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- PDB-5kny: Crystal structure of Mycobacterium tuberculosis hypoxanthine guan... -

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Basic information

Entry
Database: PDB / ID: 5kny
TitleCrystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with (3-((3R,4R)-3-(Guanin-9-yl)-4-((S)-2-hydroxy-2-phosphonoethoxy)pyrrolidin-1-yl)-3-oxopropyl)phosphonic acid
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / Phosphoribosyltransferase / Inhibitor / Complex / pyrrolidne nucleoside phosphonate / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / GMP biosynthetic process ...IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / GMP biosynthetic process / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-YPG / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.91 Å
AuthorsEng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W.
CitationJournal: To Be Published
Title: Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate
Authors: Eng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,96212
Polymers91,8794
Non-polymers2,0828
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9816
Polymers45,9402
Non-polymers1,0414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-28 kcal/mol
Surface area15630 Å2
MethodPISA
3
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9816
Polymers45,9402
Non-polymers1,0414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-26 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.523, 86.075, 79.824
Angle α, β, γ (deg.)90.000, 105.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0
411chain D and segidD0

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase


Mass: 22969.801 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: hpt, hprT, Rv3624c, MTCY15C10.28 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WHQ9, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-YPG / [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid / [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine


Mass: 496.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N6O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Li2SO4, 0.1 M Sodium acetate pH 4.5 and 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.91→44.77 Å / Num. obs: 15646 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 7.8
Reflection shellResolution: 2.91→3.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.91→44.77 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.22
RfactorNum. reflection% reflection
Rfree0.2624 1555 9.95 %
Rwork0.2008 --
obs0.2069 15623 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.95 Å2 / Biso mean: 53.2634 Å2 / Biso min: 12.65 Å2
Refinement stepCycle: final / Resolution: 2.91→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 164 29 5687
Biso mean--49.84 34.77 -
Num. residues----729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055782
X-RAY DIFFRACTIONf_angle_d0.8717903
X-RAY DIFFRACTIONf_chiral_restr0.035948
X-RAY DIFFRACTIONf_plane_restr0.004989
X-RAY DIFFRACTIONf_dihedral_angle_d11.0822004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3180X-RAY DIFFRACTION14.193TORSIONAL
12B3180X-RAY DIFFRACTION14.193TORSIONAL
13C3180X-RAY DIFFRACTION14.193TORSIONAL
14D3180X-RAY DIFFRACTION14.193TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.912-3.00590.351420.26661281142399
3.0059-3.11340.3391260.26812451371100
3.1134-3.2380.30061520.273912851437100
3.238-3.38530.27271470.228312681415100
3.3853-3.56370.29061360.213912591395100
3.5637-3.78690.27871450.20712841429100
3.7869-4.07910.23381370.194712721409100
4.0791-4.48920.25351360.171112971433100
4.4892-5.1380.22961510.151212671418100
5.138-6.47020.23051450.19612931438100
6.4702-44.77850.24311380.181317145599
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)
11.74730.4093-0.93213.1011-0.20232.1554-0.12330.2198-0.25460.14150.1869-0.04560.2137-0.12-0.06770.24450.02590.04790.0970.00050.355469.402275.412428.3507
22.7341-0.17921.22783.43340.93993.1217-0.0560.07680.09930.19480.091-0.0972-0.3335-0.007-0.02290.27840.00170.05340.09510.03730.333267.971197.941527.9286
31.11470.01171.1513.94610.63194.1413-0.23020.51920.1835-0.130.01280.2985-0.2134-0.11570.1680.2-0.10680.01840.43040.020.417959.293792.5608-8.052
41.4334-0.1581-1.09662.0206-0.12143.16280.02050.6476-0.0111-0.0921-0.1201-0.51960.18220.65860.08540.162-0.08260.05550.60930.09130.591677.754179.5545-7.4821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 17 through 201)A17 - 201
2X-RAY DIFFRACTION2(chain 'B' and resid 16 through 202)B16 - 202
3X-RAY DIFFRACTION3(chain 'C' and resid 18 through 200)C18 - 200
4X-RAY DIFFRACTION4(chain 'D' and resid 18 through 200)D18 - 200

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