SAXSdb — 3rbn

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

DNA mismatch repair protein Mlh1

Homo sapiens

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 486–751 Chain B； UniProt 486–751	Fragment：UNP residues 486-751 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；22% PEG4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.16 Å R-free 0.251

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 3RBN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P7A Crystal Structure of human MLH1 Deposited 2014-03-26	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 1–347（347 aa）	Not recorded	MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 UNX UNKNOWN LIGAND × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG4000, 10% ISOPROPANOL, 0.1 M HEPES	Resolution 2.30 Å R-free 0.254
5U5P Crystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus Musculus Complexed with a MLH1 NLS Peptide Deposited 2016-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 467–476（10 aa） Chain C 467–476（10 aa）	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.600-0.625 M sodium citrate (pH 6) 10 mM DTT	Resolution 2.17 Å R-free 0.211
6WBA Structure of Mouse Importin alpha MLH1- R470A NLS Peptide Complex Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 466–476（11 aa） Fragment：NLS peptide Chain C 466–476（11 aa） Fragment：NLS peptide	Mutation：R470A Mutation：R470A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M sodium citrate (pH 6), 0.6 M sodium citrate and 10 mM DTT	Resolution 2.15 Å R-free 0.197
6WBB Structure of Mouse Importin alpha - MLH1-E475A NLS peptide complex Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 466–476（11 aa） Fragment：NLS peptide Chain C 466–476（11 aa） Fragment：NLS peptide	Mutation：E475A Mutation：E475A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M sodium citrate (pH 6), 10 mM DTT, 0.55 M sodium citrate	Resolution 2.66 Å R-free 0.227
6WBC Structure of Mouse Importin alpha- MLH1-R472K NLS Peptide Complex Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 466–476（11 aa） Fragment：NLS peptide	Mutation：R472K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M sodium citrate (pH 6), 0.575 M sodium citrate , 10 mM DTT	Resolution 2.15 Å R-free 0.213
7M60 Structure of Mouse Importin alpha MLH1-S467A NLS Peptide Complex Deposited 2021-03-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 466–476（11 aa） Fragment：residues 466-476 Chain C 466–476（11 aa） Fragment：residues 466-476	Mutation：S467A Mutation：S467A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M sodium citrate pH6, 0.65 M sodium citrate, 10 mM DTT	Resolution 2.30 Å R-free 0.207

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MLH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–284； UniProt 486–751 Author chain B； PDBConstruct 19–284； UniProt 486–751

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	3rbn
Deposition date deposition_date	2011-03-29
Structure title title	Crystal structure of MutL protein homolog 1 isoform 1 [Homo sapiens]
Keywords keywords	Structural Genomics, Structural Genomics Consortium, SGC, DNA Mismatch Repair, Endonucleases, PROTEIN BINDING; PROTEIN BINDING
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	31.04 Å
Radius of gyration Rg (electron density) rg_electron	30.82 Å
Forward intensity I(0) i0	48165200.00
Molecular weight molecular_weight	56705.0 kDa
Excluded volume excluded_volume	71560 Å³
Envelope volume envelope_volume	88854 Å³
Hydration-shell volume shell_volume	26038 Å³
Envelope diameter envelope_diameter	109.2 Å
Shell Rg shell_rg	35.13 Å
Envelope Rg envelope_rg	30.91 Å
Shape Rg shape_rg	30.82 Å
Total Rg total_rg	31.24 Å
Total atoms total_atoms	3980
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	103.9 Å
Rg (real space) rg_real	31.39 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	4.8170e+07
I(0) uncertainty (real space) i0_real_error	7.5170e+05
Rg (reciprocal space) rg_reciprocal	31.25 Å
I(0) (reciprocal space) i0_reciprocal	48160000.0000
Solution quality estimate total_estimate	0.6008
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.5 Å
Skewness Skewness skewness	0.514
Kurtosis Kurtosis kurtosis	-0.538
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15310000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.552; Smooth: 0.809

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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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8. Citations (1)

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Unit-cell length a length_a	63.505 Å
Unit-cell length b length_b	64.700 Å
Unit-cell length c length_c	130.932 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	2.160 Å
Low-resolution limit resolution_low	45.582 Å
R factor r_factor	0.2093
R_work r_work	0.2079
R_free r_free	0.2512

Description description	DNA mismatch repair protein Mlh1
Molecular weight formula_weight	33032.5 kDa
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	4141

Crystal structure of MutL protein homolog 1 isoform 1 [Homo sapiens]

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

DNA mismatch repair protein Mlh1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
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	147

fit	/app/data/saxs_computation/rb/3rbn/3rbn.fit
pddf	/app/data/pr_computation/rb/3rbn/3rbn.pr.out
profile	/app/data/saxs_computation/rb/3rbn/3rbn.dat