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- PDB-4eei: Crystal Structure of Adenylosuccinate Lyase from Francisella tula... -

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Basic information

Entry
Database: PDB / ID: 4eei
TitleCrystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with AMP and Succinate
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha structure / AMP binding / beta-elimination / cytosole
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 / cytosol
Similarity search - Function
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) ...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
ADENOSINE MONOPHOSPHATE / : / SUCCINIC ACID / Adenylosuccinate lyase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis SCHU S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.921 Å
AuthorsMaltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with AMP and Succinate
Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,42327
Polymers100,3672
Non-polymers2,05625
Water10,827601
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,84654
Polymers200,7344
Non-polymers4,11250
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area36640 Å2
ΔGint-21 kcal/mol
Surface area59050 Å2
MethodPISA
2
A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,08722
Polymers100,3672
Non-polymers1,72020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10860 Å2
ΔGint0 kcal/mol
Surface area36480 Å2
MethodPISA
3
B: Adenylosuccinate lyase
hetero molecules

B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,75932
Polymers100,3672
Non-polymers2,39230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11560 Å2
ΔGint-29 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.759, 88.759, 254.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-852-

HOH

21B-734-

HOH

31B-871-

HOH

Detailstetramer is generated by applying x,y,z, and y,x,-z+1 to asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate lyase


Mass: 50183.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_0015, purB / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5NIQ1, adenylosuccinate lyase

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Non-polymers , 6 types, 626 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M succinic acid pH7.0, 0.1M HEPES pH7.0, 1% PEG MME 2000, 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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 78595 / Num. obs: 78595 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.5
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 4 / Num. unique all: 3857 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1C3U

1c3u


Resolution: 1.921→39.331 Å / SU ML: 0.12 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1893 2.54 %random
Rwork0.168 ---
all0.169 74476 --
obs0.169 74476 94.83 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.97 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.1718 Å20 Å2-0 Å2
2--6.1718 Å2-0 Å2
3----12.3437 Å2
Refinement stepCycle: LAST / Resolution: 1.921→39.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6751 0 127 601 7479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077192
X-RAY DIFFRACTIONf_angle_d0.9929674
X-RAY DIFFRACTIONf_dihedral_angle_d15.5542738
X-RAY DIFFRACTIONf_chiral_restr0.0641081
X-RAY DIFFRACTIONf_plane_restr0.0051237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9214-1.96940.27811260.22084695482187
1.9694-2.02270.26911230.20994803492689
2.0227-2.08220.24671310.20224882501391
2.0822-2.14940.23311250.18854955518092
2.1494-2.22620.21581310.17915028515993
2.2262-2.31540.19841290.1645051518094
2.3154-2.42070.19431360.16695126526295
2.4207-2.54830.21381330.1695147528095
2.5483-2.70790.21881380.17395234537196
2.7079-2.9170.20121390.18535304544397
2.917-3.21040.22111400.17825420556099
3.2104-3.67460.18411440.15654945638100
3.6746-4.62850.15631460.133855955741100
4.6285-39.33930.18631520.16858496001100
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)
10.394-0.0099-0.0050.3585-0.46683.8578-0.0187-0.04-0.05620.09990.02430.1450.0758-0.2549-0.01570.1566-0.00010.06540.1672-0.03040.2337-4.23310.9528142.5484
20.5268-0.120.32020.9554-0.86742.3385-0.00640.0258-0.05680.11280.03780.17430.0224-0.1597-0.03390.12610.00680.04680.1388-0.03850.18962.216112.0193134.8422
31.0212-0.65610.35572.83640.89083.24340.26520.6288-0.1114-0.9847-0.30490.3436-0.1772-0.18030.03650.41730.1064-0.1110.6947-0.04470.3787-12.022415.240790.3477
41.4724-0.54180.63061.0223-0.41181.17470.06270.2232-0.0879-0.0469-0.0716-0.11590.05590.28110.00790.123-0.00250.02030.1898-0.02020.149832.743417.1673117.5873
52.2736-2.2242-0.35795.44492.05583.46040.02650.26630.4141-0.2695-0.30580.5709-1.0936-0.99410.28190.57010.2137-0.06050.50080.09340.5567-3.338156.7301110.3878
62.0081-2.8828-1.66324.35860.83715.49370.01010.14311.0657-0.11940.0231-0.4845-0.45640.5922-0.04360.3823-0.04530.00320.28750.05690.332624.636449.8165111.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:173)
2X-RAY DIFFRACTION2chain 'A' and (resseq 174:333)
3X-RAY DIFFRACTION3chain 'A' and (resseq 334:433)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:333)
5X-RAY DIFFRACTION5chain 'B' and (resseq 334:418)
6X-RAY DIFFRACTION6chain 'B' and (resseq 419:438)

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