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

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Basic information

Entry
Database: PDB / ID: 5djh
TitleStructure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 3Mg 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: 1.451 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)31,2626
Polymers30,7471
Non-polymers5155
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-40 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.636, 58.140, 101.198
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.: 3 / 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.: 269 / 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: 36.73 %
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: 1.451→38.168 Å / Num. all: 42861 / Num. obs: 42861 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.53 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.87
Reflection shellResolution: 1.451→1.49 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.47 / % possible all: 99.2

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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: 1.451→38.168 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 15.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 2111 4.93 %Random selection
Rwork0.1487 ---
obs0.1497 42861 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→38.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 31 269 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062042
X-RAY DIFFRACTIONf_angle_d1.1732804
X-RAY DIFFRACTIONf_dihedral_angle_d11.75747
X-RAY DIFFRACTIONf_chiral_restr0.079318
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4513-1.4690.25861260.23892623X-RAY DIFFRACTION96
1.469-1.48760.26051430.22442686X-RAY DIFFRACTION97
1.4876-1.50720.24081330.21432751X-RAY DIFFRACTION97
1.5072-1.52790.23981290.18852673X-RAY DIFFRACTION97
1.5279-1.54970.22471320.19292704X-RAY DIFFRACTION97
1.5497-1.57280.21521430.17812720X-RAY DIFFRACTION97
1.5728-1.59740.22161340.1762676X-RAY DIFFRACTION97
1.5974-1.62360.18751540.16142770X-RAY DIFFRACTION98
1.6236-1.65160.23851510.16612672X-RAY DIFFRACTION98
1.6516-1.68160.16531100.1552716X-RAY DIFFRACTION97
1.6816-1.7140.18631220.15632766X-RAY DIFFRACTION98
1.714-1.74890.15861110.15412731X-RAY DIFFRACTION98
1.7489-1.7870.18261400.14942721X-RAY DIFFRACTION98
1.787-1.82850.17841520.1492689X-RAY DIFFRACTION98
1.8285-1.87430.15491290.14812798X-RAY DIFFRACTION98
1.8743-1.92490.15721500.14752698X-RAY DIFFRACTION98
1.9249-1.98160.14781390.14532706X-RAY DIFFRACTION98
1.9816-2.04550.1581550.1462718X-RAY DIFFRACTION98
2.0455-2.11860.16391210.13372739X-RAY DIFFRACTION98
2.1186-2.20350.16251450.14022748X-RAY DIFFRACTION98
2.2035-2.30370.14221440.1432702X-RAY DIFFRACTION98
2.3037-2.42520.1771520.1432724X-RAY DIFFRACTION97
2.4252-2.57710.181540.1542684X-RAY DIFFRACTION98
2.5771-2.7760.16791620.15152680X-RAY DIFFRACTION97
2.776-3.05530.1641700.14612655X-RAY DIFFRACTION97
3.0553-3.49710.14961510.13882668X-RAY DIFFRACTION96
3.4971-4.4050.14671340.11772700X-RAY DIFFRACTION97
4.405-38.18170.15481430.14662637X-RAY DIFFRACTION95
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)
10.4720.3515-0.11560.5712-0.12720.03320.0938-0.5736-0.02730.24730.05960.52270.1773-0.59670.01830.1461-0.06060.02210.39560.09880.2789-14.147128.175919.8449
21.1090.28180.33561.89660.06860.76650.004-0.0767-0.01930.03990.0378-0.07380.0349-0.0227-0.04750.0654-0.0053-0.0010.08250.00210.06697.922633.053621.5984
31.60840.2234-0.80910.9617-0.59630.966-0.03520.14450.006-0.08480.05830.00270.0233-0.111-0.04430.1071-0.0135-0.02070.11130.01230.08274.253937.84225.986
40.21410.3077-0.40540.62-0.61521.4682-0.01050.0235-0.0465-0.1371-0.0354-0.06280.13240.09240.03930.13670.00940.01360.1105-0.00060.107212.954230.99823.1375
58.2874-1.1707-3.89993.95742.95955.2623-0.14060.0834-0.0953-0.37980.0539-0.0980.41160.09940.07080.3616-0.00780.0570.16630.00660.115613.64728.4347-9.2652
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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