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- PDB-3hvu: 1.95 Angstrom Crystal Structure of Complex of Hypoxanthine-Guanin... -

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Basic information

Entry
Database: PDB / ID: 3hvu
Title1.95 Angstrom Crystal Structure of Complex of Hypoxanthine-Guanine Phosphoribosyltransferase from Bacillus anthracis with 2-(N-morpholino)ethanesulfonic acid (MES)
ComponentsHypoxanthine phosphoribosyltransferaseHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE / Hypoxanthine-guanine Phosphoribosyltransferase / 2-(N-morpholino)ethanesulfonic acid (MES) / idp01892 / Glycosyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / 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
Hypoxanthine phosphoribosyltransferase / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.95 Angstrom Crystal Structure of Complex of Hypoxanthine-Guanine Phosphoribosyltransferase from Bacillus anthracis with 2-(N-morpholino)ethanesulfonic acid (MES)
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 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 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_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_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)92,77412
Polymers91,9014
Non-polymers8738
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-69.1 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.713, 93.377, 94.900
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine 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: B9ZW32*PLUS
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: protein: 7mg/mL, 0.25M NaCl, 0.01M Tris-HCl pH 8.3; screen: PACT D3, 0.1M MMT buffer pH 6.0, 25% v/v PEG 1500, 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: May 29, 2009 / Details: Beryllium lenses
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 65972 / Num. obs: 65972 / % possible obs: 98 % / Observed criterion σ(F): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3069 / % possible all: 92.5

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H83

3h83


Resolution: 1.95→29.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.294 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Isotropic Temperature Factors were Refined
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23172 3338 5.1 %RANDOM
Rwork0.19227 ---
all0.19427 62332 --
obs0.19427 62332 98.07 %-
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: 22.879 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å2-0.3 Å2
2--5.08 Å20 Å2
3----4.05 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5852 0 52 498 6402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226290
X-RAY DIFFRACTIONr_bond_other_d0.0010.024223
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.0018554
X-RAY DIFFRACTIONr_angle_other_deg0.881310444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4815798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02825.233258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.141151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7271520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_mcbond_it1.0821.53858
X-RAY DIFFRACTIONr_mcbond_other0.3211.51562
X-RAY DIFFRACTIONr_mcangle_it1.83426320
X-RAY DIFFRACTIONr_scbond_it2.98432432
X-RAY DIFFRACTIONr_scangle_it4.5764.52234
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 252 -
Rwork0.273 4322 -
obs-4322 94.15 %
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)
11.29640.10180.86910.8694-0.23142.67160.0777-0.089-0.2152-0.02660.07530.06250.4564-0.0506-0.1530.23140.0106-0.02960.0730.06320.21479.9886-29.955331.6159
21.5021-0.0629-0.15281.6859-0.26291.035-0.0151-0.0867-0.04470.08550.1480.18170.0638-0.1426-0.13290.0909-0.0085-0.00920.04760.06890.13412.0666-12.998925.0324
32.8136-0.4720.42151.2866-0.73541.8263-0.1453-0.5607-0.04340.25530.28880.16110.0649-0.2849-0.14350.22520.0835-0.01180.16260.05810.16888.0655-21.826339.0914
43.47180.0268-2.36371.2590.10584.4710.0614-0.05830.3493-0.19070.10660.0281-0.48940.0982-0.1680.3109-0.0060.01040.01420.01690.22667.840429.507515.5893
51.3704-0.15370.17351.87720.08620.858-0.03310.03280.0279-0.05730.10790.2122-0.104-0.065-0.07480.09480.03140.03240.02670.04670.11371.11612.224322.0485
60.76380.3234-0.10651.3304-0.24071.3778-0.09540.2980.0127-0.36890.16520.1359-0.191-0.1864-0.06980.2971-0.02810.00620.16660.01990.2196.141721.38758.0876
71.9911-0.161.79791.3369-0.36643.66730.1295-0.0811-0.296-0.1520.0604-0.03190.6403-0.1693-0.18990.2741-0.01230.0020.0346-0.02430.187818.7228-29.628615.7512
81.0479-0.2086-0.21911.9978-0.16891.1444-0.0418-0.0423-0.0328-0.08490.1026-0.20360.06580.0941-0.06080.07630.0302-0.01610.0332-0.04770.109725.4985-12.056721.853
92.1091-0.06780.78761.61460.20591.1827-0.04540.4191-0.0342-0.4130.1348-0.0760.17510.2043-0.08940.2583-0.03680.01110.0979-0.01930.16120.1177-21.60757.9033
101.95070.2706-1.21660.95220.36123.8010.1012-0.1510.3015-0.01750.1337-0.0747-0.51830.1654-0.2350.24310.02310.03550.047-0.05430.211816.495529.973831.5897
111.17430.07070.31821.3860.35351.1318-0.0141-0.0760.02490.08940.151-0.2173-0.0860.1563-0.13690.0901-0.0060.02430.0509-0.06740.144424.448312.991125.182
122.7953-0.35-0.12121.4380.41230.9563-0.1303-0.50950.04440.29740.2581-0.1652-0.09130.2737-0.12780.25170.08240.01840.1983-0.06830.17718.5721.64139.0476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 35
2X-RAY DIFFRACTION2A36 - 135
3X-RAY DIFFRACTION3A136 - 179
4X-RAY DIFFRACTION4B-5 - 35
5X-RAY DIFFRACTION5B36 - 135
6X-RAY DIFFRACTION6B136 - 179
7X-RAY DIFFRACTION7C-5 - 35
8X-RAY DIFFRACTION8C36 - 135
9X-RAY DIFFRACTION9C136 - 179
10X-RAY DIFFRACTION10D-5 - 35
11X-RAY DIFFRACTION11D36 - 135
12X-RAY DIFFRACTION12D136 - 179

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