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- PDB-3gzh: Crystal structure of phosphate-bound adenylosuccinate lyase from ... -

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Basic information

Entry
Database: PDB / ID: 3gzh
TitleCrystal structure of phosphate-bound adenylosuccinate lyase from E. coli
ComponentsAdenylosuccinate lyase
KeywordsLYASE / all-helical fold / adenylosuccinate lyase / Structural Genomics / Bacterial Structural Genomics Initiative / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
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
PHOSPHATE ION / Adenylosuccinate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of phosphate-bound Escherichia coli adenylosuccinate lyase identifies His171 as a catalytic acid.
Authors: Kozlov, G. / Nguyen, L. / Pearsall, J. / Gehring, K.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9525
Polymers54,7161
Non-polymers2364
Water5,711317
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)219,80720
Polymers218,8634
Non-polymers94416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area35860 Å2
ΔGint-122.6 kcal/mol
Surface area59830 Å2
MethodPISA
2
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)219,80720
Polymers218,8634
Non-polymers94416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area17160 Å2
ΔGint-105.4 kcal/mol
Surface area78530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.316, 100.256, 150.104
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-914-

HOH

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Components

#1: Protein Adenylosuccinate lyase /


Mass: 54715.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs1603, purB, Z1860 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8X737, adenylosuccinate lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Sodium/potassium phosphate, 4% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 43947 / Num. obs: 40348 / % possible obs: 91.81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rsym value: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 2666 / Rsym value: 0.227 / % possible all: 84.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PTS

2pts


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.783 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2150 5.1 %RANDOM
Rwork0.16965 ---
all0.17185 40348 --
obs0.17185 40348 91.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.439 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--3.22 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 12 317 4052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223839
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9565221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92224.231182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37915657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3561524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022918
X-RAY DIFFRACTIONr_nbd_refined0.2110.21813
X-RAY DIFFRACTIONr_nbtor_refined0.310.22687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.2182
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.264
X-RAY DIFFRACTIONr_mcbond_it0.7921.52351
X-RAY DIFFRACTIONr_mcangle_it1.4823795
X-RAY DIFFRACTIONr_scbond_it2.70231543
X-RAY DIFFRACTIONr_scangle_it4.3414.51421
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 136 -
Rwork0.199 2666 -
obs--83.19 %

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