SAXSdb — 1lcd

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

Lac 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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–51	Not recorded	;DNA (5'-D(APAPTPTPGPTPGPAPGPCPG)-3') ; × 1 ;DNA (5'-D(CPGPCPTPCPAPCPAPAPTPT)-3') ; × 1 NA SODIUM ION × 1	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1LCD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJG NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX Deposited 1999-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：HEADPIECE, RESIDUES 1 - 62 Chain B 1–62（62 aa） Fragment：HEADPIECE, RESIDUES 1 - 62	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；315 K；Ionic strength (raw mmCIF value) SEE ARTICLE；Pressure 1 NMR sample composition SEE ARTICLE	Resolution not provided
1EFA CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF Deposited 2000-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–333（333 aa） Fragment：RESIDUES 1-333 Chain B 1–333（333 aa） Fragment：RESIDUES 1-333	Mutation：ALA109THR Mutation：ALA109THR	NPF 2-nitrophenyl beta-D-fucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, HEPES, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.60 Å R-free 0.264
1EFA CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF Deposited 2000-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–333（333 aa） Fragment：RESIDUES 1-333	Mutation：ALA109THR	NPF 2-nitrophenyl beta-D-fucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, HEPES, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.60 Å R-free 0.264
1JWL Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex Deposited 2001-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–333（333 aa） Fragment：C-terminal deletion mutant Chain B 1–333（333 aa） Fragment：C-terminal deletion mutant	Not recorded	NPF 2-nitrophenyl beta-D-fucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 4.00 Å R-free 0.261
1JWL Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex Deposited 2001-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–333（333 aa） Fragment：C-terminal deletion mutant	Not recorded	NPF 2-nitrophenyl beta-D-fucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 4.00 Å R-free 0.261
1JYE Structure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution Deposited 2001-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–349（349 aa） Fragment：C-TERMINAL DELETION MUTANT	Mutation：YES	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；Sodium Acetate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.241
1JYF Structure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion. Deposited 2001-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–349（349 aa） Fragment：C-TERMINAL DELETION	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；Sodium Citrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.252
1L1M SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1 Deposited 2002-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：N-terminal DNA-binding domain, Residues 1-62 Chain B 1–62（62 aa） Fragment：N-terminal DNA-binding domain, Residues 1-62	Mutation：V52C Mutation：V52C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 10mM KPi, 20mM KCl；Pressure ambient NMR sample composition 2mM Lac-HP62-V52C U-15N,13C, 10mM KPi, 20mM KCl, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1LBG LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY Deposited 1996-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–360（360 aa） Chain B 1–360（360 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.80 Å
1LBG LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY Deposited 1996-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 1–360（360 aa） Chain D 1–360（360 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.80 Å
1LBH INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG Deposited 1996-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–360（360 aa） Chain B 1–360（360 aa） Chain C 1–360（360 aa） Chain D 1–360（360 aa）	Not recorded	IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å
1LBI LAC REPRESSOR Deposited 1996-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–360（360 aa） Chain B 1–360（360 aa） Chain C 1–360（360 aa） Chain D 1–360（360 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1LCC STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS Deposited 1993-03-25	Parsed fields agree	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–51（51 aa）	Not recorded	NA SODIUM ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1LQC LAC REPRESSOR HEADPIECE (RESIDUES 1-56), NMR, 32 STRUCTURES Deposited 1996-08-13	Different construct Different oligomeric state Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–56（56 aa） Fragment：HEADPIECE, RESIDUES 1 - 56	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1OSL Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence Deposited 2003-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：N-terminal DNA-binding domain, residues 1-62 Chain B 1–62（62 aa） Fragment：N-terminal DNA-binding domain, residues 1-62	Mutation：V52C Mutation：V52C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；300 K；Ionic strength (raw mmCIF value) 400mM KCl, 60mM KPi；Pressure ambient NMR sample composition 2mM LAC-HP62-V52C U-15N,13C, 60mM KPI, 400mM KCL \| 90% H2O/10% D2O	Resolution not provided
1TLF UNPRECEDENTED QUATERNARY STRUCTURE OF E. COLI LAC REPRESSOR CORE TETRAMER: IMPLICATIONS FOR DNA LOOPING Deposited 1995-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 19–319（301 aa） Chain B 19–319（301 aa） Chain C 19–319（301 aa） Chain D 19–319（301 aa）	Not recorded	EMC ETHYL MERCURY ION × 4 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
2BJC NMR structure of a protein-DNA complex of an altered specificity mutant of the lac repressor headpiece that mimics the gal repressor Deposited 2005-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62 Chain B 1–62（62 aa） Fragment：DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62	Mutation：YES Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 20；Pressure 1.0 NMR sample composition 95% WATER/5% D2O	Resolution not provided
2KEI Refined Solution Structure of a Dimer of LAC repressor DNA-Binding domain complexed to its natural operator O1 Deposited 2009-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：UNP residues 1-62 Chain B 1–62（62 aa） Fragment：UNP residues 1-62	Mutation：V52C Mutation：V52C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient NMR sample composition 2 mM DNA (5'-D(DGPDAPDAPDTPDTPDGPDTPDGPDAPDGPDCPDGPDGPDAPDTPDAPDAPDCPDAPDAPDTPDTPDT)-3'), 2 mM DNA (5'-D(PDAPDAPDAPDTPDTPDGPDTPDTPDAPDTPDCPDCPDGPDCPDTPDCPDAPDCPDAPDAPDTPDTPDC)-3'), 2 mM Lac headpiece dimer, 10% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KEJ Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O2 Deposited 2009-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：UNP residues 1-62 Chain B 1–62（62 aa） Fragment：UNP residues 1-62	Mutation：V52C Mutation：V52C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient NMR sample composition 0.7 mM DNA (5'-D(DGPDAPDAPDTPDTPDGPDTPDGPDAPDGPDCPDGPDGPDAPDTPDAPDAPDCPDAPDAPDTPDTPDT)'), 0.7 mM DNA (5'-D(PDAPDAPDAPDTPDTPDGPDTPDTPDAPDTPDCPDCPDGPDCPDTPDCPDAPDCPDAPDAPDTPDTPDC)'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2KEK Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O3 Deposited 2009-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–62（62 aa） Fragment：UNP residues 1-62 Chain B 1–62（62 aa） Fragment：UNP residues 1-62	Mutation：V52C Mutation：V52C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient NMR sample composition 0.7 mM DNA (5'-strand1-3'), 0.7 mM DNA (5'-strand2-3'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2P9H High resolution structure of the Lactose Repressor bound to IPTG Deposited 2007-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 62–330（269 aa） Chain B 62–330（269 aa）	Not recorded	IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；281 K；1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 2.00 Å R-free 0.246
2PAF Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state Deposited 2007-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 62–330（269 aa） Chain B 62–330（269 aa）	Not recorded	NPF 2-nitrophenyl beta-D-fucopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；281 K；1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.50 Å R-free 0.265
2PE5 Crystal Structure of the Lac Repressor bound to ONPG in repressed state Deposited 2007-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 2–331（330 aa） Fragment：sequence database residues 2-331 Chain B 2–331（330 aa） Fragment：sequence database residues 2-331	Mutation：S61L Mutation：S61L	145 2-nitrophenyl beta-D-galactopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；281 K；1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.50 Å R-free 0.287
2PE5 Crystal Structure of the Lac Repressor bound to ONPG in repressed state Deposited 2007-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 2–331（330 aa） Fragment：sequence database residues 2-331	Mutation：S61L	145 2-nitrophenyl beta-D-galactopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；281 K；1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.50 Å R-free 0.287
3EDC Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution Deposited 2008-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–360（360 aa） Chain B 1–360（360 aa） Chain C 1–360（360 aa） Chain D 1–360（360 aa）	Not recorded	HEZ HEXANE-1,6-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；microseeded, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.10 Å R-free 0.201

21 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LACI_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–51； UniProt 1–51

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	1lcd
Deposition date deposition_date	1993-03-25
Structure title title	STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS
Keywords keywords	GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/DNA
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.39 Å
Radius of gyration Rg (electron density) rg_electron	14.07 Å
Forward intensity I(0) i0	39083200.00
Molecular weight molecular_weight	37203.0 kDa
Excluded volume excluded_volume	40983 Å³
Envelope volume envelope_volume	20550 Å³
Hydration-shell volume shell_volume	12041 Å³
Envelope diameter envelope_diameter	52.1 Å
Shell Rg shell_rg	20.16 Å
Envelope Rg envelope_rg	15.17 Å
Shape Rg shape_rg	13.96 Å
Total Rg total_rg	14.71 Å
Total atoms total_atoms	2970
Residues n_residues	219
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	49.6 Å
Rg (real space) rg_real	14.35 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	3.9080e+07
I(0) uncertainty (real space) i0_real_error	4.9090e+05
Rg (reciprocal space) rg_reciprocal	14.36 Å
I(0) (reciprocal space) i0_reciprocal	39080000.0000
Solution quality estimate total_estimate	0.7954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.0 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.382
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	497200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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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	;DNA (5'-D(APAPTPTPGPTPGPAPGPCP*G)-3') ;
Molecular weight formula_weight	3413.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	3384

AATTGTGAGCG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPGPCPTPCPAPCPAPAPTP*T)-3') ;
Molecular weight formula_weight	3293.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

CGCTCACAATT

Entity 3 Entity 3 polymer

Description description	Lac Repressor
Molecular weight formula_weight	5693.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 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	49

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1lcda_
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.5 — GalR/LacI-like bacterial regulator

CATH v4.4 (1 domains)

Domain ID domain_id	1lcdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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8. Citations (10)

;Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. ;

J.Mol.Biol. (1993)

PMID: 8230225 · DOI: 10.1006/jmbi.1993.1598 PRIMARY

;Assignment of the 1H-NMR Spectrum of a Lac Repressor Headpiece-Operator Complex in H2O and Identification of Noes. Consequences for Protein-DNA Interaction ;

Eur.J.Biochem. (1990)

Two-Dimensional NMR Study of a Protein-DNA Complex. Lac Repressor Headpiece-Operator Interaction

Biochem.Pharm. (1990)

1H NMR Study of a Complex between the Lac Repressor Headpiece and a 22 Base Pair Symmetric Lac Operator

Biochemistry (1989)

NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment

Ucla Symp.Mol.Cell.Biol., New Ser. (1989)

The Interaction of Lac Repressor Headpiece with its Operator: An NMR View

Protein Seq.Data Anal. (1988)

;Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data: Application to the DNA Binding Domain of Lac Repressor from Escherichia Coli ;

Proteins (1988)

A Two-Dimensional NMR Study of the Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment

Nato Asi Ser.,Ser.A (1987)

Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance

J.Mol.Biol. (1987)

;Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of Noes ;

Isr.J.Chem. (1986)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

fit	/app/data/saxs_computation/lc/1lcd/1lcd.fit
pddf	/app/data/pr_computation/lc/1lcd/1lcd.pr.out
profile	/app/data/saxs_computation/lc/1lcd/1lcd.dat

STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS

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

Lac 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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (10)

9. Files and Curves (10)

Files (7)

Curves (3)