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- PDB-1p9b: Structure of fully ligated Adenylosuccinate synthetase from Plasm... -

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Basic information

Entry
Database: PDB / ID: 1p9b
TitleStructure of fully ligated Adenylosuccinate synthetase from Plasmodium falciparum
ComponentsAdenylosuccinate Synthetase
KeywordsLIGASE
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / HADACIDIN / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE / NITRATE ION / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEaazhisai, K. / Jayalakshmi, R. / Gayathri, P. / Anand, R.P. / Sumathy, K. / Balaram, H. / Murthy, M.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of Fully Ligated Adenylosuccinate Synthetase from Plasmodium falciparum.
Authors: Eaazhisai, K. / Jayalakshmi, R. / Gayathri, P. / Anand, R.P. / Sumathy, K. / Balaram, H. / Murthy, M.R.
History
DepositionMay 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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 / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1666
Polymers50,0891
Non-polymers1,0775
Water5,008278
1
A: Adenylosuccinate Synthetase
hetero molecules

A: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,33112
Polymers100,1772
Non-polymers2,15410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9230 Å2
ΔGint-61 kcal/mol
Surface area30170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.579, 117.117, 80.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: -X,Y,1/2-Z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenylosuccinate Synthetase


Mass: 50088.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9U8D3, adenylosuccinate synthase

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Non-polymers , 6 types, 283 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-IMO / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O11P2
#5: Chemical ChemComp-HDA / HADACIDIN


Mass: 119.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5NO4 / Comment: medication*YM
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.08 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: PEG4000, Sodium cacodylate, pH 6.5, LIQUID DIFFUSION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
25 mMligands1drop
350 mMmagnesium acetate1drop
4100 mMsodium cacodylate1reservoirpH6.5
520-25 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.91 Å / Num. all: 164288 / Num. obs: 28913 / Redundancy: 5.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2833 / Rsym value: 0.36
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 29594 / % possible obs: 97.8 % / Num. measured all: 358593 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 97.1 % / Rmerge(I) obs: 0.363

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CIB

1cib


Resolution: 2→32.91 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 825 -random
Rwork0.199 ---
all-28327 --
obs-27502 93 %-
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.319 Å20 Å20 Å2
2--8.441 Å20 Å2
3----4.122 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 68 278 3697
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.294 --
Rwork0.244 --
obs-4336 92.1 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.331
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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