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- PDB-4efc: Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Bruc... -

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Basic information

Entry
Database: PDB / ID: 4efc
TitleCrystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560
ComponentsAdenylosuccinate lyase
KeywordsLYASE / purine biosynthesis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / 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 / glycosome / 'de novo' IMP biosynthetic process / nucleotide binding / nucleoplasm / metal ion binding / cytoplasm
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
ADENOSINE MONOPHOSPHATE / Adenylosuccinate lyase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWernimont, A.K. / Loppnau, P. / Osman, K.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Robinson, D.A. / Wyatt, P.G. / Gilbert, I.H. / Fairlamb, A.H. ...Wernimont, A.K. / Loppnau, P. / Osman, K.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Robinson, D.A. / Wyatt, P.G. / Gilbert, I.H. / Fairlamb, A.H. / Hui, R. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Adenylosuccinate Lyase from Trypanosoma Brucei, Tb427tmp.160.5560
Authors: Wernimont, A.K. / Loppnau, P. / Osman, K.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Robinson, D.A. / Wyatt, P.G. / Gilbert, I.H. / Hui, R. / Lin, Y.H.
History
DepositionMar 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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)107,39410
Polymers106,4802
Non-polymers9148
Water12,773709
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,78820
Polymers212,9604
Non-polymers1,82916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area39700 Å2
ΔGint-211 kcal/mol
Surface area54830 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-56 kcal/mol
Surface area38120 Å2
MethodPISA
3
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,39410
Polymers106,4802
Non-polymers9148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area4320 Å2
ΔGint-27 kcal/mol
Surface area42940 Å2
MethodPISA
4
A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,39610
Polymers106,4802
Non-polymers9168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area8410 Å2
ΔGint-60 kcal/mol
Surface area38820 Å2
MethodPISA
5
B: Adenylosuccinate lyase
hetero molecules

B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,39310
Polymers106,4802
Non-polymers9138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9340 Å2
ΔGint-69 kcal/mol
Surface area37950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.768, 140.744, 60.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate lyase /


Mass: 53239.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb09.160.5560 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38EJ2, adenylosuccinate lyase

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Non-polymers , 5 types, 717 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.1 M Na Formate, 0.1 M Tris pH 8, 5 mM AMP, 5 mM MgCL2, 1 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 63013 / Num. obs: 62887 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.124 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 2993 / Rsym value: 0.626 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.164 / WRfactor Rwork: 0.1322 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9132 / SU B: 6.938 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1706 / SU Rfree: 0.1455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3179 5.1 %RANDOM
Rwork0.1487 ---
all0.1508 62864 --
obs0.1508 62607 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.21 Å2 / Biso mean: 17.7924 Å2 / Biso min: 4.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7154 0 58 709 7921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227784
X-RAY DIFFRACTIONr_bond_other_d0.0010.025305
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.96810621
X-RAY DIFFRACTIONr_angle_other_deg0.913312923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3995986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72123.286350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.871151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8841564
X-RAY DIFFRACTIONr_chiral_restr0.0750.21205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218762
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021658
X-RAY DIFFRACTIONr_mcbond_it0.5241.54771
X-RAY DIFFRACTIONr_mcbond_other0.1321.51899
X-RAY DIFFRACTIONr_mcangle_it0.96427793
X-RAY DIFFRACTIONr_scbond_it1.6533013
X-RAY DIFFRACTIONr_scangle_it2.6824.52823
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 247 -
Rwork0.211 4258 -
all-4505 -
obs--98.77 %
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)
10.21630.0932-0.01670.21710.00590.02440.0302-0.0508-0.03750.0239-0.0374-0.03020.01540.01570.00720.0314-0.0087-0.0050.03420.01630.0097-47.6327-11.037529.6553
20.2773-0.1148-0.03480.2315-0.01950.09350.01320.0333-0.0465-0.0538-0.02730.03150.0337-0.01490.01410.04230.0037-0.00680.0223-0.0120.0117-58.8733-11.51540.9646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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