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- PDB-4qri: 2.35 Angstrom resolution crystal structure of hypoxanthine-guanin... -

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Basic information

Entry
Database: PDB / ID: 4qri
Title2.35 Angstrom resolution crystal structure of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
ComponentsHypoxanthine-guanine-xanthine phosphoribosyltransferase
KeywordsTRANSFERASE / hypoxanthine-guanine-xanthine phosphoribosyltransferase / Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / Glycosyltransferase / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / purine salvage pathway
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
DI(HYDROXYETHYL)ETHER / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Flores, K.J. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.35 Angstrom resolution crystal structure of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Flores, K.J. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
B: Hypoxanthine-guanine-xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,98013
Polymers47,8932
Non-polymers1,08711
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-109 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.647, 74.647, 162.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 6 - 176 / Label seq-ID: 30 - 200

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hypoxanthine-guanine-xanthine phosphoribosyltransferase


Mass: 23946.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Fiocruz L1-130 / Gene: hpt, LA_4295, LIC_13438 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q72LV5, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein: 7.4 mg/mL in 0.25 M NaCl 10 mM Tris-HCl pH 8.3 5 mM BME crystallization: The JCSG+ Suite H9 (93): 0.2 M LiSO4 0.1 BIS-TRIS 25% (w/v), VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2014 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 19969 / Num. obs: 19969 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.7
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 3.4 / Num. unique all: 958 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3O7M

3o7m


Resolution: 2.35→29.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.743 / SU ML: 0.136 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23235 1011 5.1 %RANDOM
Rwork0.18827 ---
obs0.19044 18828 99.86 %-
all-18828 --
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: 48.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 61 136 2772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192725
X-RAY DIFFRACTIONr_bond_other_d0.0040.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9963691
X-RAY DIFFRACTIONr_angle_other_deg0.93936089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2945316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58123.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26115479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9121519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212943
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02612
Refine LS restraints NCS

Ens-ID: 1 / Number: 9819 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 87 -
Rwork0.268 1325 -
obs-1325 100 %
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)
11.93190.36110.17671.6314-0.62282.04650.0278-0.0136-0.0035-0.0384-0.0315-0.10940.05820.27960.00380.19570.02280.03870.0439-0.01080.133833.064-13.439716.1885
22.5814-0.41120.30771.2558-0.27152.29260.01280.3083-0.0126-0.2312-0.1017-0.08330.27860.21620.08890.30340.01450.06030.06530.00510.169331.0982-18.18289.6862
32.4626-1.0460.46541.6599-0.11332.22940.020.2092-0.0621-0.1167-0.05570.1027-0.23870.23530.03570.2471-0.04280.01650.0473-0.0010.13630.79025.474713.2939
43.8452-1.54320.83432.7434-0.60942.1617-0.00710.04360.20090.2017-0.1118-0.2038-0.30210.36050.11890.3434-0.08420.01070.22460.02840.188741.42655.864823.1817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 85
2X-RAY DIFFRACTION2A86 - 176
3X-RAY DIFFRACTION3B6 - 131
4X-RAY DIFFRACTION4B132 - 177

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