SAXSdb — 7rck

▼

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

Mismatch repair endonuclease PMS2

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 1–365 Chain B； UniProt 1–365	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.04 Å R-free 0.234

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 7RCK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EA6 N-terminal 40kDa fragment of NhPMS2 complexed with ADP Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–364（364 aa） Fragment：N-TERMINAL 40KDA, RESIDUES 1-364	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 2.70 Å R-free 0.262
1EA6 N-terminal 40kDa fragment of NhPMS2 complexed with ADP Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–364（364 aa） Fragment：N-TERMINAL 40KDA, RESIDUES 1-364	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 2.70 Å R-free 0.262
1H7S N-terminal 40kDa fragment of human PMS2 Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa） Fragment：N-TERMINAL 40 KDA FRAGMENT	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 1.95 Å R-free 0.243
1H7S N-terminal 40kDa fragment of human PMS2 Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa） Fragment：N-TERMINAL 40 KDA FRAGMENT	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH 6.2) 0.2 M LICL	Resolution 1.95 Å R-free 0.243
1H7U hPMS2-ATPgS Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa） Fragment：GHL ATPASE, RESIDUES 1-365	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH=6.2) 0.2 M LICL, pH 6.20	Resolution 2.70 Å R-free 0.270
1H7U hPMS2-ATPgS Deposited 2001-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa） Fragment：GHL ATPASE, RESIDUES 1-365	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；2-2.4 M NA/K PHOSPHATE (PH=6.2) 0.2 M LICL, pH 6.20	Resolution 2.70 Å R-free 0.270
5U5R Crystal Structure and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a PMS2 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 × 2 PDB declaration: dimeric	Chain B 573–583（11 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) and 10 mM DTT	Resolution 2.10 Å R-free 0.207
6MFQ Crystal structure of a PMS2 variant Deposited 2018-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289.15 K；Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.	Resolution 2.60 Å R-free 0.232
6MFQ Crystal structure of a PMS2 variant Deposited 2018-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289.15 K；Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.	Resolution 2.60 Å R-free 0.232
7RCB Crystal Structure of a PMS2 VUS Deposited 2021-07-07	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa） Chain B 1–365（365 aa）	Mutation：N335S Mutation：N335S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.00 Å R-free 0.198
7RCI Crystal Structure of a PMS2 VUS with Substrate Deposited 2021-07-07	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–365（365 aa） Chain B 1–365（365 aa）	Mutation：N335S Mutation：N335S	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289.15 K；1:1 7.5 mg/mL protein with 8% v/v Tacsimate, pH 5.8, 25% w/v PEG3350	Resolution 2.12 Å R-free 0.248
9S89 N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867 Deposited 2025-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–365（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.229

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PMS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–365； UniProt 1–365 Author chain B； PDBConstruct 1–365； UniProt 1–365

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	7rck
Deposition date deposition_date	2021-07-07
Structure title title	Crystal Structure of PMS2 with Substrate
Keywords keywords	Mismatch Repair, Variant of Uncertain Significance, ATPase Domain, DNA Repair Enzyme, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	27.66 Å
Radius of gyration Rg (electron density) rg_electron	27.24 Å
Forward intensity I(0) i0	68383900.00
Molecular weight molecular_weight	62672.0 kDa
Excluded volume excluded_volume	77527 Å³
Envelope volume envelope_volume	96704 Å³
Hydration-shell volume shell_volume	30602 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	33.44 Å
Envelope Rg envelope_rg	27.42 Å
Shape Rg shape_rg	27.26 Å
Total Rg total_rg	27.79 Å
Total atoms total_atoms	4391
Residues n_residues	590
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	101.7 Å
Rg (real space) rg_real	27.70 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	6.8380e+07
I(0) uncertainty (real space) i0_real_error	1.0480e+06
Rg (reciprocal space) rg_reciprocal	27.68 Å
I(0) (reciprocal space) i0_reciprocal	68380000.0000
Solution quality estimate total_estimate	0.8360
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	98.2 Å
Skewness Skewness skewness	0.446
Kurtosis Kurtosis kurtosis	0.147
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13960000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.997

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Mismatch repair endonuclease PMS2
Molecular weight formula_weight	40513.2 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4742

MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFDS

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	344

▶

8. Citations (1)

▶

Unit-cell length a length_a	74.684 Å
Unit-cell length b length_b	75.385 Å
Unit-cell length c length_c	135.313 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	orthorhombic

Resolution resolution	2.040 Å
Low-resolution limit resolution_low	38.710 Å
R factor r_factor	0.2152
R_work r_work	0.2132
R_free r_free	0.2344

fit	/app/data/saxs_computation/rc/7rck/7rck.fit
pddf	/app/data/pr_computation/rc/7rck/7rck.pr.out
profile	/app/data/saxs_computation/rc/7rck/7rck.dat

Crystal Structure of PMS2 with Substrate

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

Mismatch repair endonuclease PMS2

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