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- PDB-2r7m: Crystal structure of FAICAR synthetase (PurP) from M. jannaschii ... -

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Basic information

Entry
Database: PDB / ID: 2r7m
TitleCrystal structure of FAICAR synthetase (PurP) from M. jannaschii complexed with AMP
Components5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
KeywordsLIGASE / ATP-grasp superfamily / ATP-binding / Magnesium / Manganese / Metal-binding / Nucleotide-binding
Function / homology
Function and homology information


formate-phosphoribosylaminoimidazolecarboxamide ligase / ligase activity, forming carbon-nitrogen bonds / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain ...IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, Y. / White, R.H. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
Authors: Zhang, Y. / White, R.H. / Ealick, S.E.
History
DepositionSep 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7356
Polymers40,8741
Non-polymers8615
Water1,69394
1
A: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)250,41236
Polymers245,2446
Non-polymers5,16830
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area40890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.446, 109.446, 256.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

21A-671-

HOH

31A-682-

HOH

41A-691-

HOH

Detailsbiological unit is a hexamer from the monomer in the asymmetric unit by the operations: (x,y,z), (-y,x-y,z), (-x+y,-x,z), (y,x,-z), (x-y,-y,-z), (-x,-x+y,-z)

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Components

#1: Protein 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase / 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate-formate ligase


Mass: 40873.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: purP / Plasmid: pET19 / Cell line (production host): B834(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q57600, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 1.2 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na acetate, pH 4.1, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 26365 / Num. obs: 26358 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.068 / Χ2: 1.878 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.384.70.36426181.184100
2.38-2.4850.30126091.301100
2.48-2.595.20.26426241.454100
2.59-2.735.20.21526151.816100
2.73-2.95.50.1526051.97100
2.9-3.125.50.11326432.277100
3.12-3.445.50.08626292.697100
3.44-3.935.40.06726403.14499.4
3.93-4.955.50.05326351.90598.3
4.95-505.60.02527470.87198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.142 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1332 5.1 %RANDOM
Rwork0.204 ---
obs0.207 26358 99.45 %-
all-26365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.206 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å21.33 Å20 Å2
2--2.66 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 53 94 2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222936
X-RAY DIFFRACTIONr_angle_refined_deg1.0932.0063965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4175353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3424.697132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.031516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022172
X-RAY DIFFRACTIONr_nbd_refined0.2140.31264
X-RAY DIFFRACTIONr_nbtor_refined0.3220.52012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.5230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.3112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.533
X-RAY DIFFRACTIONr_mcbond_it4.87721813
X-RAY DIFFRACTIONr_mcangle_it6.69532861
X-RAY DIFFRACTIONr_scbond_it5.33721262
X-RAY DIFFRACTIONr_scangle_it6.8431104
LS refinement shellResolution: 2.3→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 102 -
Rwork0.333 1792 -
all-1894 -
obs--97.63 %

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