SAXSdb — 1zym

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

ENZYME I

Escherichia coli

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 1–258 Chain B； UniProt 1–258	Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 258	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.306

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 1ZYM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EZA AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 1997-01-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
1EZB AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 17 STRUCTURES Deposited 1997-01-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
1EZC AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 17 STRUCTURES Deposited 1997-01-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
1EZD AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI NMR, 16 STRUCTURES Deposited 1997-01-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
2EZA AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 1997-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
2EZB AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 14 STRUCTURES Deposited 1997-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
2EZC AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 14 STRUCTURES Deposited 1997-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–258（258 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；313 K	Resolution not provided
2HWG Structure of phosphorylated Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system Deposited 2006-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–575（575 aa） Chain B 1–575（575 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 OXL OXALATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；The protein sample (10 mg/mL) was mixed with MgCl2 and PEP to bring each additive to a final concentration of 10 mM. After ~5 min, sodium oxalate was added to a final concentration of 10 mM. Drops containing 1:1 protein and reservoir solution were equilibrated against reservoir solution containing 22% w/v polyethylene glycol 6000, 2% saturated ammonium sulfate, and 100 mM Na+HEPES., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.70 Å R-free 0.284
2KX9 Solution Structure of the Enzyme I dimer Using Residual Dipolar Couplings and Small Angle X-Ray Scattering Deposited 2010-04-29	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–573（573 aa） Fragment：UNP residues 1-573 Chain B 1–573（573 aa） Fragment：UNP residues 1-573	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 7.4；310 K；Pressure ambient NMR sample composition 20 mM TRIS, 100 mM sodium chloride, 10 mM DTT, 4 mM MgCl2, 1 mM EDTA, 10 % D2O, 1 tablet protease inhibitor, 0.15 mM EI dimer, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L5H Solution Structure of the H189Q mutant of the Enzyme I dimer Using Residual Dipolar Couplings and Small Angle X-Ray Scattering Deposited 2010-11-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–573（573 aa） Chain B 1–573（573 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 7.4；310 K；Pressure ambient NMR sample composition 20 mM TRIS-1, 100 mM sodium chloride-2, 10 mM DTT-3, 4 mM MgCl2-4, 1 mM EDTA-5, 10 % D2O-6, 0.15 mM EI dimer-8, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MP0 Protein Phosphorylation upon a Fleeting Encounter Deposited 2014-05-08	Different construct Different mutation/modification Different oligomeric state 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 1–258（258 aa） Fragment：N-terminal Domain, residues 1-258	Not recorded	PO3 PHOSPHITE ION × 1	SOLUTION NMR NMR measurement conditions pH 7.4；313.4 K NMR sample composition 0.5 mM [U-99% 15N] N-terminal Domain of Enzyme I-1, 0.5 mM [U-99% 15N] Enzyme II of Glucose-2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1-14 mM [U-100% 1H; U-100% 12C; U-99%1 5N] N-terminal Domain of Enzyme I-3, 1-14 mM [U-99% 15N] EIN EIIAGlc-4, 1-14 mM EIN-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.4-1.5 mM [U-100% 2H; U-100% 12C; U-99% 15N] N-terminal Domain of Enzyme I-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N5T Ensemble solution structure of the phosphoenolpyruvate-Enzyme I complex from the bacterial phosphotransferase system Deposited 2015-07-28	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–575（575 aa） Chain B 1–575（575 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 7.4；310 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.4 mM [U-13C; U-15N; U-2H] EIA, 20 mM TRIS, 1 mM EDTA, 100 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2XDF Solution Structure of the Enzyme I Dimer Complexed with HPr Using Residual Dipolar Couplings and Small Angle X-Ray Scattering Deposited 2010-04-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–573（573 aa） Chain B 1–573（573 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 7.4；310 K；Pressure 1.0 NMR sample composition 90% H2O/10% D2O	Resolution not provided
3EZA COMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 1998-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–249（249 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 249	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
3EZB COMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI Deposited 1998-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–259（259 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided
3EZE COMPLEX OF THE AMINO TERMINAL DOMAIN OF ENZYME I AND THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE Deposited 1998-11-04	Different construct Different mutation/modification Different oligomeric state 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 1–259（259 aa） Fragment：AMINO-TERMINAL DOMAIN RESIDUES 1 - 259	Not recorded	PO3 PHOSPHITE ION × 1	SOLUTION NMR NMR measurement conditions pH 7；313 K	Resolution not provided

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PT1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258 Author chain B； PDBConstruct 1–258； UniProt 1–258

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	1zym
Deposition date deposition_date	1996-05-21
Structure title title	AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI
Keywords keywords	PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
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	32.64 Å
Radius of gyration Rg (electron density) rg_electron	32.97 Å
Forward intensity I(0) i0	47000700.00
Molecular weight molecular_weight	53938.0 kDa
Excluded volume excluded_volume	67695 Å³
Envelope volume envelope_volume	90353 Å³
Hydration-shell volume shell_volume	26134 Å³
Envelope diameter envelope_diameter	124.9 Å
Shell Rg shell_rg	34.68 Å
Envelope Rg envelope_rg	32.83 Å
Shape Rg shape_rg	32.96 Å
Total Rg total_rg	33.15 Å
Total atoms total_atoms	3790
Residues n_residues	495
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	119.1 Å
Rg (real space) rg_real	33.32 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	4.7000e+07
I(0) uncertainty (real space) i0_real_error	8.0990e+05
Rg (reciprocal space) rg_reciprocal	33.03 Å
I(0) (reciprocal space) i0_reciprocal	46990000.0000
Solution quality estimate total_estimate	0.7449
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.688
Kurtosis Kurtosis kurtosis	-0.104
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9154000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.525; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.369; Smooth: 0.737

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1zyma1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.10 — Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain
Family Family family	a.60.10.1 — Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain

Domain ID domain_id	d1zyma2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.1 — Phosphohistidine domain
Family Family family	c.8.1.2 — N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system

Domain ID domain_id	d1zymb1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.10 — Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain
Family Family family	a.60.10.1 — Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain

Domain ID domain_id	d1zymb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.1 — Phosphohistidine domain
Family Family family	c.8.1.2 — N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system

CATH v4.4 (4 domains)

Domain ID domain_id	1zymA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphohistidine domain

Domain ID domain_id	1zymA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PtsI, HPr-binding domain

Domain ID domain_id	1zymB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphohistidine domain

Domain ID domain_id	1zymB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — PtsI, HPr-binding domain

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8. Citations (1)

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Unit-cell length a length_a	47.420 Å
Unit-cell length b length_b	75.780 Å
Unit-cell length c length_c	170.280 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	8

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	10.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.3060

Description description	ENZYME I
Molecular weight formula_weight	28224.1 kDa
EC 编号 ec_number	2.7.3.9
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3854

AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI

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

ENZYME I

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

fit	/app/data/saxs_computation/zy/1zym/1zym.fit
pddf	/app/data/pr_computation/zy/1zym/1zym.pr.out
profile	/app/data/saxs_computation/zy/1zym/1zym.dat