SAXSdb — 9z4d

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine--tRNA ligase

Plasmodium falciparum 3D7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 91–535 Chain B； UniProt 91–535	Fragment：residues 91-535	ZN ZINC ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. Crystals were obtained as the GSU complex and soaked for 2 weeks with 10 mM Histidine in cryoprotectant. This displaced the GSU ligand resulting in an apo structure. Histidine was not bound. plate Liu-S-192 H8 , Puck: PSL-0115, Cryo: 3.4M sodium malonate	Resolution 2.87 Å R-free 0.236

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Z4D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9YRU Crystal structure of Apo Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Orthrhombic P form) Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；291 K；Berkeley D7: 100mM potassium phosphate dibasic, 100 mM potassium chloride, 30% PEG 3350. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 4mM ATP added to the protein prior to screening but ligand is not bound likely due to high phosphate concentration in the crystallant. plate 20147 D7 drop 1 , Puck: PSL-0309, Cryo: direct	Resolution 3.06 Å R-free 0.288
9YRW Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	MLI MALONATE ION × 5 GSU O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 2 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM GSU in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0114, Cryo: direct from soaking solution	Resolution 2.03 Å R-free 0.200
9YRX Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with Cysteine Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	MLI MALONATE ION × 4 CYS CYSTEINE × 2 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM cysteine in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0201, Cryo: direct from soaking solution	Resolution 2.16 Å R-free 0.215
9YRZ Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 4 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM AMP in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0203, Cryo: direct from soaking solution	Resolution 2.06 Å R-free 0.195
9YS0 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ADP in 3.4M sodium malonate. Liu-S-192 E1, Puck: PSL-0205, Cryo: direct from soaking solution	Resolution 2.14 Å R-free 0.199
9YS1 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP and Cysteine Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	CYS CYSTEINE × 2 AMP ADENOSINE MONOPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM AMP and Cysteine in 3.4M sodium malonate. plate Liu-S-192 G5 Puck: PSL-0209, Cryo: direct from soaking solution	Resolution 2.34 Å R-free 0.215
9YS2 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with cysteinyl-AMP Deposited 2025-10-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	A1CYZ 5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MLI MALONATE ION × 5 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM ATP and Cysteine in 3.4M sodium malonate. The cysteinyl-AMP intermediate formed during the soak. plate Liu-S-192 G6 Puck: PSL-0210, Cryo: direct from soaking solution	Resolution 2.22 Å R-free 0.205
9YT0 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ADP (long soak) Deposited 2025-10-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 1 month soak with 10 mM ADP in 3.4M sodium malonate. plate Liu-S-192 H3 Puck: PSL-2013, Cryo: direct from soaking solution	Resolution 2.45 Å R-free 0.216
9YT2 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with ATP (long soak) Deposited 2025-10-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 1 month soak with 10 mM ATP in 3.4M sodium malonate. plate Liu-S-192 H3 Puck: PSL-2014, Cryo: direct from soaking solution	Resolution 2.80 Å R-free 0.225
9YT3 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with 5'-Sulfamoyladenosine Deposited 2025-10-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	LMS [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE × 3 ZN ZINC ION × 2 NA SODIUM ION × 4 CL CHLORIDE ION × 24 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 7 day soak with 10 mM LMS in 3.4M sodium malonate. plate Liu-S-192 G8 Puck: PSL-2103, Cryo: direct from soaking solution	Resolution 2.77 Å R-free 0.234
9YT5 Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with GMP Deposited 2025-10-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 91–535（445 aa） Fragment：residues 91-535 Chain B 91–535（445 aa） Fragment：residues 91-535	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 4 MLI MALONATE ION × 3 ZN ZINC ION × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 7 day soak with 10 mM GMP in 3.4M sodium malonate. plate Liu-S-192 H7 Puck: PSL-2106, Cryo: direct from soaking solution	Resolution 2.90 Å R-free 0.215

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8IJP3_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–466； UniProt 91–535 Author chain B； PDBConstruct 22–466； UniProt 91–535

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z4d
Deposition date deposition_date	2025-11-10
最后修订 last_revision	2025-11-19
Structure title title	Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Cysteinyl-tRNA synthetase, CysRS ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.46 Å
Radius of gyration Rg (electron density) rg_electron	31.90 Å
Forward intensity I(0) i0	143119000.00
Molecular weight molecular_weight	99846.0 kDa
Excluded volume excluded_volume	126320 Å³
Envelope volume envelope_volume	148330 Å³
Hydration-shell volume shell_volume	39656 Å³
Envelope diameter envelope_diameter	117.5 Å
Shell Rg shell_rg	37.83 Å
Envelope Rg envelope_rg	32.09 Å
Shape Rg shape_rg	31.92 Å
Total Rg total_rg	32.29 Å
Total atoms total_atoms	7053
Residues n_residues	856
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	113.3 Å
Rg (real space) rg_real	34.02 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.4340e+08
I(0) uncertainty (real space) i0_real_error	2.0070e+06
Rg (reciprocal space) rg_reciprocal	32.58 Å
I(0) (reciprocal space) i0_reciprocal	143100000.0000
Solution quality estimate total_estimate	0.6555
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.560
Kurtosis Kurtosis kurtosis	-0.208
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	3.0310
Highest regularization parameter α highest_alpha	34480000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 0.882; Sysdev: 0.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.684

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Cysteine--tRNA ligase
Molecular weight formula_weight	54533.2 kDa
EC 编号 ec_number	6.1.1.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7055

MAHHHHHHMGTLEAQTQGPGSLPKWNQPSKEGKKITNLFVNNSLTHSKVEFIPQEGNKIKWYACGPTVYDAAHLGHARTYVSFDIIRRILVNYFKYDVFMVINITDIDDKIIKRSVEEKIGFTELARKWEYEFWEDMKSLNVLLPTAITRVSEYVGDIVKYIEKIIENKYAYVSEEGSVYFDIDEFKKSEKHFYARMEPLSVKDENKILEGEGDLGVISKKKKNAYDFALWKSSKPNEPHWDSPWGKGRPGWHIECSTMASNILGDVLDIHSGGIDLRFPHHDNELAQSEAFFDHSQWVNYFLHSGHLHIEGLKMSKSLKNFITIKNMLTKYTSNQIRILFLLNKWDNFMNYSPNGESMVQCIEIDKSFTNFFAIILMKIKNFDLNSCNLYWSDADNKLNLLFRQTKNKIHEHFLDNFNTPDALLAIQKLITEINIYMDKEKIQIGLLLEIKHYINFIFDTFGLIY

来源 Source

来源生物 organism	Plasmodium falciparum 3D7
NCBI Class编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	120.174 Å
Unit-cell length b length_b	120.174 Å
Unit-cell length c length_c	363.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.870 Å
Low-resolution limit resolution_low	47.810 Å
R factor r_factor	0.2164
R_work r_work	0.2154
R_free r_free	0.2360

fit	/app/data/saxs_computation/z4/9z4d/9z4d.fit
pddf	/app/data/pr_computation/z4/9z4d/9z4d.pr.out
profile	/app/data/saxs_computation/z4/9z4d/9z4d.dat

Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum (Hexagonal P form)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine--tRNA ligase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction