1ct9

CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI

Method: X-RAY DIFFRACTION D_max: 167.3 Å Quality: REASONABLE

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：ASPARAGINE SYNTHETASE B × 2 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：C1A	IUM URANYL (VI) ION × 8 CL CHLORIDE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 GLN GLUTAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；PEG 8000, HEPES, MAGNESIUM CHLORIDE, L-GLUTAMINE, ADENOSINE 5'-MONOPHOSPHATE, SODIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.297
2	Protein homooligomer Homooligomer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：ASPARAGINE SYNTHETASE B × 2 缺少 UniProt 身份时不显示参考序列区间	Entity 1Mutation：C1A	IUM URANYL (VI) ION × 8 CL CHLORIDE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 GLN GLUTAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；PEG 8000, HEPES, MAGNESIUM CHLORIDE, L-GLUTAMINE, ADENOSINE 5'-MONOPHOSPHATE, SODIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.297

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ct9
Deposition date deposition_date	1999-08-20
Structure title title	CRYSTAL STRUCTURE OF ASPARAGINE SYNTHETASE B FROM ESCHERICHIA COLI
Keywords keywords	AMIDOTRANSFERASE, SUBSTRATE CHANNELING, ASPARAGINE BIOSYNTHESIS, LIGASE; LIGASE
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	58.68 Å
Radius of gyration Rg (electron density) rg_electron	58.87 Å
Forward intensity I(0) i0	779168000.00
Molecular weight molecular_weight	229710.0 kDa
Excluded volume excluded_volume	283210 Å³
Envelope volume envelope_volume	401070 Å³
Hydration-shell volume shell_volume	55061 Å³
Envelope diameter envelope_diameter	178.2 Å
Shell Rg shell_rg	65.79 Å
Envelope Rg envelope_rg	56.26 Å
Shape Rg shape_rg	58.89 Å
Total Rg total_rg	58.91 Å
Total atoms total_atoms	15934
Residues n_residues	1982
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	167.3 Å
Rg (real space) rg_real	59.05 Å
Rg uncertainty (real space) rg_real_error	1.82 Å
I(0) (real space) i0_real	7.7920e+08
I(0) uncertainty (real space) i0_real_error	1.6670e+07
Rg (reciprocal space) rg_reciprocal	58.29 Å
I(0) (reciprocal space) i0_reciprocal	778200000.0000
Solution quality estimate total_estimate	0.6692
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.2 Å
Skewness Skewness skewness	0.174
Kurtosis Kurtosis kurtosis	-1.202
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40060000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.378; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.562; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	ASPARAGINE SYNTHETASE B
Molecular weight formula_weight	62575.7 kDa
EC 编号 ec_number	6.3.5.4
Mutation mutation	C1A
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	16980

ASIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDDPSGRAVGVHQSAYK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URANYL (VI) ION
Molecular weight formula_weight	270.0 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	GLUTAMINE
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1046

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ct9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1ct9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d1ct9b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1ct9b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d1ct9c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1ct9c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

Domain ID domain_id	d1ct9d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1ct9d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.1 — Class II glutamine amidotransferases

CATH v4.4 (8 domains)

Domain ID domain_id	1ct9A01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1ct9A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1ct9B01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1ct9B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1ct9C01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1ct9C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1ct9D01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

Domain ID domain_id	1ct9D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

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8. Citations (1)

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Unit-cell length a length_a	99.930 Å
Unit-cell length b length_b	127.100 Å
Unit-cell length c length_c	204.510 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	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2970

fit	/app/data/saxs_computation/ct/1ct9/1ct9.fit
pddf	/app/data/pr_computation/ct/1ct9/1ct9.pr.out
profile	/app/data/saxs_computation/ct/1ct9/1ct9.dat