SAXSdb — 5h7d

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

Putrescine aminotransferase,Immunoglobulin G-binding protein A

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Zpa963,Calmodulin × 4 （O16305） CALCIUM ION × 8	Consistent with protein count
2	Insufficient information	Heteromer	Protein 8	Zpa963,Calmodulin × 4 （O16305） CALCIUM ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 452–499； UniProt 220–267 Author chain B； PDBConstruct 452–499； UniProt 220–267 Author chain C； PDBConstruct 452–499； UniProt 220–267 Author chain D； PDBConstruct 452–499； UniProt 220–267 Author chain I； PDBConstruct 452–499； UniProt 220–267 Author chain J； PDBConstruct 452–499； UniProt 220–267 Author chain M； PDBConstruct 452–499； UniProt 220–267 Author chain N； PDBConstruct 452–499； UniProt 220–267

Putrescine aminotransferase,Immunoglobulin G-binding protein A

Staphylococcus aureus

UniProt P42588

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Zpa963,Calmodulin × 4 （O16305） CALCIUM ION × 8	Consistent with protein count
2	Insufficient information	Heteromer	Protein 8	Zpa963,Calmodulin × 4 （O16305） CALCIUM ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–451； UniProt 7–453 Author chain B； PDBConstruct 5–451； UniProt 7–453 Author chain C； PDBConstruct 5–451； UniProt 7–453 Author chain D； PDBConstruct 5–451； UniProt 7–453 Author chain I； PDBConstruct 5–451； UniProt 7–453 Author chain J； PDBConstruct 5–451； UniProt 7–453 Author chain M； PDBConstruct 5–451； UniProt 7–453 Author chain N； PDBConstruct 5–451； UniProt 7–453

Zpa963,Calmodulin

Caenorhabditis elegans

UniProt O16305

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	Putrescine aminotransferase,Immunoglobulin G-binding protein A × 4 （P38507,P42588） CALCIUM ION × 8	Consistent with protein count
2	Insufficient information	Heteromer	Protein 8	Putrescine aminotransferase,Immunoglobulin G-binding protein A × 4 （P38507,P42588） CALCIUM ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CALM_CAEEL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 58–120； UniProt 13–75 Author chain F； PDBConstruct 58–120； UniProt 13–75 Author chain G； PDBConstruct 58–120； UniProt 13–75 Author chain H； PDBConstruct 58–120； UniProt 13–75 Author chain K； PDBConstruct 58–120； UniProt 13–75 Author chain L； PDBConstruct 58–120； UniProt 13–75 Author chain O； PDBConstruct 58–120； UniProt 13–75 Author chain P； PDBConstruct 58–120； UniProt 13–75

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	5h7d
Deposition date deposition_date	2016-11-17
Structure title title	Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
Keywords keywords	synthetic protein, TRANSFERASE, IMMUNE SYSTEM-METAL BINDING PROTEIN complex; TRANSFERASE, IMMUNE SYSTEM/METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

5h7d__assembly_1__model_1

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

Download this curve (.dat)

5h7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.14 Å
Rg (electron density)	48.50 Å
Total Rg	48.75 Å
Atom count	18566
Residues	2430
Excluded volume	331700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h7d__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5h7d__assembly_2__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	Putrescine aminotransferase,Immunoglobulin G-binding protein A
Molecular weight formula_weight	54225.1 kDa
EC 编号 ec_number	2.6.1.82
Mutation mutation	N222V, G240A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,I,J,M,N
Atom count atom_count	37132

GSHMSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAMRQQVAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQA

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Zpa963,Calmodulin
Molecular weight formula_weight	13255.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H,K,L,O,P

GSHMKFNKETQEASWEIFTLPNLNGRQVAAFISSLLDDPSQSANLLAEAKKLNQIQAFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	16

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Unit-cell length a length_a	79.489 Å
Unit-cell length b length_b	155.376 Å
Unit-cell length c length_c	155.491 Å
Unit-cell angle α angle_alpha	84.84 °
Unit-cell angle β angle_beta	89.68 °
Unit-cell angle γ angle_gamma	89.56 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2075
R_work r_work	0.2038
R_free r_free	0.2409

Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex

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

Putrescine aminotransferase,Immunoglobulin G-binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Putrescine aminotransferase,Immunoglobulin G-binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Zpa963,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

5h7d__assembly_1__model_1

5h7d__assembly_1__model_1 | I(q)

5h7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex

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

Putrescine aminotransferase,Immunoglobulin G-binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putrescine aminotransferase,Immunoglobulin G-binding protein A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Zpa963,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

5h7d__assembly_1__model_1

5h7d__assembly_1__model_1 | I(q)

5h7d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)