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- PDB-5vkw: Crystal structure of adenylosuccinate lyase ADE13 from Candida al... -

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Basic information

Entry
Database: PDB / ID: 5vkw
TitleCrystal structure of adenylosuccinate lyase ADE13 from Candida albicans
ComponentsAdenylosuccinate lyase
KeywordsLYASE / adenylosuccinate lyase / adenylosuccinate / fumarate / AMP / purine biosynthesis / Candida albicans / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
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 / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / L-Aspartase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Adenylosuccinate lyase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: To Be Published
Title: Crystal structure of adenylosuccinate lyase ADE13 from Candida albicans
Authors: Stogios, P.J.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.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_symmetry

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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)109,76717
Polymers109,0212
Non-polymers74715
Water19,9791109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-119 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.030, 157.845, 374.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-505-

MG

21B-510-

MG

31A-861-

HOH

41A-923-

HOH

51A-963-

HOH

61A-1028-

HOH

71A-1146-

HOH

81B-612-

HOH

91B-817-

HOH

101B-917-

HOH

111B-919-

HOH

121B-1004-

HOH

131B-1016-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate lyase / / ASL / Adenylosuccinase


Mass: 54510.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ADE13, CAALFM_CR06150CA, orf19.3870 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1D8PT56, adenylosuccinate lyase

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Non-polymers , 6 types, 1124 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1109 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride, 0.1 M HEPES pH 7.5, 28% (w/v) PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 84905 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.063 / Rsym value: 0.163 / Net I/σ(I): 28.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 4200 / CC1/2: 0.576 / Rpim(I) all: 0.662 / Rsym value: 1.712 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VD6

2vd6


Resolution: 1.998→24.898 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1816 2.34 %RANDOM
Rwork0.1543 ---
obs0.1552 77571 91.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→24.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 34 1109 8634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117741
X-RAY DIFFRACTIONf_angle_d1.03310494
X-RAY DIFFRACTIONf_dihedral_angle_d19.5592908
X-RAY DIFFRACTIONf_chiral_restr0.0591203
X-RAY DIFFRACTIONf_plane_restr0.0071342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9984-2.05240.31471220.2555174X-RAY DIFFRACTION82
2.0524-2.11280.31761320.22475403X-RAY DIFFRACTION86
2.1128-2.18090.23331320.19395517X-RAY DIFFRACTION87
2.1809-2.25880.24071370.17795648X-RAY DIFFRACTION90
2.2588-2.34920.23011390.16865637X-RAY DIFFRACTION89
2.3492-2.45610.20681340.16395712X-RAY DIFFRACTION90
2.4561-2.58540.20571370.15555808X-RAY DIFFRACTION91
2.5854-2.74720.2141430.15335845X-RAY DIFFRACTION92
2.7472-2.9590.19461380.15535947X-RAY DIFFRACTION93
2.959-3.25620.21341450.15276028X-RAY DIFFRACTION94
3.2562-3.7260.18421480.146173X-RAY DIFFRACTION96
3.726-4.68930.14431520.12096307X-RAY DIFFRACTION97
4.6893-24.89980.17131570.15316556X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5739-2.0187-1.36343.7988-1.98794.98010.58770.3163-0.6602-0.6909-0.26050.62860.73-0.703-0.21730.3671-0.0411-0.12890.316-0.01220.449913.300613.4274149.4556
23.16020.27850.94033.40470.16532.39910.37280.4392-0.7493-0.75350.07330.28511.4064-0.6252-0.3180.6786-0.1801-0.13840.5756-0.13320.5005-6.237719.0079133.3518
30.7062-0.1490.00770.42840.06972.0670.0450.1589-0.0899-0.0672-0.04520.11480.1348-0.3102-0.02920.1480.0135-0.01130.1959-0.01880.23123.830236.4044151.6888
42.03430.28661.49170.76561.00752.9294-0.0121-0.11850.11090.09070.0283-0.0184-0.0634-0.0291-0.0250.21240.02690.030.1360.01230.236912.70554.8593186.5714
58.4774-4.2588-1.41494.355-0.96242.7417-0.29140.4431.0657-0.70250.24880.0439-0.9137-0.03680.16230.5888-0.01230.06370.30160.11830.475232.720662.763142.7956
61.6536-0.1641-1.74712.75911.01833.76490.0518-0.29990.1818-0.11010.059-0.377-0.13650.451-0.09770.21990.0446-0.0110.1991-0.00710.350518.833774.4014164.181
70.6057-0.0508-0.1670.49020.46971.62680.06290.24010.0747-0.1646-0.07790.0274-0.1936-0.13670.03670.2280.0789-0.010.2180.04460.208211.578452.5733139.7492
82.2104-0.5928-0.51711.65191.60393.6754-0.0450.6958-0.31-0.3382-0.14080.329-0.0232-0.41550.14930.41660.0474-0.03890.7159-0.00740.29393.995537.6787108.8465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:12)
2X-RAY DIFFRACTION2(chain A and resid 13:95)
3X-RAY DIFFRACTION3(chain A and resid 96:370)
4X-RAY DIFFRACTION4(chain A and resid 371:476)
5X-RAY DIFFRACTION5(chain B and resid 1:18)
6X-RAY DIFFRACTION6(chain B and resid 19:105)
7X-RAY DIFFRACTION7(chain B and resid 106:388)
8X-RAY DIFFRACTION8(chain B and resid 389:476)

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