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- PDB-5us8: 2.15 Angstrom Resolution Crystal Structure of Argininosuccinate S... -

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Basic information

Entry
Database: PDB / ID: 5us8
Title2.15 Angstrom Resolution Crystal Structure of Argininosuccinate Synthase from Bordetella pertussis
ComponentsArgininosuccinate synthase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Argininosuccinate Synthase
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate metabolic process / argininosuccinate synthase activity / urea cycle / L-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 synthase, type 1 subfamily / Argininosuccinate synthetase, catalytic/multimerisation domain body / : ...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 synthase, type 1 subfamily / 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 / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / TRIETHYLENE GLYCOL / Argininosuccinate synthase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Stam, J. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)100,5238
Polymers99,2942
Non-polymers1,2286
Water9,404522
1
A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules

A: Argininosuccinate synthase
B: Argininosuccinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,04516
Polymers198,5894
Non-polymers2,45712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area33660 Å2
ΔGint-77 kcal/mol
Surface area66270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.453, 94.453, 188.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

21B-769-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: -2 - 442 / Label seq-ID: 1 - 445

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 49647.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (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 , 5 types, 528 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 10.6 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg; Screen: Classics II (G8), 0.2M Ammonium acetate, 0.1 HEPES (pH 7.5), 25% (w/v) PEG 3350

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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: Feb 2, 2017 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 51703 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rsym value: 0.077 / Χ2: 1.012 / Net I/σ(I): 23.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2558 / CC1/2: 0.79 / Rpim(I) all: 0.298 / Rsym value: 0.759 / Χ2: 1.014 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K92

1k92


Resolution: 2.15→29.46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 8.882 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20032 2519 4.9 %RANDOM
Rwork0.15605 ---
obs0.15812 49016 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6934 0 79 522 7535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197222
X-RAY DIFFRACTIONr_bond_other_d0.0010.026711
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9779794
X-RAY DIFFRACTIONr_angle_other_deg0.893315540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8545904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16223.935338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.281151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.781560
X-RAY DIFFRACTIONr_chiral_restr0.0850.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0218113
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021486
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_it1.9133.6783598
X-RAY DIFFRACTIONr_mcbond_other1.9123.6773597
X-RAY DIFFRACTIONr_mcangle_it2.9595.5054508
X-RAY DIFFRACTIONr_mcangle_other2.965.5074509
X-RAY DIFFRACTIONr_scbond_it2.284.023623
X-RAY DIFFRACTIONr_scbond_other2.284.023623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5125.915287
X-RAY DIFFRACTIONr_long_range_B_refined6.28344.4798224
X-RAY DIFFRACTIONr_long_range_B_other6.21943.888089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28252 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 195 -
Rwork0.22 3570 -
obs--99.97 %
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)
11.5060.49470.8660.57450.22270.82020.01280.0451-0.0720.03760.03420.10540.1292-0.0429-0.04690.1673-0.0714-0.01890.03640.00880.0953-24.6226-19.7361-17.6257
22.64531.23780.65952.28571.13791.44050.0807-0.1862-0.01810.2953-0.15590.3360.2818-0.19050.07520.1838-0.06940.00760.04490.02190.1347-33.0153-18.0951-11.9369
31.1180.24860.04421.55390.30211.50730.09510.023-0.31690.0133-0.06880.13790.2965-0.329-0.02630.2815-0.0959-0.05160.0890.01450.2706-13.2239-33.5661-2.5777
41.29450.0845-0.11280.83680.11111.74990.1030.2364-0.3082-0.11980.0395-0.00970.1258-0.0085-0.14250.2255-0.0293-0.0510.055-0.05520.1285-0.518-26.4923-15.8643
50.76720.04010.01920.6977-0.1080.48850.05770.0681-0.1173-0.0258-0.0043-0.07120.03150.0516-0.05340.1674-0.044-0.0220.0348-0.02380.05424.2878-14.6317-9.6952
62.66790.5452-1.45730.7071-0.84991.45350.1543-0.36990.02560.0777-0.10310.0282-0.26860.1667-0.05120.209-0.0493-0.02540.2336-0.02490.099519.63731.794517.5703
71.2461-0.17090.81880.2455-0.02390.73130.0582-0.0286-0.1145-0.02840.0424-0.10950.15480.0866-0.10060.1987-0.0061-0.04130.1650.00260.165228.521-13.949517.5036
81.6854-0.48130.94451.1819-0.83081.79490.10010.126-0.0228-0.2489-0.1305-0.23040.29640.49230.03030.13760.0442-0.0060.17490.00060.11736.2026-11.948411.3651
91.1291-0.06150.03770.9129-0.19460.77670.1047-0.1712-0.29540.1348-0.0364-0.10810.10930.0847-0.06830.1915-0.044-0.0770.05150.03490.129810.2806-24.56368.5957
100.94730.0374-0.06440.85870.09750.47190.062-0.1368-0.08450.11370.00630.0960.0694-0.048-0.06830.1743-0.0643-0.0250.07040.04040.0461-3.3733-14.334111.099
113.34970.2358-1.81391.9978-0.50462.22270.16570.26220.4363-0.140.1930.3389-0.2235-0.2069-0.35860.2264-0.0458-0.03330.16040.01040.1536-21.8453-1.2481-12.7243
122.47040.58911.10960.14190.2640.59130.1044-0.4020.23630.0322-0.10760.0576-0.0597-0.2230.00320.24580.01430.10150.1945-0.00780.1449-10.2796-7.8715-37.0814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 119
2X-RAY DIFFRACTION2A120 - 184
3X-RAY DIFFRACTION3A185 - 233
4X-RAY DIFFRACTION4A234 - 282
5X-RAY DIFFRACTION5A283 - 394
6X-RAY DIFFRACTION6A395 - 442
7X-RAY DIFFRACTION7B-2 - 119
8X-RAY DIFFRACTION8B120 - 189
9X-RAY DIFFRACTION9B190 - 317
10X-RAY DIFFRACTION10B318 - 394
11X-RAY DIFFRACTION11B395 - 431
12X-RAY DIFFRACTION12B432 - 442

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