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- PDB-4o7t: SAICAR synthetase (Type-2) in complex with ADP, ASP and TMP -

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Basic information

Entry
Database: PDB / ID: 4o7t
TitleSAICAR synthetase (Type-2) in complex with ADP, ASP and TMP
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / SAICAR synthetase-like fold / ATP binding / CAIR binding / Aspartate binding
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 ...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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / ASPARTIC ACID / THYMIDINE-5'-PHOSPHATE / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsManjunath, K. / Jeyakanthan, J. / Sekar, K.
CitationJournal: To be Published
Title: SAICAR synthetase (Type-2) in complex with ADP, ASP and TMP
Authors: Manjunath, K. / Jeyakanthan, J. / Sekar, K.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: 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 / 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 / _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 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4816
Polymers27,4801
Non-polymers1,0015
Water1,856103
1
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules

A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,96112
Polymers54,9602
Non-polymers2,00110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5830 Å2
ΔGint-25 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.180, 155.290, 78.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-450-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 27480.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0239, purC / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: O57978, phosphoribosylaminoimidazolesuccinocarboxamide synthase

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Non-polymers , 5 types, 108 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ASP / ASPARTIC ACID


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Mosaicity: 0.64 °
Crystal growTemperature: 293 K / Method: microbatch underoil / pH: 4.6
Details: 0.2M Ammonium Sulphate, 0.1M Sodium acetate trihydrate, 30% w/v PEG monomethyl ether 2000, pH 4.6, Microbatch Underoil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2012 / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 15 / Number: 120337 / Rsym value: 0.041 / D res high: 2.1 Å / D res low: 77.645 Å / Num. obs: 15546 / % possible obs: 96.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
2.12.2194.510.1350.1357.8
2.212.3595.210.1390.1397.8
2.352.5195.810.0850.0857.8
2.512.7196.310.0640.0647.9
2.712.9797.110.0440.0447.8
2.973.3297.610.0340.0347.8
3.323.839810.0350.0357.7
3.834.798.410.0250.0257.7
4.76.6499.110.0220.0227.5
6.6442.4998.910.0190.0196.9
ReflectionResolution: 2.1→42.49 Å / Num. obs: 15546 / % possible obs: 96.6 % / Redundancy: 7.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 35.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 13.9 / Num. unique all: 17000 / % possible all: 94.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.49 Å
Translation2.5 Å42.49 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U55

3u55


Resolution: 2.1→42.49 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.846 / SU B: 4.493 / SU ML: 0.119 / SU R Cruickshank DPI: 0.229 / SU Rfree: 0.1856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 751 4.8 %RANDOM
Rwork0.1972 ---
obs0.199 15544 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.46 Å2 / Biso mean: 23.7 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--0.15 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 65 103 1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.2662.0222581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5824.9483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03115349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.067158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211402
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 51 -
Rwork0.199 1026 -
all-1077 -
obs--93.65 %

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