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- PDB-3o7m: 1.98 Angstrom resolution crystal structure of a hypoxanthine-guan... -

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Entry
Database: PDB / ID: 3o7m
Title1.98 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor'
ComponentsHypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Hypoxanthine-Guanine Phosphoribosyltransferase / Salvage of nucleosides and nucleotides / Structural Genomics / 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
BETA-MERCAPTOETHANOL / Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHalavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.98 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor'
Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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 phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
C: Hypoxanthine phosphoribosyltransferase
D: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,87019
Polymers84,5094
Non-polymers1,36115
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-157 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.499, 122.499, 119.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase


Mass: 21127.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4712, BA_5074, GBAA5074, GBAA_5074, hpt-2, hpt2 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic
References: UniProt: Q81KC7, UniProt: A0A6L8PVA4*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein at 7.4 mg/mL in 10 mM Tris/HCl, pH 8.3, 500 mM NaCl, 5 mM BME. Crystals grew from 2 M AmSO4 0.1 M bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2010 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. all: 63787 / Num. obs: 63787 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.29
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 5.15 / Num. unique all: 3146 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H83

3h83


Resolution: 1.98→29.92 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.612 / SU ML: 0.061 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20595 3231 5.1 %RANDOM
Rwork0.16723 ---
obs0.16918 60480 99.95 %-
all-60480 --
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: 33.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å2-0 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.98→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5330 0 73 558 5961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225681
X-RAY DIFFRACTIONr_bond_other_d0.0010.023848
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9837684
X-RAY DIFFRACTIONr_angle_other_deg0.81239488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7835702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51225.409257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.135151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.621520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
X-RAY DIFFRACTIONr_mcbond_it0.8841.53434
X-RAY DIFFRACTIONr_mcbond_other0.2481.51386
X-RAY DIFFRACTIONr_mcangle_it1.63425625
X-RAY DIFFRACTIONr_scbond_it2.64632247
X-RAY DIFFRACTIONr_scangle_it4.3914.52059
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 210 -
Rwork0.179 4390 -
obs-4390 99.46 %
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)
12.4977-1.2498-1.76721.87991.73043.014-0.0834-0.013-0.28110.0904-0.04510.19030.2140.04620.12850.059-0.00120.00490.02660.01440.068211.703168.10568.6065
21.26850.3542-0.06252.16410.46961.10020.0606-0.0220.0666-0.02210.0529-0.1977-0.14850.0722-0.11350.0455-0.02080.02850.0117-0.01410.042515.398883.942267.2992
30.7177-0.1978-0.10441.09530.48051.07020.02170.00320.0140.09750.0445-0.14810.01860.2727-0.06620.0505-0.0102-0.00310.08170.00490.080823.23574.752669.4239
43.35291.0257-0.91885.6089-0.80844.51210.0521-0.1287-0.22320.1714-0.15310.22570.3506-0.04240.1010.1590.08960.00810.1021-0.01410.0689-25.490259.14522.024
51.4292-0.82240.37132.7911-0.30591.4580.00920.03930.0272-0.2436-0.03880.02470.0320.24070.02960.09460.05910.00540.08270.00460.0443-24.766576.314521.3628
60.979-0.7080.21661.9861-0.07531.42560.12440.07250.0142-0.2956-0.16380.30940.0254-0.04680.03930.11450.0884-0.01850.0828-0.01520.1008-32.953773.747217.666
74.98321.5872-0.77622.6723-0.26822.72570.0665-0.2851-0.56440.2362-0.0032-0.22080.22590.1329-0.06330.14870.0977-0.02890.15460.06550.1025-18.623366.296241.8856
83.1323-1.60920.27092.53180.36271.7736-0.0403-0.31550.11730.01790.00430.04080.1298-0.14820.0360.04980.04980.01220.12380.00620.0321-32.001975.59538.8185
92.4156-0.17640.06290.58470.49451.8112-0.0429-0.35820.18780.08390.0369-0.0874-0.26440.07210.0060.16390.0921-0.0170.20550.00520.1056-21.901479.153544.396
103.9689-1.5272-2.77691.87751.09293.2519-0.02920.1099-0.2422-0.0658-0.02530.13-0.0429-0.17670.05460.0549-0.009-0.02660.0479-0.00170.05152.936474.620648.8338
112.11470.7024-0.27041.5842-0.30860.530.00250.08660.2669-0.00690.06190.0343-0.06820.0767-0.06440.0458-0.02070.01040.0253-0.00050.042216.105983.48150.2949
121.52830.1319-0.66590.7626-0.09861.6140.04140.17870.1995-0.08110.03860.1396-0.415-0.1549-0.080.15440.0073-0.02870.04890.02270.09365.297687.816648.0048
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 34
2X-RAY DIFFRACTION2A35 - 99
3X-RAY DIFFRACTION3A100 - 174
4X-RAY DIFFRACTION4B3 - 25
5X-RAY DIFFRACTION5B26 - 74
6X-RAY DIFFRACTION6B75 - 173
7X-RAY DIFFRACTION7C3 - 34
8X-RAY DIFFRACTION8C35 - 97
9X-RAY DIFFRACTION9C98 - 173
10X-RAY DIFFRACTION10D2 - 34
11X-RAY DIFFRACTION11D35 - 99
12X-RAY DIFFRACTION12D100 - 173

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