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- PDB-5dji: Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO... -

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Basic information

Entry
Database: PDB / ID: 5dji
TitleStructure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 2Mg bound
Components3'-phosphoadenosine 5'-phosphate phosphatase
KeywordsHYDROLASE / CysQ / PAP phosphatase / AMP / magnesium
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 MONOPHOSPHATE / PHOSPHATE ION / 3'-phosphoadenosine 5'-phosphate phosphatase / 3'-phosphoadenosine 5'-phosphate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 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 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 3'-phosphoadenosine 5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2375
Polymers30,7471
Non-polymers4914
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-30 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.637, 58.200, 101.510
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M magnesium acetate, 0.1 M Bis-Tris-HCl, 35% PEG550 MME

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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: 1.659→38.252 Å / Num. obs: 28723 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 38.81
Reflection shellResolution: 1.659→1.7 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.17 / % possible all: 84

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Processing

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

5djf


Resolution: 1.659→38.252 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 14.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1684 1444 5.06 %Random selection
Rwork0.1423 ---
obs0.1436 28723 95.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.659→38.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 30 295 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072035
X-RAY DIFFRACTIONf_angle_d1.1292787
X-RAY DIFFRACTIONf_dihedral_angle_d13.177743
X-RAY DIFFRACTIONf_chiral_restr0.048314
X-RAY DIFFRACTIONf_plane_restr0.006361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6594-1.68960.2087960.17062021X-RAY DIFFRACTION72
1.6896-1.72210.16361280.15882469X-RAY DIFFRACTION91
1.7221-1.75730.17081130.15062749X-RAY DIFFRACTION97
1.7573-1.79550.21021540.14392633X-RAY DIFFRACTION98
1.7955-1.83720.191500.13792700X-RAY DIFFRACTION98
1.8372-1.88320.18681290.14362689X-RAY DIFFRACTION98
1.8832-1.93410.20221490.14352708X-RAY DIFFRACTION98
1.9341-1.9910.17161380.14612675X-RAY DIFFRACTION98
1.991-2.05530.14981530.13622682X-RAY DIFFRACTION98
2.0553-2.12870.17891180.12752733X-RAY DIFFRACTION98
2.1287-2.2140.16271470.13852669X-RAY DIFFRACTION98
2.214-2.31470.13791400.13262691X-RAY DIFFRACTION98
2.3147-2.43670.17241510.13982681X-RAY DIFFRACTION98
2.4367-2.58940.16911590.15212670X-RAY DIFFRACTION98
2.5894-2.78920.16681580.1492668X-RAY DIFFRACTION98
2.7892-3.06980.17241620.14832682X-RAY DIFFRACTION97
3.0698-3.51380.16941500.13772655X-RAY DIFFRACTION97
3.5138-4.42590.16811370.13022675X-RAY DIFFRACTION97
4.4259-38.26250.14941410.15262672X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29320.3844-0.09721.29670.01080.05620.0539-0.588-0.06130.25460.02270.62740.2804-0.6850.00290.126-0.04840.01080.4030.10110.2936-14.109827.341919.8372
21.18930.21930.34641.7650.05520.7933-0.0029-0.0721-0.02490.02250.037-0.08730.0311-0.0005-0.03360.0503-0.0039-0.00180.06640.00360.05887.905233.036521.8764
30.9538-0.0218-0.58390.7499-0.47220.9601-0.01950.0817-0.0036-0.08460.0343-0.0026-0.0073-0.0309-0.0310.0979-0.0125-0.0160.09090.00780.07884.206137.93496.5889
40.22020.3882-0.52160.6745-0.92981.7329-0.02350.0124-0.0497-0.1391-0.047-0.09110.14660.15530.06140.13730.01380.01530.11610.00050.100413.1130.99273.1188
55.37390.685-2.17652.68261.98315.1547-0.06690.2652-0.1303-0.3984-0.0158-0.17370.49740.06840.05480.385-0.01140.08520.15440.00660.09713.740128.1344-9.1623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -16:17)
2X-RAY DIFFRACTION2(chain A and resid 18:123)
3X-RAY DIFFRACTION3(chain A and resid 124:164)
4X-RAY DIFFRACTION4(chain A and resid 165:249)
5X-RAY DIFFRACTION5(chain A and resid 250:267)

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