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- PDB-2ywv: Crystal structure of SAICAR synthetase from Geobacillus kaustophilus -

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Basic information

Entry
Database: PDB / ID: 2ywv
TitleCrystal structure of SAICAR synthetase from Geobacillus kaustophilus
ComponentsPhosphoribosylaminoimidazole succinocarboxamide synthetase
KeywordsLIGASE / ADP COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding
Similarity search - Function
Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / 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 ...Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / 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
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of SAICAR synthetase from Geobacillus kaustophilus
Authors: Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G.
History
DepositionApr 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Phosphoribosylaminoimidazole succinocarboxamide synthetase
B: Phosphoribosylaminoimidazole succinocarboxamide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23013
Polymers54,6552
Non-polymers1,57511
Water9,458525
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoribosylaminoimidazole succinocarboxamide synthetase
hetero molecules

A: Phosphoribosylaminoimidazole succinocarboxamide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23013
Polymers54,6552
Non-polymers1,57511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_644x+1,y-1,z-11
Buried area5030 Å2
ΔGint-148 kcal/mol
Surface area20440 Å2
MethodPISA
3
A: Phosphoribosylaminoimidazole succinocarboxamide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0676
Polymers27,3271
Non-polymers7405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Phosphoribosylaminoimidazole succinocarboxamide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1637
Polymers27,3271
Non-polymers8366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.890, 56.397, 56.410
Angle α, β, γ (deg.)76.39, 64.36, 64.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphoribosylaminoimidazole succinocarboxamide synthetase


Mass: 27327.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli)
References: UniProt: Q5L3D5, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate(pH4.6), 30%w/v PEG MME 2000 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 5, 2006
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 92845 / % possible obs: 93.9 % / Redundancy: 1.5 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.118 / Num. unique all: 9304 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GQS

2gqs


Resolution: 1.75→37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 233767.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4714 10.1 %RANDOM
Rwork0.188 ---
obs0.188 46761 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.8907 Å2 / ksol: 0.39902 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å21.18 Å21.19 Å2
2---1.63 Å2-2.31 Å2
3----0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 91 525 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 684 9.9 %
Rwork0.236 6193 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramligand.top
X-RAY DIFFRACTION3ligand.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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