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- PDB-2x75: Staphylococcus aureus adenylosuccinate lyase -

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Basic information

Entry
Database: PDB / ID: 2x75
TitleStaphylococcus aureus adenylosuccinate lyase
ComponentsADENYLOSUCCINATE LYASE
KeywordsLYASE / PURINE CYCLE / PURINE BIOSYNTHESIS
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
Similarity search - Function
Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / 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 / OXALATE ION / : / Adenylosuccinate lyase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFyfe, P.K. / Dawson, A. / Hutchison, M.T. / Cameron, S. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of Staphylococcus Aureus Adenylosuccinate Lyase (Purb) and Assessment of its Potential as a Target for Structure-Based Inhibitor Discovery.
Authors: Fyfe, P.K. / Dawson, A. / Hutchison, M.T. / Cameron, S. / Hunter, W.N.
History
DepositionFeb 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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 LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4225
Polymers49,6691
Non-polymers7534
Water1,26170
1
A: ADENYLOSUCCINATE LYASE
hetero molecules

A: ADENYLOSUCCINATE LYASE
hetero molecules

A: ADENYLOSUCCINATE LYASE
hetero molecules

A: ADENYLOSUCCINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,68920
Polymers198,6774
Non-polymers3,01216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area33880 Å2
ΔGint-121.2 kcal/mol
Surface area57710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.647, 121.265, 105.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2058-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADENYLOSUCCINATE LYASE /


Mass: 49669.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 35556 / Description: AMERICAN TYPE CULTURE COLLECTION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS
References: UniProt: C8LPI8, UniProt: Q7A0G9*PLUS, adenylosuccinate lyase

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Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPOLYETHYLENE GLYCOL PEG200 (P6G): PEG 200 USED IN CRYSTALLISATION

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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: 2.64 Å3/Da / Density % sol: 53.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9728
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9728 Å / Relative weight: 1
ReflectionResolution: 2.5→97 Å / Num. obs: 17795 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3C

1c3c


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.897 / SU B: 34.356 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.773 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28474 888 5.2 %RANDOM
Rwork0.21438 ---
obs0.21772 16310 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.805 Å2
Baniso -1Baniso -2Baniso -3
1-10.2 Å2-0 Å20 Å2
2---4.75 Å2-0 Å2
3----5.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 49 70 3578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223604
X-RAY DIFFRACTIONr_bond_other_d0.0010.022465
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9584874
X-RAY DIFFRACTIONr_angle_other_deg0.8553.0015953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58824.144181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38615645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5331529
X-RAY DIFFRACTIONr_chiral_restr0.060.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3691.52145
X-RAY DIFFRACTIONr_mcbond_other0.0731.5866
X-RAY DIFFRACTIONr_mcangle_it0.66323484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.87331459
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4354.51390
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 71 -
Rwork0.32 1221 -
obs--95.21 %
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)
10.35911.12670.87094.24792.22422.60340.0603-0.0190.00890.4535-0.07250.0262-0.03330.23010.01230.4015-0.0463-0.02220.5672-0.03170.351315.84813.51326.616
20.08670.49420.17013.10820.66713.1950.04710.00370.05970.2930.10280.07640.63180.4557-0.14990.13380.0995-0.01760.5785-0.00290.477715.03-10.1717.869
30.3109-0.3005-0.24912.75460.47652.3526-0.0383-0.0073-0.0334-0.13420.0160.13320.83210.2020.02230.44730.098-0.04990.45660.0090.352211.253-25.892-3.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 118
2X-RAY DIFFRACTION2A119 - 269
3X-RAY DIFFRACTION3A270 - 431

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