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1l3g

NMR Structure of the DNA-binding Domain of Cell Cycle Protein, Mbp1(2-124) from Saccharomyces cerevisiae

Method: SOLUTION NMR Dmax: 40.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRANSCRIPTION FACTOR Mbp1

Saccharomyces cerevisiae

UniProt P39678

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–124 Fragment：DNA-BINDING DOMAIN (RESIDUES 2-124) No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.6；288 K NMR sample composition：Mbp1 U-15N,13C 40mM Na-Phosphate, 100mM NaCl | 90% H2O/10% D2O NMR sample composition：Mbp1 U-15N, 40mM Na-Phosphate, 100mM NaCl | 90% H2O/10% D2O 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 1L3G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BM8 DNA-BINDING DOMAIN OF MBP1 Deposited 1998-07-29 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–102（99 aa） Fragment：N-TERMINAL DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.71 Å R-free 0.261
1MB1 MBP1 FROM SACCHAROMYCES CEREVISIAE Deposited 1997-07-23 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–124（124 aa） Fragment：DNA-BINDING DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；pH 6.9
Resolution 2.10 Å R-free 0.290

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MBP1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–123； UniProt 2–124

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

SAXS profile for 1l3g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l3g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l3g
Deposition date deposition_date2002-02-27
Structure title titleNMR Structure of the DNA-binding Domain of Cell Cycle Protein, Mbp1(2-124) from Saccharomyces cerevisiae
Keywords keywordscell cycle, Mlu 1 cell cycle box Binding Protein, winged helix-turn-helix proteins; CELL CYCLE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.06 Å
Radius of gyration Rg (electron density) rg_electron14.95 Å
Forward intensity I(0) i0937147000.00
Molecular weight molecular_weight264190.0 kDa
Excluded volume excluded_volume332760 ų
Envelope volume envelope_volume52239 ų
Hydration-shell volume shell_volume20666 ų
Envelope diameter envelope_diameter74.6 Å
Shell Rg shell_rg28.45 Å
Envelope Rg envelope_rg23.34 Å
Shape Rg shape_rg14.93 Å
Total Rg total_rg15.39 Å
Total atoms total_atoms36974
Residues n_residues2337
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax40.3 Å
Rg (real space) rg_real14.00 Å
Rg uncertainty (real space) rg_real_error0.06 Å
I(0) (real space) i0_real8.8820e+08
I(0) uncertainty (real space) i0_real_error7.8560e+06
Rg (reciprocal space) rg_reciprocal15.23 Å
I(0) (reciprocal space) i0_reciprocal937100000.0000
Solution quality estimate total_estimate0.6762
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.3 Å
Skewness Skewness skewness0.310
Kurtosis Kurtosis kurtosis-0.208
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.7820
Highest regularization parameter α highest_alpha406200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.949; Stabil: 0.984; Sysdev: 0.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1l3ga_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.34 — DNA-binding domain of Mlu1-box binding protein MBP1
Superfamily Superfamily superfamilyd.34.1 — DNA-binding domain of Mlu1-box binding protein MBP1
Family Family familyd.34.1.1 — DNA-binding domain of Mlu1-box binding protein MBP1

CATH v4.4 (1 domains)

Domain ID domain_id1l3gA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily10 — Transcription regulator HTH, APSES-type DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)