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- PDB-6e5y: 1.50 Angstrom Resolution Crystal Structure of Argininosuccinate S... -

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Basic information

Entry
Database: PDB / ID: 6e5y
Title1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.
ComponentsArgininosuccinate synthase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Argininosuccinate Synthase / AMP
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / arginine biosynthetic process / protein homodimerization activity / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. ...Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / 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 / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / MALONIC ACID / Argininosuccinate synthase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.50 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis in Complex with AMP.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,65312
Polymers49,6471
Non-polymers1,00511
Water8,935496
1
A: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,30524
Polymers99,2942
Non-polymers2,01122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area15650 Å2
ΔGint-219 kcal/mol
Surface area34110 Å2
MethodPISA
2
A: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,61048
Polymers198,5894
Non-polymers4,02244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area42370 Å2
ΔGint-478 kcal/mol
Surface area57140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.287, 97.287, 93.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-869-

HOH

21A-951-

HOH

31A-1028-

HOH

41A-1074-

HOH

51A-1088-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49647.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: argG, BP3537 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7VTJ9, argininosuccinate synthase

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Non-polymers , 6 types, 507 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 0.01mM ATP, 0.1mM Magnesium chloride; Screen: Classics II (A3), 2M Ammonium sulfate, 0.1 Bis-Tris (pH 5.5); Cryo: ...Details: Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 0.01mM ATP, 0.1mM Magnesium chloride; Screen: Classics II (A3), 2M Ammonium sulfate, 0.1 Bis-Tris (pH 5.5); Cryo: Reservoir + 25% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 72217 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Rsym value: 0.065 / Χ2: 1.011 / Net I/σ(I): 24.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3525 / CC1/2: 0.807 / Rpim(I) all: 0.37 / Rrim(I) all: 0.908 / Rsym value: 0.826 / Χ2: 0.995 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5US8

5us8


Resolution: 1.5→29.59 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.968 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17856 3684 5.1 %RANDOM
Rwork0.1545 ---
obs0.15575 68161 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.84 Å20 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 57 496 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0144129
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173628
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.6755650
X-RAY DIFFRACTIONr_angle_other_deg0.451.6388552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.385539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.88521.568236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.56715709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0111538
X-RAY DIFFRACTIONr_chiral_restr0.0670.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0440.024903
X-RAY DIFFRACTIONr_gen_planes_other0.040.02772
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.351.6252045
X-RAY DIFFRACTIONr_mcbond_other1.3491.6222044
X-RAY DIFFRACTIONr_mcangle_it2.0972.432621
X-RAY DIFFRACTIONr_mcangle_other2.0972.4332622
X-RAY DIFFRACTIONr_scbond_it2.1631.9082083
X-RAY DIFFRACTIONr_scbond_other2.1471.9072081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2862.7693028
X-RAY DIFFRACTIONr_long_range_B_refined5.19820.2994662
X-RAY DIFFRACTIONr_long_range_B_other5.03319.514550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 232 -
Rwork0.246 4987 -
obs--99.94 %
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)
10.34580.3452-0.68480.3626-0.71441.63720.0539-0.1036-0.01810.0376-0.0727-0.0037-0.02830.11460.01880.0618-0.0240.0160.10640.02380.093796.3918-21.687827.837
24.6367-0.8654-4.07276.55211.04795.2913-0.085-0.77640.00430.01370.1403-0.67120.25740.6707-0.05520.0527-0.0242-0.06340.33470.08440.1907109.0399-27.664442.9714
30.21210.02230.01580.39750.12040.3968-0.0064-0.0268-0.05490.0577-0.00880.00260.07620.00450.01520.02090.00230.00690.00430.00520.0451105.8387-21.89285.3766
47.29971.56535.59411.8363-2.426713.0953-0.08210.4296-0.117-0.3593-0.0329-0.08380.65570.65720.1150.39010.0619-0.02530.2396-0.05290.1632101.0071-18.2184-31.7785
50.55520.32480.44622.6291.0642.3696-0.10520.13860.0416-0.29520.1757-0.1982-0.03740.154-0.07050.0702-0.03930.04280.0828-0.00210.0757107.469810.701-19.7008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 164
2X-RAY DIFFRACTION2A165 - 184
3X-RAY DIFFRACTION3A185 - 382
4X-RAY DIFFRACTION4A383 - 394
5X-RAY DIFFRACTION5A395 - 442

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