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- PDB-5kf8: X-ray structure of a glucosamine N-Acetyltransferase from Clostri... -

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Basic information

Entry
Database: PDB / ID: 5kf8
TitleX-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum in complex with glucosamine
ComponentsPredicted acetyltransferase
KeywordsTRANSFERASE / N-acetyltransferase / acyltransferase / GNAT / tanden-GNAT
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / Chem-EP1 / 2-amino-2-deoxy-beta-D-glucopyranose / Predicted acetyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 12, 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 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5117
Polymers38,3781
Non-polymers2,1336
Water3,621201
1
A: Predicted acetyltransferase
hetero molecules

A: Predicted acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,02214
Polymers76,7572
Non-polymers4,26512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10050 Å2
ΔGint6 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.267, 44.406, 74.419
Angle α, β, γ (deg.)90.00, 121.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Predicted acetyltransferase


Mass: 38378.414 Da / Num. of mol.: 1
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
#4: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EP1 / 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID


Mass: 252.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 7-10% PEG-5000, 100 mM HEPPS, 5 mM CoA, 20 mM glucosamine

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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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25315 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 2.6 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kf1

5kf1


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.635 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21025 1258 5 %RANDOM
Rwork0.16016 ---
obs0.1627 24057 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.16 Å2
2--1.64 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 113 201 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192819
X-RAY DIFFRACTIONr_bond_other_d0.0010.022712
X-RAY DIFFRACTIONr_angle_refined_deg1.98523799
X-RAY DIFFRACTIONr_angle_other_deg0.91536262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.03923.78127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37315508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7281513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
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_it2.1281.751274
X-RAY DIFFRACTIONr_mcbond_other2.1271.7481272
X-RAY DIFFRACTIONr_mcangle_it3.0762.6121591
X-RAY DIFFRACTIONr_mcangle_other3.0752.6151592
X-RAY DIFFRACTIONr_scbond_it3.3462.0991545
X-RAY DIFFRACTIONr_scbond_other3.3342.0951537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0232.9822193
X-RAY DIFFRACTIONr_long_range_B_refined6.37414.6363344
X-RAY DIFFRACTIONr_long_range_B_other6.37314.643345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 90 -
Rwork0.239 1566 -
obs--85.01 %

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