SAXSdb — 6s5t

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

SidJ

Legionella pneumophila

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–873	Not recorded	Calmodulin-2 × 1 （P0DP24） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.15 Å

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 6S5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6K4K Crystal structure of SidJ-CaM binary complex at 2.71 A Deposited 2019-05-24	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；299 K；20% PEG 3350, 0.2M NaI	Resolution 2.71 Å R-free 0.243
6K4K Crystal structure of SidJ-CaM binary complex at 2.71 A Deposited 2019-05-24	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–873（873 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；299 K；20% PEG 3350, 0.2M NaI	Resolution 2.71 Å R-free 0.243
6K4L Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A Deposited 2019-05-24	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI	Resolution 2.95 Å R-free 0.269
6K4L Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A Deposited 2019-05-24	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–873（873 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI	Resolution 2.95 Å R-free 0.269
6K4R Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A Deposited 2019-05-26	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 CL CHLORIDE ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI, 0.1M HEPES 7.5	Resolution 3.11 Å R-free 0.279
6K4R Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A Deposited 2019-05-26	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–873（873 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；299 K；25% PEG 3350, 0.2M NaI, 0.1M HEPES 7.5	Resolution 3.11 Å R-free 0.279
6OQQ Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex Deposited 2019-04-28	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–873（873 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 MG MAGNESIUM ION × 4 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 9 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M sodium malonate, 0.01 M sodium chloride, 0.001 M magnesium chloride, 0.001 mM calcium chloride, 0.001 M AMP-CPP, 16-17% PEG 3350, 35-40% ethylene glycol	Resolution 2.10 Å R-free 0.234
6OQQ Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex Deposited 2019-04-28	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–873（873 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 2 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M sodium malonate, 0.01 M sodium chloride, 0.001 M magnesium chloride, 0.001 mM calcium chloride, 0.001 M AMP-CPP, 16-17% PEG 3350, 35-40% ethylene glycol	Resolution 2.10 Å R-free 0.234
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 97–853（757 aa）	Not recorded	CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP	Resolution 2.59 Å R-free 0.241
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 97–853（757 aa）	Not recorded	CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP	Resolution 2.59 Å R-free 0.241
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 97–851（755 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7MIS Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex Deposited 2021-04-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 97–851（755 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CA CALCIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 99–873（775 aa）	Mutation：E565A	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
7PQE Structure of SidJ/CaM bound to SdeA in post-catalysis state Deposited 2021-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 99–873（775 aa）	Mutation：E565A	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5ZTK6_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–873； UniProt 1–873

Calmodulin-2

Homo sapiens

UniProt P0DP24

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–149	Not recorded	SidJ × 1 （Q5ZTK6） ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.15 Å

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 6S5T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–148（147 aa）	Not recorded	CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP	Resolution 2.59 Å R-free 0.241
6PLM Legionella pneumophila SidJ/ Calmodulin 2 complex Deposited 2019-07-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–148（147 aa）	Not recorded	CA CALCIUM ION × 3 POP PYROPHOSPHATE 2- × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Tris pH 9.2, 0.2 M Sodium Iodide , 15% PEG 3350, 1 mM Calcium Chloride, 1 mM ATP	Resolution 2.59 Å R-free 0.241
6SZ5 Human calmodulin bound to a peptide of human NADPH oxidase 5 Deposited 2019-10-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30 mM Tris-HCl at pH 7.4, 2.5 mM CaCl2 and 2.5% (v/v) glycerol	Resolution 2.23 Å R-free 0.294
6XXF 1.7 Angstrom crystal structure of Ca/CaM:RyR2 peptide complex Deposited 2020-01-27	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium acetate pH4.5, 0.2M ammonium acetate, 10% PEG4000	Resolution 1.70 Å R-free 0.205
6Y4O Calmodulin bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain Deposited 2020-02-21	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME	Resolution 1.84 Å R-free 0.208
7MIR Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex Deposited 2021-04-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7MIS Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex Deposited 2021-04-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CA CALCIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7PPO Structure of SidJ/CaM bound to SdeA in pre-glutamylation state Deposited 2021-09-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
7PQE Structure of SidJ/CaM bound to SdeA in post-catalysis state Deposited 2021-09-17	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8K9Z Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate	Resolution 2.90 Å R-free 0.304
8K9Z Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG 3350 and 0.18 M magnesium acetate	Resolution 2.90 Å R-free 0.304
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–149（149 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–149（149 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA0 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) Deposited 2023-08-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–149（149 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking	Resolution 2.35 Å R-free 0.263
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–149（149 aa）	Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–149（149 aa）	Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342
8KA1 Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin Deposited 2023-08-02	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–149（149 aa）	Mutation：E124Q Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2	Resolution 2.82 Å R-free 0.342

11 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–149； 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	6s5t
Deposition date deposition_date	2019-07-02
Structure title title	Legionella pneumophila SidJ-Human calmodulin complex
Keywords keywords	Bacterial glutamylase, pseudo kinase, calmodulin-dependent, Legionella, SidJ, SdeA, serine ubiquitination, transferase; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	31.35 Å
Radius of gyration Rg (electron density) rg_electron	30.28 Å
Forward intensity I(0) i0	153773000.00
Molecular weight molecular_weight	98562.0 kDa
Excluded volume excluded_volume	123430 Å³
Envelope volume envelope_volume	163560 Å³
Hydration-shell volume shell_volume	43995 Å³
Envelope diameter envelope_diameter	103.8 Å
Shell Rg shell_rg	38.27 Å
Envelope Rg envelope_rg	30.51 Å
Shape Rg shape_rg	30.27 Å
Total Rg total_rg	31.02 Å
Total atoms total_atoms	6958
Residues n_residues	896
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	98.7 Å
Rg (real space) rg_real	31.22 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.5380e+08
I(0) uncertainty (real space) i0_real_error	2.1270e+06
Rg (reciprocal space) rg_reciprocal	31.28 Å
I(0) (reciprocal space) i0_reciprocal	153800000.0000
Solution quality estimate total_estimate	0.6909
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.7 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41350000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.998; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SidJ
Molecular weight formula_weight	100338.5 kDa
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	6958

MFGFIKKVLDFFGVDQSEDNPSETAVETTDVSTKIKTTDTTQEESSVKTKTVVPTQPGGSVKPETIAPDQQKKHQIKTETTTSTTKQKGPKVTLMDGHVKQYYFARRGETSTHDTSLPPPVKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLIKSNKLNSIPSQQIASHYLFLRSLANSETDGIKKNQILSLAKPLGTYLASKEPHVWKMINELIEKSEYPIIHYLKNNRAHSNFMLALIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNFYHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQNDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRLDVHSKLPQPLGQYSVKKSEILEISRGSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHDKNQDLEDLTASVKTNVHDLFVLLREGIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGLADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYLNTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSRALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGLSVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGTMQLDKEFFKQLEQVEKILSGEIKTDANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVARTNAAITIQRFWREARKNLSEKSDIDSEKPESERTTDKRL

来源 Source

来源生物 organism	Legionella pneumophila
NCBI Class编号 ncbi_taxonomy_id	446
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calmodulin-2
Molecular weight formula_weight	16852.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (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	—

Resolution resolution	4.15 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	19851

fit	/app/data/saxs_computation/s5/6s5t/6s5t.fit
pddf	/app/data/pr_computation/s5/6s5t/6s5t.pr.out
profile	/app/data/saxs_computation/s5/6s5t/6s5t.dat

Legionella pneumophila SidJ-Human calmodulin complex

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

SidJ

State in the Current Structure

Other States of the Same Protein in the Database

Calmodulin-2

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)