SAXSdb — 3cr7

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

Adenylyl-sulfate kinase

Penicillium chrysogenum

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–211 Chain B； UniProt 23–211	Fragment：UNP residues 23-211	CL CHLORIDE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.279
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 23–211 Chain D； UniProt 23–211	Fragment：UNP residues 23-211	CL CHLORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.279

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 3CR7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D6J CRYSTAL STRUCTURE OF ADENOSINE 5'-PHOSPHOSULFATE (APS) KINASE FROM PENICILLIUM CHRYSOGENUM Deposited 1999-10-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH；pH 6；298 K；1.0 M NA/K TARTRATE, O.1 M MES, PH 6.0, 0.5% POLYETHYLINIMINE, BATCH, temperature 298K	Resolution 2.00 Å R-free 0.249
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 4 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 1 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 2 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 1 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7G Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 6 AV2 ADENOSINE-5'-DIPHOSPHATE-2',3'-VANADATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.43 Å R-free 0.205
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ADX ADENOSINE-5'-PHOSPHOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258
1M7H Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer Deposited 2002-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–211（211 aa） Chain B 1–211（211 aa） Chain C 1–211（211 aa） Chain D 1–211（211 aa）	Not recorded	SO4 SULFATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ADX ADENOSINE-5'-PHOSPHOSULFATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；Na monobasic phosphate, K dibasic phosphate, succinate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.258

3 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KAPS_PENCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–189； UniProt 23–211 Author chain B； PDBConstruct 1–189； UniProt 23–211 Author chain C； PDBConstruct 1–189； UniProt 23–211 Author chain D； PDBConstruct 1–189； UniProt 23–211

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	3cr7
Deposition date deposition_date	2008-04-04
Structure title title	Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS
Keywords keywords	;APS kinase, Adenylylsulfate kinase, Transferase, sulfate metabolism, Nucleotide 2 kinase, Amino-acid biosynthesis, ATP-binding, Cysteine biosynthesis, Methionine biosynthesis, Nucleotide-binding, Phosphoprotein ;; 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	29.03 Å
Radius of gyration Rg (electron density) rg_electron	28.25 Å
Forward intensity I(0) i0	113088000.00
Molecular weight molecular_weight	81170.0 kDa
Excluded volume excluded_volume	100500 Å³
Envelope volume envelope_volume	123630 Å³
Hydration-shell volume shell_volume	36052 Å³
Envelope diameter envelope_diameter	92.2 Å
Shell Rg shell_rg	36.05 Å
Envelope Rg envelope_rg	27.98 Å
Shape Rg shape_rg	28.27 Å
Total Rg total_rg	28.96 Å
Total atoms total_atoms	5721
Residues n_residues	721
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	90.0 Å
Rg (real space) rg_real	28.92 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.1310e+08
I(0) uncertainty (real space) i0_real_error	1.5880e+06
Rg (reciprocal space) rg_reciprocal	28.97 Å
I(0) (reciprocal space) i0_reciprocal	113100000.0000
Solution quality estimate total_estimate	0.9067
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.174
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40810000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.929

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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	Adenylyl-sulfate kinase
Molecular weight formula_weight	22354.1 kDa
EC 编号 ec_number	2.7.1.25
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	6230

QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAKKELEHHHHHH

来源 Source

来源生物 organism	Penicillium chrysogenum
通用名 common_name	Penicillium notatum
NCBI Class编号 ncbi_taxonomy_id	5076
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE ;
Molecular weight formula_weight	507.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	495

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3cr7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d3cr7b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d3cr7c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

Domain ID domain_id	d3cr7d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.4 — Adenosine-5'phosphosulfate kinase (APS kinase)

CATH v4.4 (4 domains)

Domain ID domain_id	3cr7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cr7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cr7C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3cr7D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	77.580 Å
Unit-cell length b length_b	82.594 Å
Unit-cell length c length_c	139.009 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	31.715 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2790

fit	/app/data/saxs_computation/cr/3cr7/3cr7.fit
pddf	/app/data/pr_computation/cr/3cr7/3cr7.pr.out
profile	/app/data/saxs_computation/cr/3cr7/3cr7.dat

Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS

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

Adenylyl-sulfate kinase

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