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- PDB-4fe2: X-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 4fe2
TitleX-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pneumoniae complexed with AIR, ADP, Asp and Mg2+
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / alpha/beta protein / SAICAR synthetase / CAIR / Asp
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol
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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE / ASPARTIC ACID / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.288 Å
AuthorsWolf, N. / Abad-Zapatero, C. / Johnson, M.E. / Fung, L.M.-W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg(2+), AIR and Asp.
Authors: Wolf, N.M. / Abad-Zapatero, C. / Johnson, M.E. / Fung, L.W.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Sep 13, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,62615
Polymers58,4162
Non-polymers2,21013
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-38 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.074, 65.021, 86.052
Angle α, β, γ (deg.)90.00, 92.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 29208.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: purC, SP_0044 / Production host: Escherichia coli (E. coli)
References: UniProt: Q07296, phosphoribosylaminoimidazolesuccinocarboxamide synthase

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Non-polymers , 8 types, 427 molecules

#2: Chemical ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE


Mass: 295.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N3O7P
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#8: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG 200, 0.16 Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.288→85.995 Å / Num. all: 22985 / Num. obs: 21601 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 25.9
Reflection shellResolution: 2.288→2.3 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GQR

2gqr


Resolution: 2.288→85.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.88 / SU B: 8.317 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28431 1164 5.1 %RANDOM
Rwork0.19641 ---
obs0.20078 21601 98.51 %-
all-22985 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.709 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å20 Å22.44 Å2
2---2.58 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.288→85.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 140 414 4356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9975415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.355466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41625.678199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48415729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022952
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.288→2.347 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 54 -
Rwork0.204 1362 -
obs--86.76 %

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