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- PDB-1yk3: Crystal structure of Rv1347c from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1yk3
TitleCrystal structure of Rv1347c from Mycobacterium tuberculosis
ComponentsHypothetical protein Rv1347c/MT1389Hypothesis
KeywordsTRANSFERASE / acyltransferase / GCN5-related fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


catechol-containing siderophore biosynthetic process / N-acyltransferase activity / siderophore biosynthetic process / fatty acyl-CoA hydrolase activity / acyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine N-acyltransferase MbtK / Lysine N-acyltransferase MbtK
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCard, G.L. / Peterson, N.A. / Smith, C.A. / Rupp, B. / Schick, B.M. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The crystal structure of Rv1347c, a putative antibiotic resistance protein from Mycobacterium tuberculosis, reveals a GCN5-related fold and suggests an alternative function in siderophore biosynthesis
Authors: Card, G.L. / Peterson, N.A. / Smith, C.A. / Rupp, B. / Schick, B.M. / Baker, E.N.
History
DepositionJan 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Hypothetical protein Rv1347c/MT1389
B: Hypothetical protein Rv1347c/MT1389
C: Hypothetical protein Rv1347c/MT1389
D: Hypothetical protein Rv1347c/MT1389
E: Hypothetical protein Rv1347c/MT1389
F: Hypothetical protein Rv1347c/MT1389
G: Hypothetical protein Rv1347c/MT1389
H: Hypothetical protein Rv1347c/MT1389
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,51711
Polymers190,6408
Non-polymers8773
Water11,710650
1
A: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)23,8301
Polymers23,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)23,8301
Polymers23,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)23,8301
Polymers23,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein Rv1347c/MT1389
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1222
Polymers23,8301
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Hypothetical protein Rv1347c/MT1389
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1222
Polymers23,8301
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)23,8301
Polymers23,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Hypothetical protein Rv1347c/MT1389
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1222
Polymers23,8301
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)23,8301
Polymers23,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
A: Hypothetical protein Rv1347c/MT1389

C: Hypothetical protein Rv1347c/MT1389


Theoretical massNumber of molelcules
Total (without water)47,6602
Polymers47,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465x-1/2,-y+3/2,-z1
Buried area1570 Å2
ΔGint-11 kcal/mol
Surface area19700 Å2
MethodPISA
10
F: Hypothetical protein Rv1347c/MT1389

G: Hypothetical protein Rv1347c/MT1389
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9523
Polymers47,6602
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1670 Å2
ΔGint-11 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.665, 77.261, 296.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsGel filtration and dynamic light scattering studies suggest that the protein is monomeric in solution.

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Components

#1: Protein
Hypothetical protein Rv1347c/MT1389 / Hypothesis


Mass: 23830.008 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1347c / Plasmid: pET42a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P64819, UniProt: P9WK15*PLUS
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.4 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Methoxy, PEG 5000, Tris-HCl, beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONSSRL BL9-120.9795, 0.9789, 0.9118
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEMar 1, 2002Osmic mirrors
ADSC QUANTUM 42CCDMar 1, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic mirrorsSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97951
30.97891
40.91181
ReflectionResolution: 2.15→40 Å / Num. all: 96549 / Num. obs: 96453 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.2
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→36.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 174296 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1824 2.1 %RANDOM
Rwork0.227 ---
all0.229 85796 --
obs0.227 85796 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2977 Å2 / ksol: 0.326799 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-5.62 Å20 Å20 Å2
2---1.52 Å20 Å2
3----4.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-50 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12805 0 60 650 13515
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.2→2.34 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.295 13304 -
obs-13304 90.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BOG.PARAMBOG.TOP

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