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- PDB-5b6h: Crystal structure of an APRT from Yersinia pseudotuberculosis in ... -

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Basic information

Entry
Database: PDB / ID: 5b6h
TitleCrystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / adenine phosphoribosyltransferase
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
ADENOSINE MONOPHOSPHATE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis serotype I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
Model detailsSTRUCTURAL GENOMICS
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionMay 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / diffrn_radiation_wavelength / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0185
Polymers19,5891
Non-polymers4294
Water66737
1
A: Adenine phosphoribosyltransferase
hetero molecules

A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,03610
Polymers39,1792
Non-polymers8578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4940 Å2
ΔGint-86 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.875, 78.554, 53.885
Angle α, β, γ (deg.)90.000, 116.560, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 19589.320 Da / Num. of mol.: 1 / Fragment: UNP residues 7-187
Source method: isolated from a genetically manipulated source
Details: AMP complex
Source: (gene. exp.) Yersinia pseudotuberculosis serotype I (strain IP32953) (bacteria)
Strain: IP32953 / Gene: apt, YPTB0991 / Plasmid: LIC-PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q66DQ2, adenine phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M sodium malonate pH 7.0 these crystals were moved condition containing 25% PEG3350, 0.1M Tris-Hcl pH 8.5, 0.2M Sodium Acetate and soaked with 5mM AMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→48.2 Å / Num. obs: 17719 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.054 / Net I/av σ(I): 27.149 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.935.90.8123.21199.8
1.93-1.9760.665199.7
1.97-2.016.10.5181100
2.01-2.056.20.4691100
2.05-2.096.10.3571100
2.09-2.146.20.2671100
2.14-2.196.20.251100
2.19-2.256.20.2141100
2.25-2.326.20.161100
2.32-2.396.20.1441100
2.39-2.486.20.1231100
2.48-2.586.10.0991100
2.58-2.76.20.0771100
2.7-2.846.10.0661100
2.84-3.0260.0551100
3.02-3.255.80.049199.9
3.25-3.585.50.045199.8
3.58-4.095.40.042199.1
4.09-5.155.20.04198.2
5.15-404.90.043190.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MB6

4mb6


Resolution: 1.9→48.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.718 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 834 5.1 %RANDOM
Rwork0.1867 ---
obs0.1881 15497 91.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.43 Å2 / Biso mean: 26.827 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20.26 Å2
2---1.62 Å20 Å2
3---1.71 Å2
Refinement stepCycle: final / Resolution: 1.9→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 26 37 1418
Biso mean--20.97 28.76 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021382
X-RAY DIFFRACTIONr_angle_refined_deg2.3062.0071956
X-RAY DIFFRACTIONr_angle_other_deg0.91533195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0924.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.748157
X-RAY DIFFRACTIONr_chiral_restr0.1370.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211599
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
X-RAY DIFFRACTIONr_mcbond_it1.0730.996729
X-RAY DIFFRACTIONr_mcbond_other1.0710.992728
X-RAY DIFFRACTIONr_mcangle_it1.8521.48914
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 47 -
Rwork0.213 759 -
all-806 -
obs--60.97 %
Refinement TLS params.Method: refined / Origin x: 21.7073 Å / Origin y: -0.734 Å / Origin z: 7.1657 Å
111213212223313233
T0.2455 Å2-0.0443 Å20.0313 Å2-0.181 Å2-0.0168 Å2--0.0441 Å2
L1.0448 °2-0.146 °2-0.5316 °2-0.4966 °2-0.2788 °2--1.2629 °2
S0.3103 Å °-0.0624 Å °0.0333 Å °0.1131 Å °-0.1209 Å °0.1241 Å °-0.119 Å °-0.1097 Å °-0.1895 Å °

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