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- PDB-4nzp: The crystal structure of argininosuccinate synthase from Campylob... -

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Basic information

Entry
Database: PDB / ID: 4nzp
TitleThe crystal structure of argininosuccinate synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsArgininosuccinate synthase
KeywordsLIGASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Argininosuccinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsTan, K. / Gu, M. / Zhang, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of argininosuccinate synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Tan, K. / Gu, M. / Zhang, R. / Anderson, W.F. / Joachimiak, A.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Argininosuccinate synthase


Theoretical massNumber of molelcules
Total (without water)45,9101
Polymers45,9101
Non-polymers00
Water2,522140
1
A: Argininosuccinate synthase

A: Argininosuccinate synthase

A: Argininosuccinate synthase

A: Argininosuccinate synthase


Theoretical massNumber of molelcules
Total (without water)183,6414
Polymers183,6414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area23880 Å2
ΔGint-154 kcal/mol
Surface area52160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.646, 97.360, 141.526
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-628-

HOH

DetailsExperimentally unknown. It is predicted that the chain A and its three symmetry-related monomers by operators of (-x-1,y,-z), (-x-1,-y,z) and (x,-y,-z) form a tetramer.

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Components

#1: Protein Argininosuccinate synthase / / Citrulline--aspartate ligase


Mass: 45910.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: argG, Campylobacter jejuni, Cj0665c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9PHK7, argininosuccinate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 10% (w/v) PEG6000, pH 7.0, 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: Nov 1, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 19759 / Num. obs: 19759 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 16.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1J1Z

1j1z


Resolution: 2.307→29.571 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 1009 5.11 %random
Rwork0.1798 ---
obs0.183 19732 98.32 %-
all-19732 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.307→29.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 0 140 3112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073034
X-RAY DIFFRACTIONf_angle_d1.0444105
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851104
X-RAY DIFFRACTIONf_chiral_restr0.07452
X-RAY DIFFRACTIONf_plane_restr0.005531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3072-2.42880.28111370.2292589X-RAY DIFFRACTION97
2.4288-2.58090.2631520.2092673X-RAY DIFFRACTION100
2.5809-2.78010.3111480.19712698X-RAY DIFFRACTION100
2.7801-3.05960.30911490.19972682X-RAY DIFFRACTION100
3.0596-3.50170.31241550.19282688X-RAY DIFFRACTION100
3.5017-4.40940.19341420.15192720X-RAY DIFFRACTION99
4.4094-29.57320.19161260.1692673X-RAY DIFFRACTION93
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)
11.45390.5215-1.63910.965-0.10214.1483-0.08440.4674-0.1094-0.38190.0993-0.1307-0.0148-0.1934-0.03090.44410.07840.02550.483-0.08590.3644-16.8631-15.4832-27.4663
21.37940.0579-0.21851.58540.06281.44660.0791-0.0367-0.23010.04370.0321-0.05260.36980.1635-0.10630.32370.035-0.05960.25060.0080.2426-25.5126-18.3751-0.0357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 188 )
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 406 )

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