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- PDB-3h83: 2.06 Angstrom resolution structure of a hypoxanthine-guanine phos... -

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Basic information

Entry
Database: PDB / ID: 3h83
Title2.06 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor'
ComponentsHypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Hypoxanthine-Guanine Phosphoribosyltransferase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Glycosyltransferase / CSGID
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
sucrose / PHOSPHATE ION / Bifunctional protein tilS/hprT / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsHalavaty, A.S. / Shuvalova, L. / Minasov, G. / Dubrovska, I. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.06 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor'
Authors: Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Dubrovska, I. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Hypoxanthine phosphoribosyltransferase
D: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,87817
Polymers91,9014
Non-polymers1,97713
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15160 Å2
ΔGint-110 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.236, 80.549, 120.536
Angle α, β, γ (deg.)90.00, 101.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase


Mass: 22975.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: BAS0063, BA_0063, hpt-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VX6, UniProt: A0A6L7HDS1*PLUS
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: The Classic II Suite, condition B6, mixed with 1:1 v/v with protein sample (7.4 mg/mL, 0.25 M NaCl, 5 mM BME, 10 mM Tris/HCl pH 8.3), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 61007 / Num. obs: 61007 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.85
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0051refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFZ

1yfz


Resolution: 2.06→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.317 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20753 3105 5.1 %RANDOM
Rwork0.16841 ---
obs0.1704 57870 96.74 %-
all-57870 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.931 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-0.09 Å2
2--1.45 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 119 510 6524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226346
X-RAY DIFFRACTIONr_bond_other_d0.0010.024210
X-RAY DIFFRACTIONr_angle_refined_deg1.7672.0118625
X-RAY DIFFRACTIONr_angle_other_deg0.987310409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9595783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54525.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.257151167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9791520
X-RAY DIFFRACTIONr_chiral_restr0.1850.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216860
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021168
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4771.53844
X-RAY DIFFRACTIONr_mcbond_other0.4671.51561
X-RAY DIFFRACTIONr_mcangle_it2.6526275
X-RAY DIFFRACTIONr_scbond_it4.09732502
X-RAY DIFFRACTIONr_scangle_it6.344.52350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 219 -
Rwork0.184 4268 -
obs--96.81 %
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)
10.0731-0.03080.00490.10120.01910.1046-0.0018-0.0006-0.0024-0.00320.0065-0.0053-0.02270.0011-0.00470.0059-0.000300.0005-0.00030.001742.92749.910147.003
20.1148-0.0369-0.0210.0729-0.04660.1334-0.00020.0008-0.0083-0.0070.00550.0090.0238-0.0008-0.00530.0065-0.0003-0.00420.00090.00140.006539.4489-10.481147.3982
30.1613-0.0082-0.03260.12910.01080.1449-0.00740.0246-0.0064-0.0072-0.0014-0.00420.01310.02730.00870.00190.00170.00120.01130.00080.000950.3909-4.948210.6438
40.16750.00080.0180.11760.01220.158-0.00710.02140.0053-0.0076-0.00210.0087-0.0159-0.03120.00910.00370.0008-0.00240.0114-0.00030.001730.78025.41210.8322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-23 - 179
2X-RAY DIFFRACTION2B-8 - 179
3X-RAY DIFFRACTION3C0 - 179
4X-RAY DIFFRACTION4D0 - 179

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