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- PDB-1vmk: Crystal structure of Purine nucleoside phosphorylase (TM1596) fro... -

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Basic information

Entry
Database: PDB / ID: 1vmk
TitleCrystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / TM1596 / PURINE NUCLEOSIDE PHOSPHORYLASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: purine nucleoside phosphorylase
B: purine nucleoside phosphorylase
C: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4967
Polymers92,0183
Non-polymers4784
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-28 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.478, 74.601, 74.591
Angle α, β, γ (deg.)117.34, 100.95, 100.71
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
131A
141B
151C
161A
171B
181C
191A
201B
211C
221A
231B
241C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHE1AA1 - 1113 - 23
21METMETPHEPHE1BB1 - 1113 - 23
31METMETPHEPHE1CC1 - 1113 - 23
42ILEILEILEILE3AA1224
52ILEILEILEILE3BB1224
62ILEILEILEILE3CC1224
73SERSERGLYGLY1AA13 - 2725 - 39
83SERSERGLYGLY1BB13 - 2725 - 39
93SERSERGLYGLY1CC13 - 2725 - 39
104PHEPHEPROPRO1AA33 - 5245 - 64
114PHEPHEPROPRO1BB33 - 5245 - 64
124PHEPHEPROPRO1CC33 - 5245 - 64
135GLYGLYSERSER1AA61 - 22473 - 236
145GLYGLYSERSER1BB61 - 22473 - 236
155GLYGLYSERSER1CC61 - 22473 - 236
166CYSCYSCYSCYS3AA225237
176CYSCYSCYSCYS3BB225237
186CYSCYSCYSCYS3CC225237
197VALVALALAALA1AA226 - 230238 - 242
207VALVALALAALA1BB226 - 230238 - 242
217VALVALALAALA1CC226 - 230238 - 242
228GLYGLYPHEPHE1AA252 - 265264 - 277
238GLYGLYPHEPHE1BB252 - 265264 - 277
248GLYGLYPHEPHE1CC252 - 265264 - 277

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Components

#1: Protein purine nucleoside phosphorylase


Mass: 30672.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1596 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X1T2, purine-nucleoside phosphorylase
#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.56 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 0.2M MgCl2, 20.0% PEG-1000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97912
DetectorType: APS / Detector: CCD / Date: Feb 20, 2004
Details: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2→43.34 Å / Num. obs: 54061 / % possible obs: 97.72 % / Redundancy: 3.77 % / Biso Wilson estimate: 30.41 Å2 / Rsym value: 0.106 / Net I/σ(I): 12.88
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.43 % / Mean I/σ(I) obs: 2.58 / Num. unique all: 5179 / Rsym value: 0.522 / % possible all: 93.79

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a9o

1a9o


Resolution: 2.01→43.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.199 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE SOME UNMODELLED DENSITIES NEAR TO C CHAIN OF 246 WHICH MAY BELONG TO THE DISORDERED LOOP 233-246. 3. THREE GUANINE BASES ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE ARE SOME UNMODELLED DENSITIES NEAR TO C CHAIN OF 246 WHICH MAY BELONG TO THE DISORDERED LOOP 233-246. 3. THREE GUANINE BASES WERE MODELLED ACCORDING TO THE INTERPRETATION OF THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23995 2755 5.1 %RANDOM
Rwork0.20391 ---
obs0.20575 51297 97.23 %-
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: 32.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å21.25 Å21.4 Å2
2--0.05 Å20.75 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.01→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 0 34 338 5963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225751
X-RAY DIFFRACTIONr_bond_other_d0.0020.025489
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9857814
X-RAY DIFFRACTIONr_angle_other_deg0.964312659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3215728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60223.173208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7451534
X-RAY DIFFRACTIONr_chiral_restr0.0960.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026301
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021142
X-RAY DIFFRACTIONr_nbd_refined0.210.21143
X-RAY DIFFRACTIONr_nbd_other0.1990.25405
X-RAY DIFFRACTIONr_nbtor_other0.0890.23129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2310
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.212
X-RAY DIFFRACTIONr_mcbond_it2.06633812
X-RAY DIFFRACTIONr_mcbond_other0.431492
X-RAY DIFFRACTIONr_mcangle_it2.87555978
X-RAY DIFFRACTIONr_scbond_it5.20882244
X-RAY DIFFRACTIONr_scangle_it7.09111836
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22851
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3402tight positional0.040.05
2B3402tight positional0.040.05
3C3402tight positional0.040.05
1A21loose positional0.65
2B21loose positional0.615
3C21loose positional1.215
1A3402tight thermal0.20.5
2B3402tight thermal0.20.5
3C3402tight thermal0.210.5
1A21loose thermal1.510
2B21loose thermal1.9510
3C21loose thermal2.0510
LS refinement shellResolution: 2.01→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 186 5.25 %
Rwork0.314 3357 -
obs--86.37 %
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)
10.8965-0.2155-0.0140.8579-0.03230.51620.0173-0.19140.09910.0748-0.01030.0089-0.0282-0.0247-0.007-0.0151-0.00690.03090.0071-0.0249-0.016919.077-79.7178.02
20.75920.06180.21450.4860.02930.29230.02210.0660.0595-0.07320.0175-0.0137-0.0145-0.0175-0.0396-0.02980.00950.0351-0.02950.0321-0.001618.953-69.54642.251
30.70240.1297-0.08090.6890.01840.32640.03940.0044-0.0938-0.0303-0.02030.01820.04240.0075-0.0191-0.0363-0.00020.0033-0.0584-0.01160.015118.643-105.80252.547
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 265 / Label seq-ID: 13 - 277

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC

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