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- PDB-3ozb: Crystal Structure of 5'-methylthioinosine phosphorylase from Psed... -

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Basic information

Entry
Database: PDB / ID: 3ozb
TitleCrystal Structure of 5'-methylthioinosine phosphorylase from Psedomonas aeruginosa in complex with hypoxanthine
ComponentsMethylthioadenosine phosphorylase
KeywordsTRANSFERASE / 5'-methylthioinosine / phosphorylase
Function / homology
Function and homology information


S-methyl-5'-thioinosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / Probable S-methyl-5'-thioinosine phosphorylase / S-methyl-5'-thioinosine phosphorylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHo, M. / Guan, R. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2011
Title: Methylthioinosine phosphorylase from Pseudomonas aeruginosa. Structure and annotation of a novel enzyme in quorum sensing.
Authors: Guan, R. / Ho, M.C. / Almo, S.C. / Schramm, V.L.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,86716
Polymers168,6666
Non-polymers1,20110
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18260 Å2
ΔGint-110 kcal/mol
Surface area51590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.469, 99.469, 334.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Methylthioadenosine phosphorylase


Mass: 28110.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: mtnP, PA14_25210 / Plasmid: PJexpress414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q02PG8, UniProt: Q9HZK1*PLUS, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200mM potassium thiocyanate,20% PEG monomethyl ether 2000, pH 7.4, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorDetector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 42497 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.172 / Χ2: 1.035 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.97.20.95541441.0891100
2.9-3.027.20.73341971.0811100
3.02-3.157.20.54341461.061100
3.15-3.327.20.442021.0321100
3.32-3.527.20.25941961.0151100
3.52-3.797.10.18541911.0141100
3.79-4.1770.15342391.0361100
4.17-4.776.80.11942661.021100
4.77-5.986.70.11743331.0641100
5.98-206.20.0845830.9341100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 33.762 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY. HERE IS SOME UNKOWN DENSITY IN PROMIXTY TO HIS169 OF SUBUNIT B AND E AND IS NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 2126 5.1 %RANDOM
Rwork0.202 ---
obs0.205 42041 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.36 Å2 / Biso mean: 55.234 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10786 0 80 63 10929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02111112
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9715119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47251424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38822.884475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.465151698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4071591
X-RAY DIFFRACTIONr_chiral_restr0.0910.21705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218508
X-RAY DIFFRACTIONr_mcbond_it0.5571.57086
X-RAY DIFFRACTIONr_mcangle_it1.077211283
X-RAY DIFFRACTIONr_scbond_it1.57534026
X-RAY DIFFRACTIONr_scangle_it2.6964.53835
LS refinement shellResolution: 2.801→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 155 -
Rwork0.257 2860 -
all-3015 -
obs--99.44 %
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)
10.35910.3128-0.21681.3463-0.46041.45410.0393-0.0281-0.0741-0.0218-0.09950.0302-0.0727-0.18790.06020.0961-0.0873-0.01030.1628-0.01680.080345.092-1.061162.657
21.9442-0.36750.360.87820.21761.58640.12910.01060.0059-0.2112-0.19890.0388-0.1552-0.19350.06990.1570.0536-0.07350.076-0.02620.061440.79415.924131.556
31.15620.35170.1071.63690.13610.90520.0148-0.03550.0463-0.0361-0.01450.0321-0.128-0.0275-0.00020.169-0.09790.01650.0719-0.00330.038365.80426.636154.514
41.1474-0.133-0.38570.3704-0.20081.98890.0280.1064-0.104-0.0545-0.12360.01160.10110.03350.09570.18220.0240.00580.0727-0.02640.096869.828-3.339114.523
50.90090.2931-0.30661.34530.18311.5592-0.0176-0.0772-0.24650.0679-0.03-0.12470.31950.09590.04770.1905-0.0018-0.01270.01430.03690.249666.546-25.675141.95
61.1414-0.21760.25281.39750.30251.85180.101-0.0494-0.0144-0.0192-0.0498-0.18080.02070.5117-0.05120.0291-0.0251-0.00150.24790.03530.128591.1870.134142.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 258
2X-RAY DIFFRACTION2B16 - 258
3X-RAY DIFFRACTION3C16 - 257
4X-RAY DIFFRACTION4D16 - 258
5X-RAY DIFFRACTION5E17 - 258
6X-RAY DIFFRACTION6F16 - 258

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