SAXSdb — 1mjm

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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 × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–104 Chain B； UniProt 1–104	Mutation：Q44K	HALF CONSENSUS DNA OPERATOR DUPLEX × 2	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

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 1MJM	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 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 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 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 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: 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 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 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
1MJO METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT Deposited 1998-01-28	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: 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 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
1MJP METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR Deposited 1998-01-29	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 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: 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 construct Different mutation/modification Different oligomeric state 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

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	1mjm
Deposition date deposition_date	1998-01-30
Structure title title	METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE
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

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

Radius of gyration Rg (Guinier) rg_guinier	20.34 Å
Radius of gyration Rg (electron density) rg_electron	19.04 Å
Forward intensity I(0) i0	20504000.00
Molecular weight molecular_weight	30085.0 kDa
Excluded volume excluded_volume	35844 Å³
Envelope volume envelope_volume	43608 Å³
Hydration-shell volume shell_volume	19318 Å³
Envelope diameter envelope_diameter	64.6 Å
Shell Rg shell_rg	25.12 Å
Envelope Rg envelope_rg	19.25 Å
Shape Rg shape_rg	18.98 Å
Total Rg total_rg	19.96 Å
Total atoms total_atoms	2094
Residues n_residues	228
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	61.0 Å
Rg (real space) rg_real	20.23 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	2.0500e+07
I(0) uncertainty (real space) i0_real_error	2.6740e+05
Rg (reciprocal space) rg_reciprocal	20.25 Å
I(0) (reciprocal space) i0_reciprocal	20500000.0000
Solution quality estimate total_estimate	0.7591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2194000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 0.996; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HALF CONSENSUS DNA OPERATOR DUPLEX
Molecular weight formula_weight	3045.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	2271

GAGACGTCTC

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mjma_
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	d1mjmb_
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 (2 domains)

Domain ID domain_id	1mjmA00
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	1mjmB00
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

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8. Citations (1)

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Unit-cell length a length_a	39.960 Å
Unit-cell length b length_b	64.000 Å
Unit-cell length c length_c	114.470 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	2.200 Å
Low-resolution limit resolution_low	25.400 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2820

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

METHIONINE APOREPRESSOR MUTANT (Q44K) COMPLEXED TO HALF OF THE CONSENSUS OPERATOR SEQUENCE

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)