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- PDB-1o5o: Crystal structure of Uracil phosphoribosyltransferase (TM0721) fr... -

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Basic information

Entry
Database: PDB / ID: 1o5o
TitleCrystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / TM0721 / URACIL PHOSPHORIBOSYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / nucleoside metabolic process / kinase activity / GTP binding / magnesium ion binding / cytosol
Similarity search - Function
Uracil phosphoribosyltransferase, bacterial-type / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,42117
Polymers99,2604
Non-polymers2,16113
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-239 kcal/mol
Surface area30710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.078, 87.406, 90.826
Angle α, β, γ (deg.)90.00, 115.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
12A
22C
32A
42C
13B
23D
33B
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETILEILE3AA1 - 10013 - 112
211METMETILEILE3BB1 - 10013 - 112
311METMETILEILE3CC1 - 10013 - 112
411METMETILEILE3DD1 - 10013 - 112
521ALAALALYSLYS3AA116 - 209128 - 221
621ALAALALYSLYS3BB116 - 209128 - 221
721ALAALALYSLYS3CC116 - 209128 - 221
821ALAALALYSLYS3DD116 - 209128 - 221
112GLYGLYTYRTYR3AA101 - 115113 - 127
212GLYGLYTYRTYR3CC101 - 115113 - 127
322U5PU5PU5PU5P1AH600
422U5PU5PU5PU5P1CM602
113GLYGLYTYRTYR3BB101 - 115113 - 127
213GLYGLYTYRTYR3DD101 - 115113 - 127
323U5PU5PU5PU5P1BK601
423U5PU5PU5PU5P1DQ603

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Uracil phosphoribosyltransferase / / UMP pyrophosphorylase / UPRTase


Mass: 24814.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0721 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZI0, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.44 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 2.4M ammonium sulfate, 0.1M bicine pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2003 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 41796 / Num. obs: 41796 / % possible obs: 100 % / Redundancy: 3.72 % / Biso Wilson estimate: 51.25 Å2 / Rsym value: 0.102 / Net I/σ(I): 10.16
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.66 % / Mean I/σ(I) obs: 1.49 / Num. unique all: 4138 / Rsym value: 0.752 / % possible all: 99.71

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i5e

1i5e


Resolution: 2.3→30.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.204 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. UNLIKE IN SUBUNITS A,C, THERE IS ONLY WEAK DENSITY FOR THE BOUND PRODUCT IN SUBUNITS B AND D, BUT IT WAS MODELLED BY NCS. THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. UNLIKE IN SUBUNITS A,C, THERE IS ONLY WEAK DENSITY FOR THE BOUND PRODUCT IN SUBUNITS B AND D, BUT IT WAS MODELLED BY NCS. THE VARIABLE OCCUPANCY MAY RESULT FROM DIFFERENT CRYSTAL CONTACTS OF ADJACENT RESIDUES 101-114, WHICH ARE ALSO INVOLVED IN DOMAIN SWAPPING. 3. SULFATE IONS NOT IN THE ACTIVE SITE (705-709) WERE MODELLED AT HALF OCCUPANCY WHICH RESULTED IN MORE REALISTIC B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23635 2126 5.1 %RANDOM
Rwork0.16658 ---
obs0.17004 39885 99.68 %-
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: 45.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.13 Å2
2--0.53 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 129 355 7038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226789
X-RAY DIFFRACTIONr_bond_other_d0.0020.026511
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.019227
X-RAY DIFFRACTIONr_angle_other_deg0.915315149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39224.569267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.403151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851539
X-RAY DIFFRACTIONr_chiral_restr0.0960.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027258
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021193
X-RAY DIFFRACTIONr_nbd_refined0.190.21281
X-RAY DIFFRACTIONr_nbd_other0.1880.26693
X-RAY DIFFRACTIONr_nbtor_other0.0910.24429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2337
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.24
X-RAY DIFFRACTIONr_mcbond_it0.9661.54546
X-RAY DIFFRACTIONr_mcangle_it1.3926801
X-RAY DIFFRACTIONr_scbond_it2.21632784
X-RAY DIFFRACTIONr_scangle_it3.4664.52426
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1141tight positional0.060.05
12B1141tight positional0.060.05
13C1141tight positional0.050.05
14D1141tight positional0.060.05
11A1817loose positional0.395
12B1817loose positional0.475
13C1817loose positional0.435
14D1817loose positional0.415
11A1141tight thermal1.6110
12B1141tight thermal1.3210
13C1141tight thermal1.3710
14D1141tight thermal1.7310
11A1817loose thermal1.9510
12B1817loose thermal1.7110
13C1817loose thermal1.5810
14D1817loose thermal1.8510
21A118tight positional0.030.05
21A151loose positional0.485
21A118tight thermal0.8410
21A151loose thermal1.0110
31B118tight positional0.050.05
31B151loose positional0.615
31B118tight thermal1.4710
31B151loose thermal1.4310
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 161 5.39 %
Rwork0.25 2826 -
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)
13.8222-0.9086-0.66022.30090.23162.5665-0.139-0.44540.41210.21670.2136-0.4005-0.10450.0981-0.0746-0.19810.0574-0.0572-0.1924-0.1593-0.144329.7931.39735.52
22.6741-0.2331-0.53041.29-0.1683.19310.0069-0.0606-0.04310.09240.0651-0.07790.18210.2198-0.0719-0.20450.1346-0.0195-0.2409-0.0337-0.241238.442-24.78625.169
32.7006-0.45130.153.32860.0441.36710.17180.3937-0.1212-0.2125-0.0940.13870.1602-0.0328-0.0778-0.15530.1092-0.0074-0.1269-0.0248-0.328822.292-16.9571.16
42.1743-0.117-0.14223.20860.38471.9321-0.022-0.0333-0.0104-0.008-0.0050.16310.033-0.18150.027-0.26550.08950.0106-0.2034-0.0213-0.2434.115-5.31821.163
516.6869.0809-1.5599.67840.21624.0485-0.1427-0.80332.0019-0.23510.17220.703-0.7058-0.0667-0.0295-0.03140.0844-0.1045-0.1423-0.19520.057918.20613.6138.981
69.5714-4.15672.117215.6958-6.687810.93410.0667-0.3209-0.71050.3962-0.18310.1841.21720.3560.1164-0.03690.0969-0.0355-0.0965-0.1136-0.217242.668-37.30312.769
70.49650.4509-2.783115.1251-9.350918.76470.27150.4695-0.4321-1.0104-0.5965-0.70690.17140.58760.325-0.02430.20070.00090.0177-0.0444-0.138335.636-26.664-3.991
822.42660.4805-10.72082.9397-1.08139.11310.22490.37010.08910.224-0.19830.37690.7034-1.1652-0.0267-0.1069-0.0212-0.03890.1-0.1451-0.2419-0.8775.80934.715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 4812 - 60
21AA68 - 10080 - 112
31AA116 - 209128 - 221
41BB49 - 6761 - 79
52BB1 - 4813 - 60
62BB68 - 10080 - 112
72BB116 - 209128 - 221
82AA49 - 6761 - 79
93CC0 - 4812 - 60
103CC68 - 10080 - 112
113CC116 - 209128 - 221
123DD49 - 6761 - 79
134DD0 - 4812 - 60
144DD68 - 10080 - 112
154DD116 - 209128 - 221
164CC49 - 6761 - 79
175AA101 - 115113 - 127
186BB101 - 115113 - 127
197CC101 - 115113 - 127
208DD101 - 115113 - 127

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