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- PDB-5djk: Structure of M. tuberculosis CysQ, a PAP phosphatase with PO4 and... -

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Basic information

Entry
Database: PDB / ID: 5djk
TitleStructure of M. tuberculosis CysQ, a PAP phosphatase with PO4 and 2Ca bound
Components3'-phosphoadenosine 5'-phosphate phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CysQ / PAP phosphatase / calcium / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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
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: 1.799 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,9455
Polymers30,7471
Non-polymers1984
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-38 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.257, 58.225, 101.415
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 219 / 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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M calcium chloride, 0.1 M Bis-Tris-HCl, 30% 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: Mar 27, 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: 1.799→31.529 Å / Num. all: 22686 / Num. obs: 22686 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.54 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.89
Reflection shellResolution: 1.799→1.838 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.87 / % possible all: 96.9

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Processing

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

5djf


Resolution: 1.799→31.529 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 1168 5.14 %Random selection
Rwork0.1551 ---
obs0.1569 22686 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→31.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 8 219 2121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071958
X-RAY DIFFRACTIONf_angle_d1.0652678
X-RAY DIFFRACTIONf_dihedral_angle_d12.325713
X-RAY DIFFRACTIONf_chiral_restr0.043303
X-RAY DIFFRACTIONf_plane_restr0.004353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7994-1.83850.22611270.23152472X-RAY DIFFRACTION96
1.8385-1.88130.24461290.21862500X-RAY DIFFRACTION99
1.8813-1.92840.2351420.19882490X-RAY DIFFRACTION99
1.9284-1.98050.23161270.17842534X-RAY DIFFRACTION100
1.9805-2.03880.18171310.16462485X-RAY DIFFRACTION99
2.0388-2.10450.1821210.16382554X-RAY DIFFRACTION99
2.1045-2.17970.23711220.15732518X-RAY DIFFRACTION99
2.1797-2.2670.15651420.15152516X-RAY DIFFRACTION99
2.267-2.37010.21161550.14932533X-RAY DIFFRACTION99
2.3701-2.4950.18721170.15592501X-RAY DIFFRACTION99
2.495-2.65130.20941640.16392495X-RAY DIFFRACTION99
2.6513-2.85590.17851510.15232510X-RAY DIFFRACTION99
2.8559-3.1430.18911560.15352465X-RAY DIFFRACTION99
3.143-3.59730.1921180.13622536X-RAY DIFFRACTION99
3.5973-4.53010.15811450.12572506X-RAY DIFFRACTION99
4.5301-31.53380.17221290.15742528X-RAY DIFFRACTION100
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)
10.027-0.01220.1210.04670.01860.7352-0.0908-0.0865-0.21260.0612-0.11870.4027-0.0406-0.3838-0.02180.1043-0.0201-0.00180.21950.0320.203-9.583829.797318.9735
20.64360.10910.22631.02990.17140.3406-0.0267-0.0723-0.0460.02250.0569-0.11710.02350.01610.00190.0733-0.0044-0.00230.096-0.00070.10277.954233.241821.9
30.4767-0.2990.11620.2611-0.0910.28030.04570.12530.03-0.14630.001-0.0144-0.0971-0.11080.05460.1424-0.00980.00180.11830.00990.08974.073338.81764.6503
40.21830.4158-0.54830.3306-0.53330.767-0.03-0.0053-0.0333-0.1486-0.0529-0.10610.06030.0925-0.01270.16160.00760.03820.12040.00670.112313.108630.91522.7828
50.46010.0507-0.65310.1292-0.17541.016-0.15880.3098-0.0979-0.28290.1442-0.06480.16-0.29210.18650.556-0.12290.22140.2569-0.09560.036713.081728.4257-9.3481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 12:17)
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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