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- PDB-6d9s: The (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosph... -

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Basic information

Entry
Database: PDB / ID: 6d9s
TitleThe (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase)
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / HPRT / hypoxanthine phosphoribosyltransferase
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / DI(HYDROXYETHYL)ETHER / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsSatyshur, K.A. / Dubiel, K. / Anderson, B. / Wolak, C. / Keck, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM084003 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM07215 United States
National Science Foundation (NSF, United States)DGE-1256259 United States
CitationJournal: Elife / Year: 2019
Title: Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction.
Authors: Anderson, B.W. / Liu, K. / Wolak, C. / Dubiel, K. / She, F. / Satyshur, K.A. / Keck, J.L. / Wang, J.D.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,89912
Polymers41,0072
Non-polymers1,89210
Water2,126118
1
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,79824
Polymers82,0154
Non-polymers3,78320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area17310 Å2
ΔGint-76 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.611, 82.611, 174.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypoxanthine phosphoribosyltransferase / HPRT


Mass: 20503.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: hpt, hprT, hpt1, tilS, BA_0063, A9486_05730, ABW01_27435, BASH2_00187, BVG01_28865, CN272_24955, CN488_12230, CN504_22375, COE56_22980, COJ30_24475, COK92_19380, COL95_25280, MCCC1A01412_27610
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A1S0QLD4, UniProt: B9ZW32*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2 M ammonium tartrate dibasic, pH 6.6, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 40594 / % possible obs: 99.6 % / Redundancy: 8.1 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.164 / Χ2: 2.289 / Net I/σ(I): 16.41
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 3928 / CC1/2: 0.724 / Rpim(I) all: 0.489 / Χ2: 0.982 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H83

3h83


Resolution: 2.105→40.2 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.49
RfactorNum. reflection% reflection
Rfree0.2439 1986 4.91 %
Rwork0.2017 --
obs0.2037 40414 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.105→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 116 118 3058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032995
X-RAY DIFFRACTIONf_angle_d0.8124053
X-RAY DIFFRACTIONf_dihedral_angle_d14.2721814
X-RAY DIFFRACTIONf_chiral_restr0.048472
X-RAY DIFFRACTIONf_plane_restr0.003488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1054-2.15810.3391310.3392520X-RAY DIFFRACTION93
2.1581-2.21640.37511360.32392704X-RAY DIFFRACTION99
2.2164-2.28160.34251410.29662715X-RAY DIFFRACTION99
2.2816-2.35530.3021440.28922743X-RAY DIFFRACTION99
2.3553-2.43940.32981400.27682703X-RAY DIFFRACTION100
2.4394-2.53710.2721430.25782734X-RAY DIFFRACTION100
2.5371-2.65250.27711400.25032742X-RAY DIFFRACTION100
2.6525-2.79230.31231430.26152738X-RAY DIFFRACTION100
2.7923-2.96720.34871420.27042769X-RAY DIFFRACTION100
2.9672-3.19630.32771400.25282766X-RAY DIFFRACTION100
3.1963-3.51770.29091440.21952768X-RAY DIFFRACTION100
3.5177-4.02640.24561460.17962797X-RAY DIFFRACTION100
4.0264-5.07120.17121430.13832788X-RAY DIFFRACTION98
5.0712-40.20720.20031530.17622941X-RAY DIFFRACTION99
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)
12.2972-0.05061.02872.79392.58572.9783-0.4114-0.4937-0.0730.44910.2882-0.5432-0.19711.0021-0.10830.8330.062-0.12270.6872-0.06880.652672.9158-21.270530.896
26.34875.64091.87465.43760.752.4360.30110.01940.29341.4821-0.37360.549-0.357-0.52270.21180.81330.22010.05730.6351-0.01980.542555.4947-28.847432.8526
32.4563-2.992-2.6139.70845.85623.9474-0.0115-0.072-0.06870.44040.28140.36480.0936-0.89020.00510.63120.12830.0690.7767-0.04780.584143.1085-35.880724.3205
43.50841.1956-2.25920.3702-0.3576.06240.04090.19270.170.22680.0172-0.0904-0.29660.0224-0.13390.51080.2246-0.00720.54740.0180.54257.1964-32.414916.4492
54.69914.5475-5.86974.4729-5.94968.13240.32620.3548-0.06060.5347-0.01020.2961-0.655-0.3311-0.01850.5210.1716-0.05440.7438-0.01380.513152.7409-30.29855.5886
60.44870.63580.27791.5607-0.40482.9432-0.02210.24990.25120.25710.26990.2264-0.759-0.4459-0.29550.62960.30980.01130.7418-0.0390.616251.6497-24.411711.1388
75.89625.07983.01947.44664.82665.5759-0.364-0.11420.7182-0.48860.10580.6717-1.1486-0.68830.11280.75220.33390.030.61880.00220.509750.2136-20.437517.0497
87.893-0.2642-1.22642.03971.00312.1808-0.00540.20950.5795-0.02210.1314-0.0875-0.66140.0175-0.08860.70220.1509-0.01160.50010.00580.475867.4015-19.799322.9113
97.717-3.02354.55735.1524-4.62834.6480.25730.6803-0.7226-0.86080.14450.32261.1616-0.0301-0.36220.64470.0159-0.02220.8694-0.15450.729653.3328-50.3784-30.4139
105.4320.7530.2557.53665.94284.6744-0.0260.4954-0.1711-0.8903-0.55660.6405-0.6756-0.71110.64910.57480.1417-0.06240.82070.10340.552550.7992-26.9516-29.7259
112.17421.7495-1.35872.082-0.37554.8864-0.15310.1336-0.0568-0.0204-0.1109-0.09-0.2843-0.23910.2820.41670.151-0.04360.7275-0.02990.524357.0524-27.5151-18.0732
128.6428-5.42564.14396.6326-3.20182.0992-0.987-0.1893-1.23560.41191.30660.76770.4647-4.1668-0.55120.83-0.07570.17041.78930.10730.705144.2756-41.3643-0.3669
132.29980.19590.9292.3294-1.21885.1468-0.08260.05940.13490.20260.17930.2166-0.3258-0.8297-0.05950.40140.18810.02170.7557-0.04530.480850.4634-29.7194-8.269
143.2829-0.59911.03147.46544.75698.73580.02080.35170.0954-0.1773-0.34980.7673-0.5415-1.36020.33950.40490.21120.05590.93350.04410.462444.864-28.6618-13.3877
153.86783.5038-0.19234.364-2.6835.2049-0.2651-0.21110.18680.31810.37740.107-0.655-1.55890.00410.34050.20110.0031.21420.02360.581840.6296-33.2312-19.6496
168.62951.98754.50376.1052-1.02853.28860.17030.0594-0.52450.07010.45480.18260.6253-0.6256-0.57950.47630.00190.03540.75770.05630.531851.8808-49.3384-22.1644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:14)
2X-RAY DIFFRACTION2(chain A and resid 15:25)
3X-RAY DIFFRACTION3(chain A and resid 26:36)
4X-RAY DIFFRACTION4(chain A and resid 37:74)
5X-RAY DIFFRACTION5(chain A and resid 75:94)
6X-RAY DIFFRACTION6(chain A and resid 95:118)
7X-RAY DIFFRACTION7(chain A and resid 119:140)
8X-RAY DIFFRACTION8(chain A and resid 141:179)
9X-RAY DIFFRACTION9(chain B and resid 0:13)
10X-RAY DIFFRACTION10(chain B and resid 14:31)
11X-RAY DIFFRACTION11(chain B and resid 32:69)
12X-RAY DIFFRACTION12(chain B and resid 70:77)
13X-RAY DIFFRACTION13(chain B and resid 78:115)
14X-RAY DIFFRACTION14(chain B and resid 116:135)
15X-RAY DIFFRACTION15(chain B and resid 136:149)
16X-RAY DIFFRACTION16(chain B and resid 150:179)

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