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- PDB-2qga: Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound -

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Basic information

Entry
Database: PDB / ID: 2qga
TitlePlasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound
ComponentsAdenylosuccinate lyase
KeywordsLYASE / malaria / adenylosuccinate lyase / Pv003765 / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
: / Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...: / Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Adenylosuccinate lyase / Adenylosuccinate lyase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLunin, V.V. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. ...Lunin, V.V. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Hills, T. / Altamentova, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Plasmodium vivax adenylosuccinate lyase Pv003765 with AMP bound
Authors: Lunin, V.V. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Hills, T. / Altamentova, S. / ...Authors: Lunin, V.V. / Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Sundstrom, M. / Weigelt, J. / Edwards, A.E. / Hui, R. / Hills, T. / Altamentova, S. / Structural Genomics Consortium (SGC)
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors state that the sequence is obtained from Pv003765 (www.plasmodb.org). Electron ...SEQUENCE The authors state that the sequence is obtained from Pv003765 (www.plasmodb.org). Electron density maps also support lysine at position 364.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,65510
Polymers106,4962
Non-polymers1,1598
Water15,006833
1
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
hetero molecules

B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,31020
Polymers212,9924
Non-polymers2,31816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area36250 Å2
ΔGint-268 kcal/mol
Surface area59050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.247, 179.545, 68.575
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-901-

CA

21C-902-

CA

31B-1252-

HOH

41C-1013-

HOH

51C-1123-

HOH

61C-1262-

HOH

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Components

#1: Protein Adenylosuccinate lyase


Mass: 53248.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: asl / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a
References: UniProt: Q8WSJ9, UniProt: A5KBL5*PLUS, adenylosuccinate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M Ammonia Sulfate, 0.2M K/Na Tartrate, 0.1M Na Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 93338 / Num. obs: 93338 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.102 / Net I/σ(I): 13.48
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 9285 / Rsym value: 0.54 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hvg

2hvg


Resolution: 2.01→33.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.183 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21013 4686 5 %RANDOM
Rwork0.1752 ---
obs0.17693 88647 99.82 %-
all-88647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.08 Å2
2---1.11 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7297 0 68 833 8198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.96410231
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72324.644351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.468151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0811536
X-RAY DIFFRACTIONr_chiral_restr0.1070.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025576
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23797
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.25302
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2614
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.2183
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.270
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.050.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.54738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49927389
X-RAY DIFFRACTIONr_scbond_it2.42833234
X-RAY DIFFRACTIONr_scangle_it3.6264.52841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 349 -
Rwork0.235 6416 -
obs--98.66 %

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