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- PDB-5zc7: Crystal structure of APRT from Y. pseudotuberculosis with bound a... -

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Basic information

Entry
Database: PDB / ID: 5zc7
TitleCrystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 space group).
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / adenine phosphoribosyltransferase / metal mediated assembly / adenine
Function / homology
Function and homology information


adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / cytosol
Similarity search - Function
Adenine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENINE / NICKEL (II) ION / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis serotype I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionFeb 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,87211
Polymers40,3322
Non-polymers5409
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-51 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.074, 121.074, 50.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-200-

NI

21A-204-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 20165.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis serotype I (strain IP32953) (bacteria)
Strain: IP32953 / Gene: apt, YPTB0991 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q66DQ2, adenine phosphoribosyltransferase

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Non-polymers , 6 types, 150 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate with 5mM adenine, 1mM Nickel Chloride and 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28327 / % possible obs: 99.5 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.039 / Rrim(I) all: 0.128 / Χ2: 0.959 / Net I/σ(I): 6.3 / Num. measured all: 299633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.036.70.68113320.750.2640.7340.95296
2.03-2.077.20.64713940.7690.2430.6940.99697.5
2.07-2.118.10.57513780.8210.2050.6130.97898.4
2.11-2.1590.54413900.870.1860.5770.97699.4
2.15-2.2100.49414130.9070.1620.5210.9799.9
2.2-2.2510.70.43114200.9440.1370.4531.01100
2.25-2.3111.20.37814040.9660.1170.3961.008100
2.31-2.3711.60.35314440.9690.1080.3690.952100
2.37-2.4411.70.31713890.9790.0960.3310.951100
2.44-2.5211.70.28214450.9820.0860.2950.963100
2.52-2.6111.70.23713980.9860.0720.2480.939100
2.61-2.7111.50.20314070.9890.0620.2120.954100
2.71-2.8411.20.16814330.9910.0520.1760.939100
2.84-2.9910.90.14414150.9930.0450.1510.982100
2.99-3.17100.11514260.9940.0380.1211.03100
3.17-3.429.30.08414240.9960.0290.0890.989100
3.42-3.7612.40.06614290.9980.020.0690.937100
3.76-4.3112.40.05514410.9990.0160.0580.88100
4.31-5.4312.20.05114460.9990.0150.0530.883100
5.43-5011.60.05214990.9980.0160.0540.94699.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.063 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 1269 4.6 %RANDOM
Rwork0.1602 ---
obs0.1618 26119 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.91 Å2 / Biso mean: 27.793 Å2 / Biso min: 14.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å2-0 Å2
2--0.34 Å20 Å2
3----1.11 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 30 141 2930
Biso mean--27.9 29.37 -
Num. residues----363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0192852
X-RAY DIFFRACTIONr_bond_other_d0.0040.022726
X-RAY DIFFRACTIONr_angle_refined_deg2.4131.9963875
X-RAY DIFFRACTIONr_angle_other_deg1.17336322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69124.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8151514
X-RAY DIFFRACTIONr_chiral_restr0.1460.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213156
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 80 -
Rwork0.223 1521 -
all-1601 -
obs--76.31 %
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)
10.37490.02190.11070.2635-0.0130.0985-0.00630.01830.03170.0366-0.02950.01870.00840.01960.03580.0243-0.0031-0.00240.019-0.020.095342.7209-29.94460.6844
20.83620.30560.35040.25410.21870.2058-0.05480.00850.0548-0.0323-0.02510.1246-0.0282-0.01060.07990.00860.003-0.02520.0154-0.0280.119822.7073-30.2517-9.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 205
2X-RAY DIFFRACTION2B7 - 203

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