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- PDB-3mgd: Crystal Structure of predicted acetyltransferase with acetyl-CoA ... -

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Basic information

Entry
Database: PDB / ID: 3mgd
TitleCrystal Structure of predicted acetyltransferase with acetyl-CoA from Clostridium acetobutylicum at the resolution 1.9A, Northeast Structural Genomics Consortium Target CaR165
ComponentsPredicted acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / N-acetyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / 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 / Predicted acetyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target CaR165
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: 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 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted acetyltransferase
B: Predicted acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6524
Polymers37,0332
Non-polymers1,6192
Water5,278293
1
A: Predicted acetyltransferase
hetero molecules

A: Predicted acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6524
Polymers37,0332
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7940 Å2
ΔGint-42 kcal/mol
Surface area15300 Å2
MethodPISA
2
B: Predicted acetyltransferase
hetero molecules

B: Predicted acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6524
Polymers37,0332
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8180 Å2
ΔGint-40 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.933, 56.341, 99.721
Angle α, β, γ (deg.)90.000, 98.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Predicted acetyltransferase


Mass: 18516.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C0160 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q97MN4
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M HEPES, 10% PEG8000, 10 mM CoA, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2010 / Details: MIRROR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 48682 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.68 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.6 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.69 Å / SU ML: 0.22 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 1274 5.09 %
Rwork0.1798 --
obs0.1823 26309 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.37 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.3204 Å21.1877 Å2-4.5082 Å2
2---0 Å22.9333 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 102 293 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072704
X-RAY DIFFRACTIONf_angle_d1.1483673
X-RAY DIFFRACTIONf_dihedral_angle_d25.1571105
X-RAY DIFFRACTIONf_chiral_restr0.078401
X-RAY DIFFRACTIONf_plane_restr0.017463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-1.97470.25931600.19172551X-RAY DIFFRACTION98
1.9747-2.06460.30621320.19072641X-RAY DIFFRACTION99
2.0646-2.17340.241410.18472621X-RAY DIFFRACTION99
2.1734-2.30950.24011320.18792630X-RAY DIFFRACTION99
2.3095-2.48770.25621310.18432663X-RAY DIFFRACTION100
2.4877-2.73790.23441510.19392646X-RAY DIFFRACTION100
2.7379-3.13360.21311350.18252680X-RAY DIFFRACTION100
3.1336-3.94640.24371310.16142657X-RAY DIFFRACTION100
3.9464-28.69740.18971610.17272670X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -3.2773 Å / Origin y: 28.6964 Å / Origin z: 25.3519 Å
111213212223313233
T0.102 Å2-0.0206 Å20.0025 Å2-0.0714 Å2-0.0008 Å2--0.1102 Å2
L0.1639 °2-0.1161 °2-0.228 °2-0.0147 °20.1118 °2--1.2178 °2
S-0.0357 Å °0.0117 Å °-0.0123 Å °0.0087 Å °-0.0004 Å °-0.015 Å °0.0575 Å °0.0097 Å °0.0341 Å °
Refinement TLS groupSelection details: ALL

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