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- PDB-4u7j: Crystal structure of Argininosuccinate synthase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4u7j
TitleCrystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile
ComponentsArgininosuccinate synthase
KeywordsLIGASE / SSGCID / Argininosuccinate synthase / Citrulline-aspartate ligase / Mycobacterium thermoresistibile / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / L-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 ...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 / Arginosuccinate synthase C-terminal 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
Argininosuccinate synthase
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Argininosuccinate synthase from Mycobacterium thermoresistibile
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fischer, E.S. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / 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_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)91,23317
Polymers90,3552
Non-polymers87815
Water13,421745
1
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,46634
Polymers180,7114
Non-polymers1,75630
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area31470 Å2
ΔGint-93 kcal/mol
Surface area52090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.940, 144.440, 57.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#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 (bacteria)
Strain: ATCC 19527 / Gene: argG, KEK_01915 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7CBN9, argininosuccinate synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents JCSG+ screen, D6: 20% PEG 8000, 200mM MgCl2, 100mM Tris/HCl pH 8.5; cryo 20% EG; MythA.00809.a.B1.PW37508 at 30.1mg/ml, tray 256225d6, puck zrb0-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 80159 / Num. obs: 80159 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.15 % / Biso Wilson estimate: 18.98 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Χ2: 0.979 / Net I/σ(I): 22.11 / Num. measured all: 493282
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.86.170.8580.5283.3936061583858380.578100
1.8-1.840.9050.4284.2235283570056990.468100
1.84-1.90.9380.3345.4234498557855770.365100
1.9-1.960.9630.2636.933306539153900.288100
1.96-2.020.9750.2098.6132517524652430.22899.9
2.02-2.090.9860.15411.4831323507650710.16999.9
2.09-2.170.990.13113.4130403490248960.14399.9
2.17-2.260.9940.10416.6229319473847360.114100
2.26-2.360.9950.08819.0628206453745350.096100
2.36-2.470.9970.07821.3226934433643350.085100
2.47-2.610.9980.06325.2925744414541430.069100
2.61-2.770.9980.05330.0224423394839460.05899.9
2.77-2.960.9990.04534.1722706366436620.0599.9
2.96-3.20.9990.03839.7321440347834770.041100
3.2-3.50.9990.03147.3319444317531740.034100
3.5-3.910.9990.02654.3617798292229220.029100
3.91-4.520.9990.02458.6715642257725770.026100
4.52-5.530.9990.02359.0613215221022100.026100
5.53-7.830.9990.02556.4110056173717360.02899.9
7.830.9990.02260.07496410229920.02497.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.91 Å46.65 Å
Translation3.91 Å46.65 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
ARPmodel building
PHENIX(phenix.refine: dev_1756)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kh1 modified with CCP4 program CHAINSAW

1kh1


Resolution: 1.75→44.668 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3972 4.96 %Random selection
Rwork0.1455 76169 --
obs0.1473 80141 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.5 Å2 / Biso mean: 23.8913 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: final / Resolution: 1.75→44.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 54 745 6829
Biso mean--34.16 31.8 -
Num. residues----785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076281
X-RAY DIFFRACTIONf_angle_d1.0458540
X-RAY DIFFRACTIONf_chiral_restr0.044969
X-RAY DIFFRACTIONf_plane_restr0.0051116
X-RAY DIFFRACTIONf_dihedral_angle_d11.9312275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.77130.26791250.196326712796100
1.7713-1.79380.24351490.184526772826100
1.7938-1.81740.19671270.181727172844100
1.8174-1.84230.20161270.173426882815100
1.8423-1.86860.19971590.164426862845100
1.8686-1.89650.22081320.163226822814100
1.8965-1.92610.22141300.163727242854100
1.9261-1.95770.20561640.157726522816100
1.9577-1.99150.22261310.153127092840100
1.9915-2.02770.19721530.151726562809100
2.0277-2.06670.1831520.144627112863100
2.0667-2.10890.18091470.136926602807100
2.1089-2.15470.18121440.135627272871100
2.1547-2.20480.17411490.131626782827100
2.2048-2.260.15911440.131427102854100
2.26-2.32110.1481600.13226812841100
2.3211-2.38940.17591350.141127092844100
2.3894-2.46650.19891390.148427222861100
2.4665-2.55460.16791440.14727232867100
2.5546-2.65690.16821470.135127132860100
2.6569-2.77780.15271260.14427532879100
2.7778-2.92420.21051480.148527192867100
2.9242-3.10740.18491450.150827202865100
3.1074-3.34720.18221280.152127832911100
3.3472-3.68390.20831270.139127712898100
3.6839-4.21670.16731480.129627842932100
4.2167-5.31120.1411480.13228232971100
5.3112-44.68220.1921440.162920306499
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)
14.77560.8117-0.3080.6216-0.29511.0250.0170.3478-0.0661-0.0750.0104-0.2307-0.02690.2507-0.02040.1871-0.01420.03430.1858-0.03630.211677.264616.243342.9592
21.84520.2629-0.36640.9523-0.23180.2058-0.0289-0.0516-0.0404-0.01940.0113-0.2633-0.03920.08710.01630.171-0.0156-0.00650.1694-0.02180.275.330312.863852.4961
30.3331-0.01440.03620.4255-0.08380.3872-0.02550.00010.0466-0.00370.0236-0.0346-0.07690.0401-0.00040.1445-0.00120.00010.1254-0.00620.125652.926920.500755.2517
41.261-0.0028-0.27862.8283-2.75073.0196-0.1002-0.00310.05650.17260.33650.3444-0.226-0.3948-0.26410.17730.0095-0.00480.1423-0.02470.188223.58758.63964.0783
54.1997-3.33794.69473.7639-3.67668.84150.02910.04920.0234-0.239-0.07460.4946-0.3524-0.75150.00170.3020.12640.05590.33880.04350.381210.572319.885181.2097
63.3346-0.249-0.75821.04420.24981.56830.0341-0.31970.24010.21290.0450.4039-0.2448-0.2948-0.04970.26030.06470.08580.2330.00430.270324.050722.330986.6303
71.1582-0.1585-0.16121.1234-0.04930.9890.00550.0440.02530.08450.06350.302-0.1455-0.2773-0.03070.18890.05710.02440.19470.02640.193622.62716.386575.4304
80.3810.19860.33250.51860.29951.0964-0.0233-0.05560.06840.0162-0.00210.0646-0.0899-0.09220.01540.1560.03420.00550.133-0.00550.140540.307628.594270.7579
90.294-0.1024-0.10770.58470.11570.2718-0.02650.0036-0.00290.06640.0512-0.10350.00170.0569-0.02740.11350.0071-0.01620.1098-0.00850.091657.039510.112870.6208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 78 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 186 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 354 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 355 through 398 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 26 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 78 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 79 through 181 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 274 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 275 through 398 )B0

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