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- PDB-2cnu: Atomic resolution structure of SAICAR-synthase from Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 2cnu
TitleAtomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid
ComponentsPHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
KeywordsLIGASE / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYN LIGASE / ACETYLATION / ATP BINDING PROTEIN / PURINE BIOSYNTHESIS
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsUrusova, D.V. / Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Popov, A.N. / Lamzin, V.S. / Melik-Adamyan, W.R.
CitationJournal: To be Published
Title: Saicar Synthase: Substrate Recognition, Conformational Flexibility and Catalysis.
Authors: Urusova, D.V. / Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Popov, A.N. / Lamzin, V.S. / Melik-Adamyan, W.R.
History
DepositionMay 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,61711
Polymers34,5451
Non-polymers1,07210
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.023, 62.497, 78.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE / SAICAR SYNTHETASE


Mass: 34545.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P27616, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.1 Å3/Da / Density % sol: 40.8 %
Crystal growpH: 7.5
Details: TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1997 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.05→24 Å / Num. obs: 131992 / % possible obs: 94.4 % / Redundancy: 4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.999refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A48

1a48


Resolution: 1.05→23.97 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.854 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.159 6644 5 %RANDOM
Rwork0.132 ---
obs0.134 125306 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.05→23.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 62 708 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222937
X-RAY DIFFRACTIONr_bond_other_d0.0020.022701
X-RAY DIFFRACTIONr_angle_refined_deg2.2421.9874011
X-RAY DIFFRACTIONr_angle_other_deg2.05636383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9711519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9711519
X-RAY DIFFRACTIONr_chiral_restr0.1470.249
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023175
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02559
X-RAY DIFFRACTIONr_nbd_refined0.3520.29
X-RAY DIFFRACTIONr_nbd_other0.3520.2729
X-RAY DIFFRACTIONr_nbtor_refined0.2230.22963
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.21774
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.284
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.481.52197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.98822830
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.04431411
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9564.51155
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 452
Rwork0.265 8431

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