PDB-8up6: Structure of atypical asparaginase from Rhodospirillum rubrum (mu...

ID or keywords:

Entry

Database: PDB / ID: 8up6

Title

Structure of atypical asparaginase from Rhodospirillum rubrum (mutant K19A) in complex with L-Asp

Components

Asparaginase

Keywords

HYDROLASE / Asparaginase / wild type / atypical / enzyme

Function / homology

Function and homology information

asparaginase / asparaginase activity / membrane
Similarity search - Function

Biological species

Rhodospirillum rubrum ATCC 11170 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Lubkowski, J. / Wlodawer, A. / Zhang, D.

Funding support

1items

Citation

Journal: Protein Sci. / Year: 2024
Title: RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases.
Authors: Zhang, D. / Czapinska, H. / Bochtler, M. / Wlodawer, A. / Lubkowski, J.

History

Deposition	Oct 21, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8up6.cif.gz	142.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8up6.ent.gz	111.9 KB	Display	PDB format
PDBx/mmJSON format	8up6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8up6_validation.pdf.gz	477.9 KB	Display	wwPDB validaton report
Full document	8up6_full_validation.pdf.gz	482.5 KB	Display
Data in XML	8up6_validation.xml.gz	29.1 KB	Display
Data in CIF	8up6_validation.cif.gz	42.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/up/8up6 ftp://data.pdbj.org/pub/pdb/validation_reports/up/8up6	HTTPS FTP

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Related structure data

Related structure data	8uooC 8uorC 8uouC 8uowC 8up3C 8up7C 8up8C 8up9C 8upcC C: citing same article (ref.)
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	#171 - Mar 2014 Neurotransmitter Transporters similarity (1)

Deposited unit

A: Asparaginase

B: Asparaginase

C: Asparaginase

D: Asparaginase

hetero molecules

79.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.045, 77.327, 115.025
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Asparaginase Mass: 19743.393 Da / Num. of mol.: 4 / Mutation: K19A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria) Gene: Rru_A3730 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q2RMX1, asparaginase
#2: Chemical	ChemComp-ASP / ASPARTIC ACID Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₇NO₄
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 uL 18 mg/mL protein in 50 mM HEPES, 150 mM sodium chloride, 20 mM L-Asp + 0.2 uL reservoir (Molecular Dimensions Morpheus F9 + 20 mM L-Asp, pH 8.5) PH range: 7.5-8.0

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Data collection

Diffraction

Mean temperature: 100 K / Ambient temp details: Stream of liquid nitrogen / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2022

Radiation

Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→40 Å / Num. obs: 71088 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.068 / R_pim(I) all: 0.02 / R_rim(I) all: 0.071 / Χ²: 0.965 / Net I/σ(I): 9.2 / Num. measured all: 917685

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.73	11.9	0.753	3496	0.947	0.986	0.222	0.786	0.864	99.8
1.73-1.76	13	0.717	3532	0.961	0.99	0.204	0.747	0.865	99.9
1.76-1.79	13.5	0.621	3540	0.971	0.993	0.174	0.646	0.887	99.9
1.79-1.83	13.6	0.531	3486	0.977	0.994	0.148	0.552	0.9	100
1.83-1.87	13.7	0.421	3525	0.989	0.997	0.117	0.438	0.914	99.9
1.87-1.91	13.4	0.351	3522	0.989	0.997	0.099	0.365	0.962	100
1.91-1.96	13.3	0.29	3543	0.991	0.998	0.082	0.302	0.973	99.9
1.96-2.02	13.1	0.218	3510	0.995	0.999	0.062	0.227	0.963	99.8
2.02-2.07	12.6	0.186	3547	0.996	0.999	0.054	0.194	0.999	99.9
2.07-2.14	11.6	0.156	3526	0.996	0.999	0.047	0.163	0.987	99.7
2.14-2.22	13.7	0.133	3526	0.997	0.999	0.037	0.138	0.981	99.9
2.22-2.31	13.7	0.107	3544	0.998	1	0.03	0.111	0.988	99.8
2.31-2.41	13.6	0.087	3552	0.998	1	0.025	0.091	0.95	99.9
2.41-2.54	13.3	0.07	3556	0.999	1	0.02	0.073	0.962	100
2.54-2.7	13	0.062	3578	0.999	1	0.018	0.064	0.94	100
2.7-2.91	12.5	0.052	3568	0.999	1	0.016	0.055	0.949	99.8
2.91-3.2	11.9	0.043	3592	0.999	1	0.013	0.045	1.002	99.5
3.2-3.66	13.6	0.038	3615	0.999	1	0.011	0.04	1.112	99.9
3.66-4.61	12.1	0.034	3576	0.999	1	0.011	0.036	1.105	97.6
4.61-40	11.3	0.034	3754	0.998	0.999	0.011	0.036	1.012	97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→38.89 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.026 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.205	1431	2 %	RANDOM
R_work	0.181	-	-	-
obs	0.182	69304	99.3 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 17.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	0 Å²	0 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	0.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→38.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4881	0	57	384	5322

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	5032
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4937
X-RAY DIFFRACTION	r_angle_refined_deg	1.776	1.639	6801
X-RAY DIFFRACTION	r_angle_other_deg	1.499	1.576	11358
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.697	5	666
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.069	20.298	235
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.235	15	803
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.513	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	668
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5702
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1066
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.771	1.621	2670
X-RAY DIFFRACTION	r_mcbond_other	1.77	1.621	2669
X-RAY DIFFRACTION	r_mcangle_it	2.648	2.42	3328
X-RAY DIFFRACTION	r_mcangle_other	2.648	2.421	3329
X-RAY DIFFRACTION	r_scbond_it	2.81	2.075	2362
X-RAY DIFFRACTION	r_scbond_other	2.81	2.076	2363
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.422	2.943	3472
X-RAY DIFFRACTION	r_long_range_B_refined	5.795	20.306	5432
X-RAY DIFFRACTION	r_long_range_B_other	5.751	20.105	5355
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.75 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.28	65	-
R_work	0.23	4889	-
obs	-	-	95.45 %

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