PDB-8jbd: Crystal structure of Adenylosuccinate lyase from Thermus thermoph...

ID or keywords:

Entry

Database: PDB / ID: 8jbd

Title

Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB

Components

Adenylosuccinate lyase

Keywords

LYASE / ADENYLOSUCCINATE LYASE PURINE BIOSYNTHESIS THERMUS THERMOPHILUS

Function / homology

Function and homology information

adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process
Similarity search - Function

Biological species

Thermus thermophilus HB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Nemoto, N. / Kawai, G. / Sampei, G.

Funding support

1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.
Authors: Nemoto, N. / Kawai, G. / Sampei, G.I.

History

Deposition	May 8, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 15, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8jbd.cif.gz	147.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8jbd_validation.pdf.gz	447.9 KB	Display	wwPDB validaton report
Full document	8jbd_full_validation.pdf.gz	457.6 KB	Display
Data in XML	8jbd_validation.xml.gz	25.9 KB	Display
Data in CIF	8jbd_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/8jbd ftp://data.pdbj.org/pub/pdb/validation_reports/jb/8jbd	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7)

Deposited unit

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

A: Adenylosuccinate lyase

B: Adenylosuccinate lyase

defined by author&software
Evidence: gel filtration
205 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	158.657, 158.657, 151.634
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Adenylosuccinate lyase Mass: 51259.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA1513 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SI61
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 0.1M Sodium acetate trihydrate (pH 4.6), 1.0M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.37→50 Å / Num. obs: 86898 / % possible obs: 100 % / Redundancy: 11.2 % / R_merge(I) obs: 0.077 / Χ²: 0.894 / Net I/σ(I): 30.8
Reflection shell	Resolution: 2.37→2.45 Å / Redundancy: 11.3 % / R_merge(I) obs: 0.353 / Mean I/σ(I) obs: 6.83 / Num. unique obs: 8688 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.38→19.992 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.914 / WR_factor R_free: 0.248 / WR_factor R_work: 0.205 / SU B: 4.95 / SU ML: 0.121 / Average fsc free: 0.9307 / Average fsc work: 0.9444 / Cross valid method: FREE R-VALUE / ESU R: 0.235 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2485	2262	4.974 %
R_work	0.2047	43213	-
all	0.207	-	-
obs	-	45475	99.743 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 43.549 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	0.001 Å²	0 Å²
2-	-	0.001 Å²	-0 Å²
3-	-	-	-0.004 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→19.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4860	0	0	251	5111

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	4939
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4867
X-RAY DIFFRACTION	r_angle_refined_deg	1.714	1.638	6672
X-RAY DIFFRACTION	r_angle_other_deg	1.405	1.572	11148
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.068	5	603
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.648	19.5	280
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.217	15	845
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.528	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	624
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5473
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1117
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	1143
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	4528
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	2369
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	2463
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	187
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.023	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.33	0.2	36
X-RAY DIFFRACTION	r_nbd_other	0.216	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.241	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	4.366	4.248	2463
X-RAY DIFFRACTION	r_mcbond_other	4.366	4.248	2462
X-RAY DIFFRACTION	r_mcangle_it	5.928	6.326	3049
X-RAY DIFFRACTION	r_mcangle_other	5.927	6.327	3050
X-RAY DIFFRACTION	r_scbond_it	5.579	4.931	2470
X-RAY DIFFRACTION	r_scbond_other	5.574	4.931	2470
X-RAY DIFFRACTION	r_scangle_it	8.306	7.146	3617
X-RAY DIFFRACTION	r_scangle_other	8.302	7.146	3617
X-RAY DIFFRACTION	r_lrange_it	10.609	50.796	5606
X-RAY DIFFRACTION	r_lrange_other	10.621	50.696	5577

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.38-2.441	0.292	154	0.198	3114	0.202	3270	0.911	0.941	99.9388	0.198
2.441-2.507	0.251	158	0.178	3000	0.181	3160	0.929	0.951	99.9367	0.178
2.507-2.578	0.217	146	0.181	2968	0.183	3114	0.947	0.95	100	0.181
2.578-2.656	0.266	139	0.183	2875	0.187	3015	0.919	0.947	99.9668	0.183
2.656-2.742	0.236	164	0.193	2766	0.195	2930	0.927	0.942	100	0.193
2.742-2.836	0.245	134	0.188	2699	0.191	2834	0.927	0.944	99.9647	0.188
2.836-2.941	0.23	131	0.201	2610	0.203	2741	0.936	0.937	100	0.201
2.941-3.058	0.268	153	0.211	2505	0.214	2658	0.908	0.93	100	0.211
3.058-3.191	0.254	132	0.208	2410	0.211	2542	0.915	0.933	100	0.208
3.191-3.342	0.228	127	0.196	2312	0.197	2439	0.938	0.948	100	0.196
3.342-3.518	0.21	107	0.204	2241	0.204	2348	0.953	0.95	100	0.204
3.518-3.724	0.229	106	0.199	2116	0.2	2222	0.939	0.952	100	0.199
3.724-3.971	0.251	120	0.194	1974	0.197	2095	0.933	0.948	99.9523	0.194
3.971-4.275	0.249	82	0.192	1877	0.195	1959	0.93	0.947	100	0.192
4.275-4.662	0.211	92	0.182	1747	0.183	1839	0.955	0.958	100	0.182
4.662-5.177	0.227	100	0.201	1564	0.203	1664	0.958	0.96	100	0.201
5.177-5.912	0.371	80	0.273	1421	0.278	1501	0.91	0.929	100	0.273
5.912-7.088	0.282	58	0.254	1252	0.255	1310	0.927	0.931	100	0.254
7.088-9.447	0.217	48	0.2	1023	0.201	1071	0.953	0.955	100	0.2
9.447-19.992	0.326	31	0.266	719	0.268	752	0.922	0.927	99.734	0.266

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