SAXSdb — 1cjb

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

PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)

Plasmodium falciparum

UniProt P20035

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–231 Chain B； UniProt 1–231	Not recorded	MG MAGNESIUM ION × 8 IRP (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE × 4 POP PYROPHOSPHATE 2- × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.239
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–231 Chain D； UniProt 1–221	Not recorded	MG MAGNESIUM ION × 8 IRP (1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE × 4 POP PYROPHOSPHATE 2- × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.239

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 1CJB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VFA Crystal structure of a chimera of Plasmodium falciparum and human hypoxanthine-guanine phosphoribosyl transferases Deposited 2007-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–56（56 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain A 171–231（61 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain B 1–56（56 aa） Fragment：RESIDUES 1-56,49-160,171-231 Chain B 171–231（61 aa） Fragment：RESIDUES 1-56,49-160,171-231	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1M TRIS PH 8.0, 2.0M AMMONIUM SULPHATE	Resolution 2.80 Å R-free 0.278
3OZF Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with hypoxanthine Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa） Chain C 1–231（231 aa） Chain D 1–231（231 aa）	Not recorded	HPA HYPOXANTHINE × 4 POP PYROPHOSPHATE 2- × 4 PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.94 Å R-free 0.237
3OZG Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate Deposited 2010-09-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–231（231 aa） Chain B 1–231（231 aa）	Not recorded	SSI [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid × 4 POP PYROPHOSPHATE 2- × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.99 Å R-free 0.264
3OZG Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate Deposited 2010-09-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–231（231 aa） Chain D 1–231（231 aa）	Not recorded	SSI [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid × 4 POP PYROPHOSPHATE 2- × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K	Resolution 1.99 Å R-free 0.264
7TUX Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid Deposited 2022-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–231（231 aa）	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 9 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
7TUX Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid Deposited 2022-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–231（231 aa）	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 12 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
7TUX Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid Deposited 2022-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–231（231 aa）	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 10 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195
7TUX Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid Deposited 2022-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–231（231 aa）	Not recorded	YBM [(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 5 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM Lithium Acetate, 20% PEG3350	Resolution 1.62 Å R-free 0.195

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HGXR_PLAFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 1–231 Author chain B； PDBConstruct 1–231； UniProt 1–231 Author chain C； PDBConstruct 1–231； UniProt 1–231 Author chain D； PDBConstruct 1–231； UniProt 1–221

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	1cjb
Deposition date deposition_date	1999-04-08
Structure title title	MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE
Keywords keywords	MALARIA, PURINE SALVAGE, PHOSPHORIBOSYLTRANSFERASE, TRANSITION STATE INHIBITOR, TRANSFERASE; 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	45.23 Å
Radius of gyration Rg (electron density) rg_electron	45.15 Å
Forward intensity I(0) i0	156719000.00
Molecular weight molecular_weight	106130.0 kDa
Excluded volume excluded_volume	133760 Å³
Envelope volume envelope_volume	188440 Å³
Hydration-shell volume shell_volume	34477 Å³
Envelope diameter envelope_diameter	137.4 Å
Shell Rg shell_rg	51.36 Å
Envelope Rg envelope_rg	43.06 Å
Shape Rg shape_rg	45.16 Å
Total Rg total_rg	45.42 Å
Total atoms total_atoms	7469
Residues n_residues	914
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	126.5 Å
Rg (real space) rg_real	45.52 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	1.5670e+08
I(0) uncertainty (real space) i0_real_error	2.5160e+06
Rg (reciprocal space) rg_reciprocal	45.23 Å
I(0) (reciprocal space) i0_reciprocal	156700000.0000
Solution quality estimate total_estimate	0.6766
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-1.212
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11270000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.465; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.397; Smooth: 0.000

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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	PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)
Molecular weight formula_weight	26386.5 kDa
EC 编号 ec_number	2.4.2.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7876

MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKATSL

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI Class编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	(1S)-1(9-DEAZAHYPOXANTHIN-9YL)1,4-DIDEOXY-1,4-IMINO-D-RIBITOL-5-PHOSPHATE
Molecular weight formula_weight	346.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 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	407

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cjba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1cjbb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1cjbc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

Domain ID domain_id	d1cjbd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.61 — PRTase-like
Superfamily Superfamily superfamily	c.61.1 — PRTase-like
Family Family family	c.61.1.1 — Phosphoribosyltransferases (PRTases)

CATH v4.4 (4 domains)

Domain ID domain_id	1cjbA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1cjbB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1cjbC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

Domain ID domain_id	1cjbD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2020 —

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8. Citations (1)

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Unit-cell length a length_a	105.490 Å
Unit-cell length b length_b	110.390 Å
Unit-cell length c length_c	173.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2390

fit	/app/data/saxs_computation/cj/1cjb/1cjb.fit
pddf	/app/data/pr_computation/cj/1cjb/1cjb.pr.out
profile	/app/data/saxs_computation/cj/1cjb/1cjb.dat

MALARIAL PURINE PHOSPHORIBOSYLTRANSFERASE

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

PROTEIN (HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE)

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