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- PDB-4xfj: Crystal structure of Argininosuccinate synthase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4xfj
TitleCrystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine
ComponentsArgininosuccinate synthase
KeywordsLIGASE / SSGCID / Argininosuccinate synthase / Citrulline--aspartate ligase / Mycobacterium thermoresistibile / AMPPNP / Arginine / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Single helix bin / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. ...Single helix bin / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ARGININE / Argininosuccinate synthase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile in complex with AMPPNP and Arginine
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,16315
Polymers90,3552
Non-polymers1,80813
Water15,079837
1
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,32730
Polymers180,7114
Non-polymers3,61626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area32150 Å2
ΔGint-127 kcal/mol
Surface area50210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.830, 143.410, 58.030
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 Argininosuccinate synthase / Citrulline--aspartate ligase


Mass: 45177.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria)
Gene: argG, KEK_01915 / Plasmid: MythA.00809.a.B1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CBN9, argininosuccinate synthase

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Non-polymers , 5 types, 850 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.76
Details: Optimization screen: 100mM Tris pH 8.67, 200mM MgCl2, 20% PEG 8000; MythA.00809.a.B1.PW37508 at 20.mg/ml with 5mM AMPPNP, 5mM Arg, 2.5mM MgCl2; cryo: 20% EG, 2.5mM AMPPNP, 5mM Arg, 0.5mM ...Details: Optimization screen: 100mM Tris pH 8.67, 200mM MgCl2, 20% PEG 8000; MythA.00809.a.B1.PW37508 at 20.mg/ml with 5mM AMPPNP, 5mM Arg, 2.5mM MgCl2; cryo: 20% EG, 2.5mM AMPPNP, 5mM Arg, 0.5mM MgCl2, 5mM Asp; tray 258539d3, puck yyj4-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 114110 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.05 / Χ2: 0.978 / Net I/σ(I): 23.4 / Num. measured all: 558771
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.594.90.8220.4653.3141003836983600.5299.9
1.59-1.630.8840.3794.1140022814981440.42499.9
1.63-1.680.9050.3154.8939018794679440.353100
1.68-1.730.9380.2566.0337879770877070.287100
1.73-1.790.9570.2057.5636862750474960.22999.9
1.79-1.850.9740.1649.4235503724472360.18499.9
1.85-1.920.9840.12812.0734230700470000.14399.9
1.92-20.9890.10215.0832950676867610.11499.9
2-2.090.9940.07420.131505646864580.08299.8
2.09-2.190.9960.0624.0130123619061730.06899.7
2.19-2.310.9970.0528.428928592758950.05699.5
2.31-2.450.9980.04431.4927395559855740.04999.6
2.45-2.620.9980.03736.5125929527352350.04299.3
2.62-2.830.9990.03142.6424130493648820.03598.9
2.83-3.10.9990.02748.3522159453044910.0399.1
3.1-3.470.9990.02257.8220183414341120.02599.3
3.47-40.9990.01967.3117869366736620.02199.9
4-4.910.01671.2815286313931330.01899.8
4.9-6.9310.01767.8911729246424580.01999.8
6.93-5010.01572.526068144913890.01795.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: dev_1894)refinement
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u7j

4u7j


Resolution: 1.55→36.896 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 4897 4.3 %Random selection
Rwork0.1358 108917 --
obs0.1378 113814 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 22.417 Å2 / Biso min: 7.45 Å2
Refinement stepCycle: final / Resolution: 1.55→36.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6065 0 114 840 7019
Biso mean--34 30.99 -
Num. residues----792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096476
X-RAY DIFFRACTIONf_angle_d1.2318847
X-RAY DIFFRACTIONf_chiral_restr0.051996
X-RAY DIFFRACTIONf_plane_restr0.0061152
X-RAY DIFFRACTIONf_dihedral_angle_d12.7082355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.241620.1663595375799
1.5676-1.58610.23221590.156335713730100
1.5861-1.60540.21441630.149136073770100
1.6054-1.62570.21231600.143835713731100
1.6257-1.64710.21511640.142936453809100
1.6471-1.66970.21551600.134535723732100
1.6697-1.69350.19921630.128536103773100
1.6935-1.71880.19651610.130636023763100
1.7188-1.74570.20841610.126535913752100
1.7457-1.77430.18531640.123436383802100
1.7743-1.80490.20151620.123536053767100
1.8049-1.83770.14641610.123235893750100
1.8377-1.87310.19841640.124636273791100
1.8731-1.91130.19841620.125436113773100
1.9113-1.95280.20691610.123135973758100
1.9528-1.99830.15961640.128536363800100
1.9983-2.04820.17781620.125236193781100
2.0482-2.10360.1881620.122636103772100
2.1036-2.16550.17141650.120836123777100
2.1655-2.23540.19261640.121936463810100
2.2354-2.31530.17081630.12613610377399
2.3153-2.4080.17461640.129736403804100
2.408-2.51750.19511630.135936303793100
2.5175-2.65020.17691630.13373615377899
2.6502-2.81620.18411620.14013626378899
2.8162-3.03360.18271640.14883654381899
3.0336-3.33870.1881670.14673671383899
3.3387-3.82130.15041640.133136983862100
3.8213-4.81280.15391690.134237623931100
4.8128-36.90690.19981740.16283857403199

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