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- PDB-3bhg: Crystal structure of adenylosuccinate lyase from Legionella pneum... -

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Basic information

Entry
Database: PDB / ID: 3bhg
TitleCrystal structure of adenylosuccinate lyase from Legionella pneumophila
ComponentsAdenylosuccinate lyase
KeywordsLYASE / adenylosuccinate lyase / Legionella pneumophila / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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 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 ...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
Adenylosuccinate lyase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Li, H. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of adenylosuccinate lyase from Legionella pneumophila.
Authors: Chang, C. / Li, H. / Freeman, L. / Joachimiak, A.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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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)52,5784
Polymers52,2931
Non-polymers2843
Water4,918273
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)210,31116
Polymers209,1744
Non-polymers1,13712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.216, 109.216, 157.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

21A-751-

HOH

31A-760-

HOH

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Components

#1: Protein Adenylosuccinate lyase


Mass: 52293.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Species: Legionella pneumophila / Strain: Philadelphia 1, DSM 7513 / Gene: lpg0801 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q5ZXD1, adenylosuccinate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-tris, 2.0 M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 37623 / Num. obs: 37453 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 18.3 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 59
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 16.1 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 4.75 / Num. unique all: 3650 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.416 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19529 1861 5 %RANDOM
Rwork0.1663 ---
all0.16772 37130 --
obs0.16772 37130 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.611 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---1.65 Å20 Å2
3---3.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 16 273 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223618
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9514918
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62924.909165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41615614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6971516
X-RAY DIFFRACTIONr_chiral_restr0.090.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022724
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21716
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22555
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.2156
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.244
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.52306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09723631
X-RAY DIFFRACTIONr_scbond_it1.96231473
X-RAY DIFFRACTIONr_scangle_it2.9884.51283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 128 -
Rwork0.231 2486 -
obs--95.3 %
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)
14.8114.3498-0.58859.5139-0.7360.51080.1847-0.0810.30510.45390.01680.3713-0.5203-0.3783-0.2015-0.01490.09650.061-0.02460.0152-0.0273-17.422318.81245.8039
21.9048-0.0551-1.54492.4283-0.64614.01960.17840.18920.308-0.1878-0.09790.0353-0.7798-0.4038-0.08050.11360.1102-0.0152-0.15380.0678-0.0254-7.077535.2906-18.6316
30.28570.02280.00750.3674-0.00050.89620.01070.0210.07430.080.00540.0086-0.18060.0199-0.0161-0.0257-0.00240.0094-0.0951-0.00020.00983.014816.81034.7497
42.51961.8596-1.57531.5478-0.2515.7280.0165-0.32120.27360.41120.2022-0.0843-0.2125-0.1263-0.21870.03150.0307-0.0413-0.00710.0144-0.003213.1512.440633.1994
510.8471-2.4464-1.48851.1276-0.1755.9065-0.1645-0.7962-0.75010.47210.0992-0.13460.56130.63850.06530.17170.0777-0.13180.07920.0548-0.101325.0722-2.049940.9997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 226 - 25
2X-RAY DIFFRACTION2AA23 - 12126 - 124
3X-RAY DIFFRACTION3AA122 - 371125 - 374
4X-RAY DIFFRACTION4AA372 - 380375 - 383
5X-RAY DIFFRACTION4AA445 - 456448 - 459
6X-RAY DIFFRACTION5AA381 - 444384 - 447

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