SAXSdb — 9cca

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

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24	;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2 ; × 12 （Q7K740,Q8IIK4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDX1_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 117–416； UniProt 2–301 Author chain B； PDBConstruct 117–416； UniProt 2–301 Author chain C； PDBConstruct 117–416； UniProt 2–301 Author chain D； PDBConstruct 117–416； UniProt 2–301 Author chain E； PDBConstruct 117–416； UniProt 2–301 Author chain F； PDBConstruct 117–416； UniProt 2–301 Author chain M； PDBConstruct 117–416； UniProt 2–301 Author chain N； PDBConstruct 117–416； UniProt 2–301 Author chain O； PDBConstruct 117–416； UniProt 2–301 Author chain P； PDBConstruct 117–416； UniProt 2–301 Author chain Q； PDBConstruct 117–416； UniProt 2–301 Author chain R； PDBConstruct 117–416； UniProt 2–301

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

Plasmodium falciparum

UniProt Q7K740

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CSP_PLAF7
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 4–17； UniProt 101–114 Author chain A； PDBConstruct 419–432； UniProt 101–114 Author chain A； PDBConstruct 18–37； UniProt 131–150 Author chain A； PDBConstruct 433–452； UniProt 131–150 Author chain A； PDBConstruct 38–111； UniProt 310–383 Author chain A； PDBConstruct 453–526； UniProt 310–383 Author chain B； PDBConstruct 4–17； UniProt 101–114 Author chain B； PDBConstruct 419–432； UniProt 101–114 Author chain B； PDBConstruct 18–37； UniProt 131–150 Author chain B； PDBConstruct 433–452； UniProt 131–150 Author chain B； PDBConstruct 38–111； UniProt 310–383 Author chain B； PDBConstruct 453–526； UniProt 310–383 Author chain C； PDBConstruct 4–17； UniProt 101–114 Author chain C； PDBConstruct 419–432； UniProt 101–114 Author chain C； PDBConstruct 18–37； UniProt 131–150 Author chain C； PDBConstruct 433–452； UniProt 131–150 Author chain C； PDBConstruct 38–111； UniProt 310–383 Author chain C； PDBConstruct 453–526； UniProt 310–383 Author chain D； PDBConstruct 4–17； UniProt 101–114 Author chain D； PDBConstruct 419–432； UniProt 101–114 Author chain D； PDBConstruct 18–37； UniProt 131–150 Author chain D； PDBConstruct 433–452； UniProt 131–150 Author chain D； PDBConstruct 38–111； UniProt 310–383 Author chain D； PDBConstruct 453–526； UniProt 310–383 Author chain E； PDBConstruct 4–17； UniProt 101–114 Author chain E； PDBConstruct 419–432； UniProt 101–114 Author chain E； PDBConstruct 18–37； UniProt 131–150 Author chain E； PDBConstruct 433–452； UniProt 131–150 Author chain E； PDBConstruct 38–111； UniProt 310–383 Author chain E； PDBConstruct 453–526； UniProt 310–383 Author chain F； PDBConstruct 4–17； UniProt 101–114 Author chain F； PDBConstruct 419–432； UniProt 101–114 Author chain F； PDBConstruct 18–37； UniProt 131–150 Author chain F； PDBConstruct 433–452； UniProt 131–150 Author chain F； PDBConstruct 38–111； UniProt 310–383 Author chain F； PDBConstruct 453–526； UniProt 310–383 Author chain M； PDBConstruct 4–17； UniProt 101–114 Author chain M； PDBConstruct 419–432； UniProt 101–114 Author chain M； PDBConstruct 18–37； UniProt 131–150 Author chain M； PDBConstruct 433–452； UniProt 131–150 Author chain M； PDBConstruct 38–111； UniProt 310–383 Author chain M； PDBConstruct 453–526； UniProt 310–383 Author chain N； PDBConstruct 4–17； UniProt 101–114 Author chain N； PDBConstruct 419–432； UniProt 101–114 Author chain N； PDBConstruct 18–37； UniProt 131–150 Author chain N； PDBConstruct 433–452； UniProt 131–150 Author chain N； PDBConstruct 38–111； UniProt 310–383 Author chain N； PDBConstruct 453–526； UniProt 310–383 Author chain O； PDBConstruct 4–17； UniProt 101–114 Author chain O； PDBConstruct 419–432； UniProt 101–114 Author chain O； PDBConstruct 18–37； UniProt 131–150 Author chain O； PDBConstruct 433–452； UniProt 131–150 Author chain O； PDBConstruct 38–111； UniProt 310–383 Author chain O； PDBConstruct 453–526； UniProt 310–383 Author chain P； PDBConstruct 4–17； UniProt 101–114 Author chain P； PDBConstruct 419–432； UniProt 101–114 Author chain P； PDBConstruct 18–37； UniProt 131–150 Author chain P； PDBConstruct 433–452； UniProt 131–150 Author chain P； PDBConstruct 38–111； UniProt 310–383 Author chain P； PDBConstruct 453–526； UniProt 310–383 Author chain Q； PDBConstruct 4–17； UniProt 101–114 Author chain Q； PDBConstruct 419–432； UniProt 101–114 Author chain Q； PDBConstruct 18–37； UniProt 131–150 Author chain Q； PDBConstruct 433–452； UniProt 131–150 Author chain Q； PDBConstruct 38–111； UniProt 310–383 Author chain Q； PDBConstruct 453–526； UniProt 310–383 Author chain R； PDBConstruct 4–17； UniProt 101–114 Author chain R； PDBConstruct 419–432； UniProt 101–114 Author chain R； PDBConstruct 18–37； UniProt 131–150 Author chain R； PDBConstruct 433–452； UniProt 131–150 Author chain R； PDBConstruct 38–111； UniProt 310–383 Author chain R； PDBConstruct 453–526； UniProt 310–383 Author chain G； PDBConstruct 4–17； UniProt 101–114 Author chain G； PDBConstruct 336–349； UniProt 101–114 Author chain G； PDBConstruct 18–37； UniProt 131–150 Author chain G； PDBConstruct 350–369； UniProt 131–150 Author chain G； PDBConstruct 38–111； UniProt 310–383 Author chain G； PDBConstruct 370–443； UniProt 310–383 Author chain H； PDBConstruct 4–17； UniProt 101–114 Author chain H； PDBConstruct 336–349； UniProt 101–114 Author chain H； PDBConstruct 18–37； UniProt 131–150 Author chain H； PDBConstruct 350–369； UniProt 131–150 Author chain H； PDBConstruct 38–111； UniProt 310–383 Author chain H； PDBConstruct 370–443； UniProt 310–383 Author chain I； PDBConstruct 4–17； UniProt 101–114 Author chain I； PDBConstruct 336–349； UniProt 101–114 Author chain I； PDBConstruct 18–37； UniProt 131–150 Author chain I； PDBConstruct 350–369； UniProt 131–150 Author chain I； PDBConstruct 38–111； UniProt 310–383 Author chain I； PDBConstruct 370–443； UniProt 310–383 Author chain J； PDBConstruct 4–17； UniProt 101–114 Author chain J； PDBConstruct 336–349； UniProt 101–114 Author chain J； PDBConstruct 18–37； UniProt 131–150 Author chain J； PDBConstruct 350–369； UniProt 131–150 Author chain J； PDBConstruct 38–111； UniProt 310–383 Author chain J； PDBConstruct 370–443； UniProt 310–383 Author chain K； PDBConstruct 4–17； UniProt 101–114 Author chain K； PDBConstruct 336–349； UniProt 101–114 Author chain K； PDBConstruct 18–37； UniProt 131–150 Author chain K； PDBConstruct 350–369； UniProt 131–150 Author chain K； PDBConstruct 38–111； UniProt 310–383 Author chain K； PDBConstruct 370–443； UniProt 310–383 Author chain L； PDBConstruct 4–17； UniProt 101–114 Author chain L； PDBConstruct 336–349； UniProt 101–114 Author chain L； PDBConstruct 18–37； UniProt 131–150 Author chain L； PDBConstruct 350–369； UniProt 131–150 Author chain L； PDBConstruct 38–111； UniProt 310–383 Author chain L； PDBConstruct 370–443； UniProt 310–383 Author chain S； PDBConstruct 4–17； UniProt 101–114 Author chain S； PDBConstruct 336–349； UniProt 101–114 Author chain S； PDBConstruct 18–37； UniProt 131–150 Author chain S； PDBConstruct 350–369； UniProt 131–150 Author chain S； PDBConstruct 38–111； UniProt 310–383 Author chain S； PDBConstruct 370–443； UniProt 310–383 Author chain T； PDBConstruct 4–17； UniProt 101–114 Author chain T； PDBConstruct 336–349； UniProt 101–114 Author chain T； PDBConstruct 18–37； UniProt 131–150 Author chain T； PDBConstruct 350–369； UniProt 131–150 Author chain T； PDBConstruct 38–111； UniProt 310–383 Author chain T； PDBConstruct 370–443； UniProt 310–383 Author chain U； PDBConstruct 4–17； UniProt 101–114 Author chain U； PDBConstruct 336–349； UniProt 101–114 Author chain U； PDBConstruct 18–37； UniProt 131–150 Author chain U； PDBConstruct 350–369； UniProt 131–150 Author chain U； PDBConstruct 38–111； UniProt 310–383 Author chain U； PDBConstruct 370–443； UniProt 310–383 Author chain V； PDBConstruct 4–17； UniProt 101–114 Author chain V； PDBConstruct 336–349； UniProt 101–114 Author chain V； PDBConstruct 18–37； UniProt 131–150 Author chain V； PDBConstruct 350–369； UniProt 131–150 Author chain V； PDBConstruct 38–111； UniProt 310–383 Author chain V； PDBConstruct 370–443； UniProt 310–383 Author chain W； PDBConstruct 4–17； UniProt 101–114 Author chain W； PDBConstruct 336–349； UniProt 101–114 Author chain W； PDBConstruct 18–37； UniProt 131–150 Author chain W； PDBConstruct 350–369； UniProt 131–150 Author chain W； PDBConstruct 38–111； UniProt 310–383 Author chain W； PDBConstruct 370–443； UniProt 310–383 Author chain X； PDBConstruct 4–17； UniProt 101–114 Author chain X； PDBConstruct 336–349； UniProt 101–114 Author chain X； PDBConstruct 18–37； UniProt 131–150 Author chain X； PDBConstruct 350–369； UniProt 131–150 Author chain X； PDBConstruct 38–111； UniProt 310–383 Author chain X； PDBConstruct 370–443； UniProt 310–383

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2 ;

Plasmodium falciparum

UniProt Q8IIK4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 24	;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ; × 12 （C6KT50,Q7K740）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDX2_PLAF7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 117–333； UniProt 3–219 Author chain H； PDBConstruct 117–333； UniProt 3–219 Author chain I； PDBConstruct 117–333； UniProt 3–219 Author chain J； PDBConstruct 117–333； UniProt 3–219 Author chain K； PDBConstruct 117–333； UniProt 3–219 Author chain L； PDBConstruct 117–333； UniProt 3–219 Author chain S； PDBConstruct 117–333； UniProt 3–219 Author chain T； PDBConstruct 117–333； UniProt 3–219 Author chain U； PDBConstruct 117–333； UniProt 3–219 Author chain V； PDBConstruct 117–333； UniProt 3–219 Author chain W； PDBConstruct 117–333； UniProt 3–219 Author chain X； PDBConstruct 117–333； UniProt 3–219

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	9cca
Deposition date deposition_date	2024-06-21
Structure title title	Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)
Keywords keywords	synthase, complex, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9cca__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9cca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cca__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	60.45 Å
Rg (electron density)	60.19 Å
Total Rg	60.18 Å
Atom count	82341
Residues	5287
Excluded volume	734380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cca__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;
Molecular weight formula_weight	58417.1 kDa
EC 编号 ec_number	4.3.3.6
Mutation mutation	K198R,K289C,S293C in Pdx1 (Uniprot numbering: K83R,K174C,S178C)
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,M,N,O,P,Q,R
Atom count atom_count	82341

MTGNPDPNANPNVDPNANPNANPNANPNANPNANPNAEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFNVVNSGGSGTENHKDDAVLLKHGWCEMLKGGVIMDVKSVEQAKIAEEAGAIGVMVLENIPSELRNKEGVARSVDPSKVEEIKKCVSINVLARVRIGHFVEAQILEELKIDMIDESEVLTIADEMHHIDKHKFKTPFVCGCTNLGEALRRISEGASMIRTKGEAGTGNIIEAIKHIRTVNNEICYLCCLSDSEVYHFAKKINAPIDLVLLTKKLKRLPVVNFAAGGVATPADAAMCMQLGMDGVFVGSGIFESENPRKMAASIVSAVSNFNNPKILLDVSMNLGKAMCGSTRVSDKWKNKNEEHTKFLTPQTGNPDPNANPNVDPNANPNANPNANPNANPNANPNAEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFNVVNSGGSLEHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2 ;
Molecular weight formula_weight	49843.6 kDa
EC 编号 ec_number	4.3.3.6,3.5.1.2
Mutation mutation	N179Q,N242Q,H310N in Pdx2 (Uniprot numbering: N65Q,N128Q,H196N)
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L,S,T,U,V,W,X

MTGNPDPNANPNVDPNANPNANPNANPNANPNANPNAEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFNVVNSGGSGTEITIGVLSLQGDFEPHINHFIKLQIPSLNIIQVRNVHDLGLCDGLVIPGGESTTVRRCCAYEQDTLYNALVHFIHVLKKPIWGTCAGCILLSKNVENIKLYSNFGNKFSFGGLDITICRNFYGSQQDSFICSLNIISDSSAFKKDLTAACIRAPYIREILSDEVKVLATFSHESYGPNIIAAVEQNNCLGTVFNPELLPHTAFQQYFYEKVKNYKYSTGNPDPNANPNVDPNANPNANPNANPNANPNANPNAEPSDKHIKEYLNKIQNSLSTEWSPCSVTCGNGIQVRIKPGSANKPKDELDYANDIEKKICKMEKCSSVFNVVNSGGSLEHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.95 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	251050

Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)

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

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

State in the Current Structure

Other States of the Same Protein in the Database

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

State in the Current Structure

Other States of the Same Protein in the Database

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2 ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cca__assembly_1__model_1

9cca__assembly_1__model_1 | I(q)

9cca__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)

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

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cca__assembly_1__model_1

9cca__assembly_1__model_1 | I(q)

9cca__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)