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- PDB-5kf1: X-ray structure of a glucosamine N-Acetyltransferase from Clostri... -

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Basic information

Entry
Database: PDB / ID: 5kf1
TitleX-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, apo form, pH 5
ComponentsPredicted acetyltransferase
KeywordsTRANSFERASE / N-acetyltransferase / GNAT / tandem-GNAT
Function / homology: / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / COENZYME A / Predicted acetyltransferase
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolden, H.M. / Thoden, J.B. / Dopkins, B.J. / tipton, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural Studies on a Glucosamine/Glucosaminide N-Acetyltransferase.
Authors: Dopkins, B.J. / Tipton, P.A. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)79,9737
Polymers76,7572
Non-polymers3,2165
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-26 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.864, 65.694, 90.486
Angle α, β, γ (deg.)90.00, 106.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted acetyltransferase


Mass: 38378.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: CA_C0184 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q97ML2
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8-11% PEG-8000, 100 mH HOMOPIPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46396 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.9 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL FROM SAD DATA SET

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.614 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2253 4.9 %RANDOM
Rwork0.184 ---
obs0.187 44132 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.51 Å2
2---0.88 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 152 252 5596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195497
X-RAY DIFFRACTIONr_bond_other_d0.0010.025265
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9877411
X-RAY DIFFRACTIONr_angle_other_deg0.85312135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3445631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77123.882255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60615998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7061526
X-RAY DIFFRACTIONr_chiral_restr0.1060.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021319
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0412.9982517
X-RAY DIFFRACTIONr_mcbond_other3.0392.9972514
X-RAY DIFFRACTIONr_mcangle_it4.1324.4823140
X-RAY DIFFRACTIONr_mcangle_other4.1324.4833141
X-RAY DIFFRACTIONr_scbond_it4.2363.4812980
X-RAY DIFFRACTIONr_scbond_other4.2353.4812980
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3445.0194269
X-RAY DIFFRACTIONr_long_range_B_refined7.6324.6376578
X-RAY DIFFRACTIONr_long_range_B_other7.62924.646579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 137 -
Rwork0.287 2967 -
obs--86.22 %

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