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- PDB-5k7x: Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikos... -

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Basic information

Entry
Database: PDB / ID: 5k7x
TitleFully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP and Hadacidin
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / Adenylosuccinate synthetase / Pyrococcus horikoshii OT3 / GTP / IMP / Hadacidin
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / HADACIDIN / INOSINIC ACID / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsXie, Y. / Cheng, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473114 China
CitationJournal: To Be Published
Title: Crystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3
Authors: Xie, Y. / Kishisita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
C: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
E: Adenylosuccinate synthetase
F: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,60030
Polymers224,5116
Non-polymers6,08924
Water1,04558
1
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86710
Polymers74,8372
Non-polymers2,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-55 kcal/mol
Surface area22750 Å2
MethodPISA
2
C: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86710
Polymers74,8372
Non-polymers2,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-56 kcal/mol
Surface area23200 Å2
MethodPISA
3
E: Adenylosuccinate synthetase
F: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86710
Polymers74,8372
Non-polymers2,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-56 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.348, 130.549, 168.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Adenylosuccinate synthetase / AdSS / IMP--aspartate ligase


Mass: 37418.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: purA, PH0438 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58187, adenylosuccinate synthase

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Non-polymers , 5 types, 82 molecules

#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Chemical
ChemComp-HDA / HADACIDIN


Mass: 119.076 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5NO4 / Comment: anticancer, medication*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2016 / Details: Silicon
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55976 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D7U

2d7u


Resolution: 2.803→39.123 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2634 2690 4.88 %
Rwork0.2062 --
obs0.2089 55164 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→39.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15624 0 384 58 16066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716314
X-RAY DIFFRACTIONf_angle_d1.11122116
X-RAY DIFFRACTIONf_dihedral_angle_d16.9116102
X-RAY DIFFRACTIONf_chiral_restr0.0612436
X-RAY DIFFRACTIONf_plane_restr0.0052838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8025-2.85350.33921090.27551933X-RAY DIFFRACTION68
2.8535-2.90830.3011090.2632254X-RAY DIFFRACTION79
2.9083-2.96770.30571220.26162455X-RAY DIFFRACTION85
2.9677-3.03220.35211340.26512656X-RAY DIFFRACTION94
3.0322-3.10270.3261380.26872817X-RAY DIFFRACTION97
3.1027-3.18030.33051320.26522845X-RAY DIFFRACTION99
3.1803-3.26620.37331450.2572859X-RAY DIFFRACTION100
3.2662-3.36230.27651560.24442831X-RAY DIFFRACTION100
3.3623-3.47070.28441440.23052865X-RAY DIFFRACTION100
3.4707-3.59470.26391580.20932862X-RAY DIFFRACTION100
3.5947-3.73850.27881410.20662896X-RAY DIFFRACTION100
3.7385-3.90850.2421660.20142850X-RAY DIFFRACTION99
3.9085-4.11440.29791300.19292880X-RAY DIFFRACTION99
4.1144-4.37180.24581640.18692857X-RAY DIFFRACTION99
4.3718-4.70890.23521460.1682871X-RAY DIFFRACTION99
4.7089-5.18180.23331400.17962899X-RAY DIFFRACTION99
5.1818-5.92940.24841490.19132918X-RAY DIFFRACTION99
5.9294-7.46190.23971750.20362928X-RAY DIFFRACTION100
7.4619-39.1270.1921320.1642998X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -10.1182 Å / Origin y: 30.2758 Å / Origin z: -34.7333 Å
111213212223313233
T0.2349 Å20.0763 Å2-0.0315 Å2-0.2945 Å2-0.031 Å2--0.306 Å2
L0.1846 °2-0.1667 °20.0796 °2-0.3892 °2-0.0137 °2--0.1313 °2
S0.0691 Å °-0.0017 Å °-0.0742 Å °-0.1007 Å °-0.0159 Å °0.0148 Å °-0.0229 Å °-0.0399 Å °-0.0477 Å °
Refinement TLS groupSelection details: all

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