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- PDB-2hvg: Crystal Structure of Adenylosuccinate Lyase from Plasmodium Vivax -

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Basic information

Entry
Database: PDB / ID: 2hvg
TitleCrystal Structure of Adenylosuccinate Lyase from Plasmodium Vivax
ComponentsAdenylosuccinate lyase
KeywordsLYASE / alpha helical / Structural Genomics / Structural Genomics Consortium / SGC
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
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 / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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
Adenylosuccinate lyase / Adenylosuccinate lyase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWernimont, A.K. / Dong, A. / Lew, J. / Wasney, G.A. / Vedadi, M. / Ren, H. / Alam, Z. / Qiu, W. / Kozieradzki, I. / Weigelt, J. ...Wernimont, A.K. / Dong, A. / Lew, J. / Wasney, G.A. / Vedadi, M. / Ren, H. / Alam, Z. / Qiu, W. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJul 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Remark 999SEQUENCE Authors state that LYS at position 364 is correct.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,08615
Polymers110,8372
Non-polymers1,24913
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-185 kcal/mol
Surface area37620 Å2
MethodPISA
2
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,17130
Polymers221,6744
Non-polymers2,49826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area35180 Å2
ΔGint-506 kcal/mol
Surface area59390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.419, 177.599, 68.613
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-872-

HOH

21B-662-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 3 / Auth seq-ID: 3 - 445 / Label seq-ID: 22 - 464

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Adenylosuccinate lyase


Mass: 55418.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: p28a-thrombin-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Oxford
References: UniProt: Q8WSJ9, UniProt: A5KBL5*PLUS, adenylosuccinate lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7 M NH42SO4, 0.1 M Na Citrate, 0.2 M K/Na Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 62678 / Num. obs: 62489 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 6.03 / Num. unique all: 6259 / Rsym value: 0.212 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.767 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25078 3170 5.1 %RANDOM
Rwork0.20694 ---
all0.21001 62489 --
obs0.20919 59305 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.342 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20.3 Å2
2---2.34 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7154 0 65 564 7783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9619944
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78124.524336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3061534
X-RAY DIFFRACTIONr_chiral_restr0.0980.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025384
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23587
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25096
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.2146
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.54591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16627208
X-RAY DIFFRACTIONr_scbond_it1.92133111
X-RAY DIFFRACTIONr_scangle_it2.9694.52736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1724tight positional0.030.05
1706loose positional0.345
1724tight thermal0.170.5
1706loose thermal1.2210
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 231 -
Rwork0.214 4196 -
obs-4196 95.7 %

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