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- PDB-6unc: The crystal structure of Phosphopantetheinyl Hydrolase (PptH) fro... -

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Basic information

Entry
Database: PDB / ID: 6unc
TitleThe crystal structure of Phosphopantetheinyl Hydrolase (PptH) from Mycobacterium tuberculosis
ComponentsMetallophos domain-containing protein
KeywordsHYDROLASE / Phosphopantetheinyl Hydrolase / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology[acyl-carrier-protein] phosphodiesterase / [acyl-carrier-protein] phosphodiesterase activity / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / metal ion binding / : / : / [Acyl-carrier-protein] phosphodiesterase PptH
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMosior, J.W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01AI095208 United States
Welch FoundationA-0015 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Structural insights into phosphopantetheinyl hydrolase PptH from Mycobacterium tuberculosis.
Authors: Mosior, J. / Bourland, R. / Soma, S. / Nathan, C. / Sacchettini, J.
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallophos domain-containing protein
B: Metallophos domain-containing protein
C: Metallophos domain-containing protein
D: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,95912
Polymers145,5164
Non-polymers4438
Water4,486249
1
A: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4903
Polymers36,3791
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4903
Polymers36,3791
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4903
Polymers36,3791
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4903
Polymers36,3791
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Metallophos domain-containing protein
hetero molecules

B: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9806
Polymers72,7582
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2760 Å2
ΔGint-52 kcal/mol
Surface area22450 Å2
MethodPISA
6
C: Metallophos domain-containing protein
hetero molecules

D: Metallophos domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9806
Polymers72,7582
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2910 Å2
ΔGint-52 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.190, 92.534, 183.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 15 through 30 or (resid 31...A15 - 92
121(chain 'A' and (resid 15 through 30 or (resid 31...A94 - 106
131(chain 'A' and (resid 15 through 30 or (resid 31...A108 - 109
141(chain 'A' and (resid 15 through 30 or (resid 31...A112 - 134
151(chain 'A' and (resid 15 through 30 or (resid 31...A136 - 198
161(chain 'A' and (resid 15 through 30 or (resid 31...A201 - 290
211(chain 'B' and (resid 15 through 57 or (resid 58...B15 - 92
221(chain 'B' and (resid 15 through 57 or (resid 58...B94 - 106
231(chain 'B' and (resid 15 through 57 or (resid 58...B108 - 109
241(chain 'B' and (resid 15 through 57 or (resid 58...B112 - 134
251(chain 'B' and (resid 15 through 57 or (resid 58...B136 - 198
261(chain 'B' and (resid 15 through 57 or (resid 58...B201 - 290
311(chain 'C' and ((resid 15 through 17 and (name N...C15 - 92
321(chain 'C' and ((resid 15 through 17 and (name N...C94 - 106
331(chain 'C' and ((resid 15 through 17 and (name N...C108 - 109
341(chain 'C' and ((resid 15 through 17 and (name N...C112 - 134
351(chain 'C' and ((resid 15 through 17 and (name N...C136 - 198
361(chain 'C' and ((resid 15 through 17 and (name N...C201 - 290
411(chain 'D' and (resid 15 through 30 or (resid 31...D15 - 92
421(chain 'D' and (resid 15 through 30 or (resid 31...D94 - 106
431(chain 'D' and (resid 15 through 30 or (resid 31...D108 - 109
441(chain 'D' and (resid 15 through 30 or (resid 31...D112 - 134
451(chain 'D' and (resid 15 through 30 or (resid 31...D136 - 198
461(chain 'D' and (resid 15 through 30 or (resid 31...D201 - 290

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Components

#1: Protein
Metallophos domain-containing protein


Mass: 36379.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2795c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 AI / References: UniProt: I6YEE1
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3 M ammonium tartrate dibasic; 0.1 M bis-tris propane pH 7.0 with protein: condition 1:1 (protein: condition)
PH range: 6.7-7.0

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→44.87 Å / Num. obs: 84008 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.059 / Rrim(I) all: 0.111 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8417 / CC1/2: 0.57 / Rpim(I) all: 0.601 / Rrim(I) all: 1.137

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.86 Å / SU ML: 0.3368 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9084
RfactorNum. reflection% reflection
Rfree0.2215 4324 5.15 %
Rwork0.1858 --
obs0.1876 83990 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 8 249 9287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229346
X-RAY DIFFRACTIONf_angle_d0.576312817
X-RAY DIFFRACTIONf_chiral_restr0.04521346
X-RAY DIFFRACTIONf_plane_restr0.00471663
X-RAY DIFFRACTIONf_dihedral_angle_d13.82345457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36161460.32242645X-RAY DIFFRACTION99.68
2.53-2.560.331450.31212723X-RAY DIFFRACTION99.48
2.56-2.590.30241420.2912614X-RAY DIFFRACTION99.53
2.59-2.620.36921430.29572694X-RAY DIFFRACTION99.65
2.62-2.660.31211420.29232677X-RAY DIFFRACTION99.61
2.66-2.690.37081410.28812621X-RAY DIFFRACTION99.71
2.69-2.730.36231480.27812683X-RAY DIFFRACTION99.4
2.73-2.770.35991440.27142639X-RAY DIFFRACTION99.68
2.77-2.820.29451420.26352659X-RAY DIFFRACTION99.57
2.82-2.860.29511430.24762695X-RAY DIFFRACTION99.75
2.86-2.910.27911720.24072641X-RAY DIFFRACTION99.82
2.91-2.960.30931500.23462688X-RAY DIFFRACTION99.93
2.96-3.020.24691140.22792633X-RAY DIFFRACTION99.75
3.02-3.080.2891580.21792672X-RAY DIFFRACTION99.68
3.08-3.150.2531390.20662628X-RAY DIFFRACTION99.64
3.15-3.220.30871270.19722718X-RAY DIFFRACTION99.79
3.22-3.30.21091650.20122668X-RAY DIFFRACTION99.79
3.3-3.390.23341360.20292634X-RAY DIFFRACTION99.6
3.39-3.490.22791520.19322662X-RAY DIFFRACTION99.79
3.49-3.610.20071230.18652700X-RAY DIFFRACTION99.65
3.61-3.730.21911630.16492619X-RAY DIFFRACTION99.11
3.73-3.880.20131430.16332674X-RAY DIFFRACTION99.37
3.88-4.060.19091440.15082626X-RAY DIFFRACTION99.18
4.06-4.270.19931580.15252617X-RAY DIFFRACTION99.07
4.27-4.540.17891500.14112662X-RAY DIFFRACTION99.19
4.54-4.890.16861470.13832631X-RAY DIFFRACTION98.65
4.89-5.380.17891240.15362634X-RAY DIFFRACTION98.29
5.38-6.160.17331240.16142689X-RAY DIFFRACTION99.12
6.16-7.760.19491460.17542615X-RAY DIFFRACTION98.93
7.76-44.860.16331530.14562605X-RAY DIFFRACTION97.73

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