0336-2.01521.6927-0.0573-0.0674-0.0435-0.38480.02250.21960.39790.25990.03480.17270.1013-0.02470.25010.02060.193944.5539171.37787.4053
31.87671.1669-0.34422.12760.21722.8066-0.240.176-0.0492-0.60130.1640.0430.6820.03140.07610.407-0.0269-0.01230.02590.02420.102239.7174157.40431.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 117
2X-RAY DIFFRACTION2A118 - 204
3X-RAY DIFFRACTION3A205 - 333

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