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- PDB-2pgr: Crystal structure of adenosine deaminase from Plasmodium vivax in... -

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Basic information

Entry
Database: PDB / ID: 2pgr
TitleCrystal structure of adenosine deaminase from Plasmodium vivax in complex with pentostatin
Componentsadenosine deaminase
KeywordsHYDROLASE / Metallo-dependent hydrolase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa Consortium / MSGPP / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI / Protein Structure Initiative
Function / homology
Function and homology information


S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / adenosine deaminase / 2'-deoxyadenosine deaminase activity / purine ribonucleoside monophosphate biosynthetic process / adenosine deaminase activity / purine ribonucleoside salvage / metal ion binding
Similarity search - Function
Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETONITRILE / 2'-DEOXYCOFORMYCIN / Adenosine deaminase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLarson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.
Authors: Larson, E.T. / Deng, W. / Krumm, B.E. / Napuli, A. / Mueller, N. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Lauricella, A. / DeTitta, G. / Luft, J. / Zucker, F. / Hol, W.G. / Verlinde, C.L. / Merritt, E.A.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF ...SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT PLASMODB, THE AUTHORITATIVE SEQUENCE REPOSITORY FOR PLASMODIUM SPECIES, WITH ACCESSION CODE PV111245. DUE TO CLONING PROCESS, THE CRYSTALLIZED POLYPEPTIDE HAS ADDITION OF AN UNCLEAVABLE N-TERMINAL HIS TAG (RESIDUES -7 TO 0).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8935
Polymers43,4771
Non-polymers4164
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.488, 146.386, 50.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein adenosine deaminase


Mass: 43477.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: Pv111245 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5KE01, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DCF / 2'-DEOXYCOFORMYCIN


Mass: 268.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N4O4 / Comment: anticancer*YM
#4: Chemical ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 33% PEG 20000, 0.1 M TAPS (pH 9.0), 0.1 M Sodium phosphate (monobasic), 16% acetonitrile, 5 mM adenosine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91722 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2007 / Details: mirrors
RadiationMonochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91722 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 23772 / Num. obs: 23772 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.103 / Χ2: 0.874 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.09 / Num. unique all: 2375 / Χ2: 0.926 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PGF

2pgf


Resolution: 2.3→37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.06 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUPS WERE DEFINED USING THE TLSMD SERVER: J.PAINTER & E.A.MERRITT (2006) ACTA CRYST. D62, 439-450, J.PAINTER & E.A.MERRITT (2006) J. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUPS WERE DEFINED USING THE TLSMD SERVER: J.PAINTER & E.A.MERRITT (2006) ACTA CRYST. D62, 439-450, J.PAINTER & E.A.MERRITT (2006) J.APPL.CRYST. 39, 109-111. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1171 4.9 %RANDOM
Rwork0.168 ---
all0.171 ---
obs0.171 23771 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.985 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2---1.77 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 26 110 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223039
X-RAY DIFFRACTIONr_bond_other_d0.0010.022054
X-RAY DIFFRACTIONr_angle_refined_deg0.8831.974101
X-RAY DIFFRACTIONr_angle_other_deg0.783.0015028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2915366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48325.405148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67815565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.601158
X-RAY DIFFRACTIONr_chiral_restr0.050.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
X-RAY DIFFRACTIONr_nbd_refined0.1860.2657
X-RAY DIFFRACTIONr_nbd_other0.1630.22171
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21525
X-RAY DIFFRACTIONr_nbtor_other0.080.21444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2122
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.25
X-RAY DIFFRACTIONr_mcbond_it1.4582.52336
X-RAY DIFFRACTIONr_mcbond_other0.3242.5732
X-RAY DIFFRACTIONr_mcangle_it1.7153.752938
X-RAY DIFFRACTIONr_scbond_it2.56841400
X-RAY DIFFRACTIONr_scangle_it3.49661163
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 104 -
Rwork0.207 1613 -
obs-1717 98.68 %
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)
15.0455-0.9754-4.37633.15760.51185.5888-0.27230.7243-0.4695-0.21670.06540.32250.2635-0.67260.2069-0.0133-0.070.00730.0608-0.10860.15495.0777.24224.605
21.1763-0.4224-0.09642.07620.11060.9832-0.04290.0015-0.20570.3905-0.0628-0.03980.06370.09080.10570.1305-0.04250.040.06170.00420.079124.6759.6935.856
31.4881-0.79750.53145.1247-0.69171.51350.0603-0.33780.03591.03930.0179-0.04030.28790.0871-0.07830.3098-0.0653-0.02980.07280.0255-0.044930.00315.04548.45
41.86280.7850.88832.9470.9461.87870.03960.1298-0.25330.10850.0437-0.32190.14680.2387-0.08330.0543-0.00310.03090.05510.00340.072434.20811.29228.316
50.8531.3773-0.89454.57043.04999.5459-0.03690.0572-0.0168-0.00880.1757-0.198-0.07770.2882-0.13880.034-0.01960.01830.07110.02350.099839.9625.91629.409
61.82920.6354-0.73932.11270.56352.5032-0.02930.0550.1607-0.0131-0.05430.0314-0.30370.13550.08360.1053-0.0618-0.01580.03240.0160.044928.32435.17530.44
76.8804-2.0794-0.01732.39240.037620.01820.14120.18981.0013-0.15550.1227-0.01-0.44180.1572-0.2640.0987-0.0038-0.0625-0.0920.01810.231114.00740.39327.938
81.217-0.24010.44682.8753-0.43961.6485-0.0041-0.03710.02710.2966-0.09710.3644-0.1422-0.13970.10130.0738-0.03950.05980.0623-0.03950.086215.5624.09934.753
92.93610.613-0.90983.9752-0.83110.8696-0.01580.3508-0.1615-0.3738-0.10.3116-0.1275-0.11910.11580.0353-0.0273-0.03290.0862-0.06550.082513.54119.0121.997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
115 - 2813 - 36
2229 - 6437 - 72
3365 - 9973 - 107
44100 - 167108 - 175
55168 - 194176 - 202
66195 - 258203 - 266
77259 - 269267 - 277
88270 - 322278 - 330
99323 - 363331 - 371

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