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Basic information

Entry
Database: PDB / ID: 5knp
TitleCrystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(Hypoxanthin-9-yl)pyrrolidin-3-yl)-oxymethanephosphonic acid
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/INHIBITOR / inhibitor / complex / phosphoribosyltransferase / nucleoside phosphonates / 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-6W7 / PYROPHOSPHATE 2- / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.1Sep 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_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)94,03820
Polymers91,8794
Non-polymers2,15916
Water2,954164
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)47,01910
Polymers45,9402
Non-polymers1,0808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-44 kcal/mol
Surface area15090 Å2
MethodPISA
3
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,01910
Polymers45,9402
Non-polymers1,0808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-45 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.264, 85.678, 154.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-6W7 / [(3~{S},4~{R})-4-(6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid / [3S,4R]-(4-(Hypoxanthin-9-yl)pyrrolidin-3-yl)-oxymethanephosphonic acid


Mass: 315.222 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O5P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: The well solution: 20% PEG8000, 0.1 M Tris-HCl pH 8.5 and 0.2 M MgCl2. The drop consisted of an equal volume of well solution and protein inhibitor complex

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→46.44 Å / Num. obs: 27104 / % possible obs: 97.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHT

4rht


Resolution: 2.45→46.44 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.31
RfactorNum. reflection% reflection
Rfree0.2979 1997 7.38 %
Rwork0.23 --
obs0.235 27051 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.31 Å2 / Biso mean: 45.4514 Å2 / Biso min: 4.52 Å2
Refinement stepCycle: final / Resolution: 2.45→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 164 164 5838
Biso mean--51.2 34.64 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055838
X-RAY DIFFRACTIONf_angle_d0.5587914
X-RAY DIFFRACTIONf_chiral_restr0.022926
X-RAY DIFFRACTIONf_plane_restr0.002993
X-RAY DIFFRACTIONf_dihedral_angle_d13.082078
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4459-2.50710.36551400.30711772191298
2.5071-2.57490.33741420.30851773191598
2.5749-2.65060.35271430.30961788193198
2.6506-2.73620.36391420.31161779192198
2.7362-2.8340.36181420.31481789193198
2.834-2.94740.33361420.29351781192398
2.9474-3.08150.35111440.27671802194698
3.0815-3.2440.3471410.25741770191198
3.244-3.44720.28111430.23111779192297
3.4472-3.71320.31681410.2281780192197
3.7132-4.08670.28321430.19581792193597
4.0867-4.67760.23941430.16851790193396
4.6776-5.89130.2351430.18081804194795
5.8913-46.44950.27751480.19071855200393
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)
18.0741-0.1424-0.86781.907-0.0162.6632-0.32441.08940.354-0.46880.2026-0.052-0.2490.05110.12320.4514-0.0392-0.02480.42780.00510.162-29.254910.8926-39.9248
21.161-1.67740.9544.638-4.6125.54980.70661.1879-0.6263-0.9935-0.5787-0.58591.05652.6886-0.24570.44140.05740.03271.1504-0.3970.8882-3.60437.2786-31.1812
33.68580.2233-0.44413.40070.92341.6641-0.0941-0.22940.11340.20670.2193-0.16720.02710.0882-0.11980.34120.0146-0.03840.2769-0.00020.189-19.31229.1762-22.835
47.58590.1861-0.8736.3924-0.1411.72070.2147-0.02980.26890.0511-0.03070.2573-0.5986-0.2043-0.15060.3286-0.00740.01310.23650.05870.1991-33.543915.1917-31.0743
55.5824-1.0245-2.29893.0116-0.09843.32620.07710.3773-0.187-0.4675-0.15010.13560.1118-0.00260.08270.3926-0.0034-0.0160.1516-0.05950.2037-22.9718-10.6662-40.2023
66.04541.97844.59017.06973.30228.6530.046-0.0780.8096-0.37620.00970.87690.3533-0.7846-0.05470.4145-0.0757-0.01570.30160.13750.3455-38.123-6.3243-27.5969
72.9134-0.138-0.13161.297-0.69186.320.1791-0.2586-0.09770.22730.020.22990.4721-0.1222-0.18920.2899-0.0160.05520.18740.00350.2737-31.742-5.2049-22.5055
83.7527-5.5448-2.61178.38185.09529.0879-0.5315-0.34240.0670.49030.4282-0.37890.90870.23320.03190.388-0.0886-0.00880.34860.02960.3603-30.6346-14.7275-20.9136
97.9339-1.8626-3.1764.36833.79314.469-0.2362-0.144-0.82820.59910.15460.43920.5634-0.01190.07860.394-0.0002-0.00660.19420.03350.3555-31.5148-19.3651-27.4796
105.35144.64592.82956.28922.15957.6391-0.0905-0.2905-0.58150.2887-0.0754-0.41670.24470.45790.17840.2240.10740.01540.389-0.06290.3387-14.9788-12.3752-31.474
114.13680.9535-3.01262.90710.25035.27070.01480.2307-0.36280.02950.2665-1.26980.91150.517-0.24310.30510.0593-0.10550.2741-0.16470.4177-10.4194-9.7204-34.5042
126.3678-5.0043-1.34677.88921.6915.1457-0.3517-1.137-0.29630.89350.43370.64720.020.02830.06360.4208-0.10680.13420.52370.00130.3424-36.0325-3.108719.9359
132.4729-0.29340.88292.6681-0.37097.9325-0.167-0.051-0.31440.1516-0.0495-0.43230.031-0.0711-0.06740.2399-0.01440.06280.30340.00370.4005-27.967-8.27455.3221
141.8455-0.7596-0.93224.78770.98343.84550.0494-0.0126-0.2870.1067-0.2590.24020.3823-0.32130.22640.2957-0.0335-0.00080.34390.03670.3303-36.9361-9.38145.5913
150.8046-0.4805-2.12889.65874.45246.74040.55820.33860.5334-0.05210.04440.8669-0.1487-0.7138-0.54520.32850.14340.06650.5070.13110.5351-42.58869.661813.414
164.5112-2.00150.66428.1436-1.93395.3337-0.1719-0.83420.00381.4682-0.0716-0.1664-0.5650.49980.21510.5159-0.07950.03320.5054-0.01530.2836-17.13576.615418.8591
173.3685-1.1812-3.21274.76712.0558.52270.1124-0.060.06730.081-0.18790.0529-0.10670.23670.07190.2335-0.0519-0.02890.30280.03790.2318-23.7548.20563.2438
184.253-0.99210.82576.2008-0.66429.37910.198-0.1060.0842-0.3082-0.2094-0.2109-0.13890.56780.07160.294-0.08510.01070.24990.04750.3596-13.791912.31153.7877
193.41970.38450.30646.64512.80412.7243-0.3279-0.029-0.041-0.06570.4116-0.86210.1820.6579-0.02370.26530.0174-0.01640.46960.13850.4671-8.519-1.454211.6026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 47 )A17 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 58 )A48 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 151 )A59 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 200 )A152 - 200
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 47 )B18 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 68 )B48 - 68
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 116 )B69 - 116
8X-RAY DIFFRACTION8chain 'B' and (resid 117 through 141 )B117 - 141
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 167 )B142 - 167
10X-RAY DIFFRACTION10chain 'B' and (resid 168 through 187 )B168 - 187
11X-RAY DIFFRACTION11chain 'B' and (resid 188 through 201 )B188 - 201
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 48 )C17 - 48
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 107 )C49 - 107
14X-RAY DIFFRACTION14chain 'C' and (resid 108 through 186 )C108 - 186
15X-RAY DIFFRACTION15chain 'C' and (resid 187 through 202 )C187 - 202
16X-RAY DIFFRACTION16chain 'D' and (resid 17 through 55 )D17 - 55
17X-RAY DIFFRACTION17chain 'D' and (resid 56 through 116 )D56 - 116
18X-RAY DIFFRACTION18chain 'D' and (resid 117 through 157 )D117 - 157
19X-RAY DIFFRACTION19chain 'D' and (resid 158 through 202 )D158 - 202

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