SAXSdb — 7ppo

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

Ubiquitinating/deubiquitinating enzyme SdeA

Legionella pneumophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Calmodulin-dependent glutamylase SidJ × 1 （Q5ZTK6） Calmodulin × 1 （P0DP24） MAGNESIUM ION × 1 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDEA_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–979； UniProt 231–1190

Calmodulin-dependent glutamylase SidJ

Legionella pneumophila

UniProt Q5ZTK6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitinating/deubiquitinating enzyme SdeA × 1 （Q5ZTK4） Calmodulin × 1 （P0DP24） MAGNESIUM ION × 1 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIDJ_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 19–793； UniProt 99–873

Calmodulin

Homo sapiens

UniProt P0DP24

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ubiquitinating/deubiquitinating enzyme SdeA × 1 （Q5ZTK4） Calmodulin-dependent glutamylase SidJ × 1 （Q5ZTK6） MAGNESIUM ION × 1 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALM2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 20–168； UniProt 1–149

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	7ppo
Deposition date deposition_date	2021-09-14
Structure title title	Structure of SidJ/CaM bound to SdeA in pre-glutamylation state
Keywords keywords	Glutamylase, Pseudokinase, phosphoribosyl, ubiquitination, Complex, LIGASE; LIGASE
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.

7ppo__assembly_1__model_1

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

Download this curve (.dat)

7ppo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ppo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.55 Å
Rg (electron density)	35.86 Å
Total Rg	36.39 Å
Atom count	10989
Residues	1381
Excluded volume	195070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ppo__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Ubiquitinating/deubiquitinating enzyme SdeA
Molecular weight formula_weight	111200.4 kDa
EC 编号 ec_number	3.4.22.-,2.3.2.-,2.4.2.31
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10990

HHHHHHSAGLEVLFQGPMVGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKYHEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVDLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVVSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFPGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIFLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTXSEFSVYLPEDVALVPVKVTLDGKTQKGENRYVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNEVEAVQYSHLSTGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEEARQAKRQMDAIKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELREQIQSARQELESLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGISNLSNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISA

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calmodulin-dependent glutamylase SidJ
Molecular weight formula_weight	91827.0 kDa
EC 编号 ec_number	6.-.-.-
Mutation mutation	E565A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

HHHHHHSAGLEVLFQGPMVKQYYFARRGETSTHDTSLPPPVKVLSGRSIPLKEIPFETTRNELVQIYLTSVDQLIKSNKLNSIPSQQIASHYLFLRSLANSETDGIKKNQILSLAKPLGIYLASKEPHVWKTINELIEKSEYPIIHYLKNNRAHSNFMLALIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNFYHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQNDVVAVKVQKRGEPKSTLEEEFQMADYLLKHQSRLDVYSKLPQPLGQYSVKKSEILEISRGSLDFERFKTLIGDSKDLEVYVYKAPLTYFTYLHDKNQDLEDLTASVKTNVHDLFVLLREGIMFPQLADIFHTHFGEDEREDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGLADLGDSLPITSLFTSSDFTKHYFSALLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYLNTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSRALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGLSVDGTHQDLGGYNRESPLRELEKLLYATVTLIEGTMQLDKEFFKQLQQVEKILSGEIKTDANSCFEAVAQLLDLARPRCHFQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVAKTNAAITIQRFWRETRKNLSENSDIESEKPESERTTDKRLK

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	446
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Calmodulin
Molecular weight formula_weight	19066.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HHHHHHSSGLEVLFQGPHMMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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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	2.91 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	140022

Structure of SidJ/CaM bound to SdeA in pre-glutamylation state

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

Ubiquitinating/deubiquitinating enzyme SdeA

State in the Current Structure

Other States of the Same Protein in the Database

Calmodulin-dependent glutamylase SidJ

State in the Current Structure

Other States of the Same Protein in the Database

Calmodulin

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

7ppo__assembly_1__model_1

7ppo__assembly_1__model_1 | I(q)

7ppo__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Structure of SidJ/CaM bound to SdeA in pre-glutamylation state

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

Ubiquitinating/deubiquitinating enzyme SdeA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Calmodulin-dependent glutamylase SidJ

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Calmodulin

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

7ppo__assembly_1__model_1

7ppo__assembly_1__model_1 | I(q)

7ppo__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)