SAXSdb — 1mjo

▼

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

METHIONINE REPRESSOR

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–DNA Homooligomer Protein × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 1–104 Chain B； UniProt 1–104 Chain C； UniProt 1–104 Chain D； UniProt 1–104	Mutation：Q44K	CONSENSUS DNA OPERATOR DUPLEX WITH THE CENTRAL TA STEP MUTATED TO AT × 2 SAM S-ADENOSYLMETHIONINE × 4 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；PROTEIN (10MG/ML) + SAM (1MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 28-38% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 6.0-7.0	Resolution 2.10 Å R-free 0.241

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 1MJO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CMA MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE Deposited 1992-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.00, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å
1CMB THREE DIMENSIONAL CRYSTAL STRUCTURES OF ESCHERICHIA COLI MET REPRESSOR WITH AND WITHOUT COREPRESSOR Deposited 1992-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1CMC THREE DIMENSIONAL CRYSTAL STRUCTURES OF E. COLI MET REPRESSOR WITH AND WITHOUT COREPRESSOR Deposited 1992-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Not recorded	MG MAGNESIUM ION × 2 SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1MJ2 METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO A CONSENSUS OPERATOR SEQUENCE Deposited 1998-01-27	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa） Chain C 1–104（104 aa） Chain D 1–104（104 aa）	Mutation：Q44K Mutation：Q44K Mutation：Q44K Mutation：Q44K	SAM S-ADENOSYLMETHIONINE × 4 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.40 Å R-free 0.260
1MJK METHIONINE REPRESSOR MUTANT APOREPRESSOR (Q44K) FROM ESCHERICHIA COLI Deposited 1998-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：Q44K Mutation：Q44K	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 16-28% PEG 600, 1.5% NAIO4, 100MM POTASSIUM PHOSPHATE BUFFER, PH 7.0.	Resolution 2.15 Å R-free 0.223
1MJL METHIONINE REPRESSOR MUTANT (Q44K) COMPLEX WITH THE COREPRESSOR SAM (S-ADENOSYL METHIONINE) FROM ESCHERICHIA COLI Deposited 1998-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：Q44K Mutation：Q44K	SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (10MG/ML) + SAM (1MG/ ML) WAS CRYSTALLIZED FROM 10-30% PEG 600, 100MM SODIUM CACODYLATE BUFFER, PH 4.6-5.2., pH 7.0	Resolution 2.10 Å R-free 0.197
1MJM METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE Deposited 1998-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：Q44K Mutation：Q44K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (10MG/ML) + DNA (3.8MG/ML) WAS CRYSTALLISED FROM 8-14% P4000, 100MM CITRATE BUFFER, PH 5.0-6.0, 20% GLYCEROL, pH 7.0	Resolution 2.20 Å R-free 0.282
1MJP METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR Deposited 1998-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa）	Mutation：Q44K Mutation：Q44K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (10MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 40% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 7.0.	Resolution 3.40 Å R-free 0.309
1MJQ METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO AN ALTERED MET CONSENSUS OPERATOR SEQUENCE Deposited 1998-01-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 1–104（104 aa） Chain B 1–104（104 aa） Chain C 1–104（104 aa） Chain D 1–104（104 aa）	Mutation：Q44K Mutation：Q44K Mutation：Q44K Mutation：Q44K	SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (10MG/ML) + SAM(1.5MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 28-38% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 6.0-7.0, 40MM CACL2	Resolution 2.40 Å R-free 0.268
1MJQ METHIONINE REPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO AN ALTERED MET CONSENSUS OPERATOR SEQUENCE Deposited 1998-01-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain G 1–104（104 aa） Chain H 1–104（104 aa） Chain I 1–104（104 aa） Chain J 1–104（104 aa）	Mutation：Q44K Mutation：Q44K Mutation：Q44K Mutation：Q44K	SAM S-ADENOSYLMETHIONINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN (10MG/ML) + SAM(1.5MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 28-38% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 6.0-7.0, 40MM CACL2	Resolution 2.40 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	METJ_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain B； PDBConstruct 1–104； UniProt 1–104 Author chain C； PDBConstruct 1–104； UniProt 1–104 Author chain D； PDBConstruct 1–104； UniProt 1–104

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1mjo
Deposition date deposition_date	1998-01-28
Structure title title	METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT
Keywords keywords	;TRANSCRIPTION REGULATION, METJ, METHIONINE REPRESSOR, SHEET-HELIX-HELIX, S-ADENOSYL METHIONINE, DNA, COMPLEX (TRANSCRIPTION REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.91 Å
Radius of gyration Rg (electron density) rg_electron	25.14 Å
Forward intensity I(0) i0	79956200.00
Molecular weight molecular_weight	61300.0 kDa
Excluded volume excluded_volume	73048 Å³
Envelope volume envelope_volume	90549 Å³
Hydration-shell volume shell_volume	29891 Å³
Envelope diameter envelope_diameter	82.0 Å
Shell Rg shell_rg	32.64 Å
Envelope Rg envelope_rg	25.16 Å
Shape Rg shape_rg	25.14 Å
Total Rg total_rg	25.87 Å
Total atoms total_atoms	4261
Residues n_residues	453
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.7 Å
Rg (real space) rg_real	25.83 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	7.9960e+07
I(0) uncertainty (real space) i0_real_error	9.8350e+05
Rg (reciprocal space) rg_reciprocal	25.86 Å
I(0) (reciprocal space) i0_reciprocal	79960000.0000
Solution quality estimate total_estimate	0.9082
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8674000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.965

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CONSENSUS DNA OPERATOR DUPLEX WITH THE CENTRAL TA STEP MUTATED TO AT
Molecular weight formula_weight	5819.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,G
Atom count atom_count	4771

TTAGACGTCATGACGTCTA

Entity 2 Entity 2 polymer

Description description	METHIONINE REPRESSOR
Molecular weight formula_weight	12028.6 kDa
Mutation mutation	Q44K
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

AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPETWEY

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 3 Entity 3 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	510

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1mjoa_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.5 — Met repressor, MetJ (MetR)

Domain ID domain_id	d1mjob_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.5 — Met repressor, MetJ (MetR)

Domain ID domain_id	d1mjoc_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.5 — Met repressor, MetJ (MetR)

Domain ID domain_id	d1mjod_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.5 — Met repressor, MetJ (MetR)

CATH v4.4 (4 domains)

Domain ID domain_id	1mjoA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	140 — MET Apo-Repressor, subunit A
Homologous superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

Domain ID domain_id	1mjoB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	140 — MET Apo-Repressor, subunit A
Homologous superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

Domain ID domain_id	1mjoC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	140 — MET Apo-Repressor, subunit A
Homologous superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

Domain ID domain_id	1mjoD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	140 — MET Apo-Repressor, subunit A
Homologous superfamily homologous superfamily	10 — MET Apo-Repressor, subunit A

▶

8. Citations (1)

▶

Unit-cell length a length_a	117.505 Å
Unit-cell length b length_b	117.505 Å
Unit-cell length c length_c	90.208 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	31.800 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2410

fit	/app/data/saxs_computation/mj/1mjo/1mjo.fit
pddf	/app/data/pr_computation/mj/1mjo/1mjo.pr.out
profile	/app/data/saxs_computation/mj/1mjo/1mjo.dat

METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT

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

METHIONINE REPRESSOR

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 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)