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- PDB-5djg: Structure of M. tuberculosis CysQ, a PAP phosphatase with PAP, Mg... -

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Basic information

Entry
Database: PDB / ID: 5djg
TitleStructure of M. tuberculosis CysQ, a PAP phosphatase with PAP, Mg, and Li bound
Components3'-phosphoadenosine 5'-phosphate phosphatase
KeywordsHYDROLASE / CysQ / PAP phosphatase / PAP / lithium
Function / homology
Function and homology information


Sulfate assimilation / inositol monophosphate phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity ...Sulfate assimilation / inositol monophosphate phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / sulfate assimilation / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cobalt ion binding / manganese ion binding / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
: / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / : / 3'-phosphoadenosine 5'-phosphate phosphatase / 3'-phosphoadenosine 5'-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsFisher, A.J. / Erickson, A.I.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound.
Authors: Erickson, A.I. / Sarsam, R.D. / Fisher, A.J.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3'-phosphoadenosine 5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2054
Polymers30,7471
Non-polymers4583
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-21 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.665, 58.060, 101.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3'-phosphoadenosine 5'-phosphate phosphatase / CysQ / PAP phosphatase / 3'(2') / 5'-bisphosphate nucleotidase / 5-bisphosphonucleoside 3'(2')- ...CysQ / PAP phosphatase / 3'(2') / 5'-bisphosphate nucleotidase / 5-bisphosphonucleoside 3'(2')-phosphohydrolase / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase / DPNPase / Fructose-1 / 6-bisphosphatase / FBPase / Inositol-1-monophosphatase / IMPase / Inositol-1-phosphatase


Mass: 30746.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysQ, MT2189 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WKJ0, UniProt: P9WKJ1*PLUS, 3'(2'),5'-bisphosphate nucleotidase, fructose-bisphosphatase, inositol-phosphate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 25% PEG8000, 1 mM PAP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2014
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.951→38.151 Å / Num. all: 17281 / Num. obs: 17281 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.39 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.44
Reflection shellResolution: 1.951→2 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.43 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
XDSJuly 4, 2012data reduction
XSCALENovember 11, 2013data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DJF

5djf


Resolution: 1.951→38.151 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.9 / Phase error: 16.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 906 5.19 %Random selection
Rwork0.158 ---
obs0.1595 17281 92.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.951→38.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 29 273 2239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072026
X-RAY DIFFRACTIONf_angle_d1.1452773
X-RAY DIFFRACTIONf_dihedral_angle_d13.16730
X-RAY DIFFRACTIONf_chiral_restr0.048312
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9515-2.00890.21781160.22212033X-RAY DIFFRACTION76
2.0089-2.07370.22971190.17932464X-RAY DIFFRACTION92
2.0737-2.14790.23541170.16562594X-RAY DIFFRACTION95
2.1479-2.23380.18491430.17042536X-RAY DIFFRACTION95
2.2338-2.33550.18461510.15722484X-RAY DIFFRACTION95
2.3355-2.45860.24951080.15792541X-RAY DIFFRACTION95
2.4586-2.61260.18161690.16912478X-RAY DIFFRACTION95
2.6126-2.81430.19691500.15492525X-RAY DIFFRACTION95
2.8143-3.09740.18241600.15292506X-RAY DIFFRACTION95
3.0974-3.54530.14771290.14442482X-RAY DIFFRACTION93
3.5453-4.46560.14671380.13452476X-RAY DIFFRACTION93
4.4656-38.15780.19591230.16232522X-RAY DIFFRACTION95

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