← Back to search
5lod

Crystal structure of HhaI DNA methyltransferase in APO form

Method: X-RAY DIFFRACTION Dmax: 107.5 Å Quality: GOOD
▼

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

Modification methylase HhaI

Haemophilus parahaemolyticus

UniProt P05102

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 1–327 Chain B； UniProt 1–327 Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；AMMONIUM SULFATE 50 mM, CITRATE 100mM, 32% (w/v) PEG-4000 Resolution 1.90 Å R-free 0.219

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 5LOD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10MH TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET Deposited 1998-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；10% (W/V) PEG 8000 50 MM CALCIUM ACETATE 50 MM SODIUM CACODYLATE PH 6.5
Resolution 2.55 Å
1FJX STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY Deposited 2000-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：T250G SO4 SULFATE ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.7 M ammonium sulfate 20% (w/v) glucose 50 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 16K
Resolution 2.26 Å R-free 0.283
1HMY CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE Deposited 1993-08-05 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 1–327（327 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1M0E ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE Deposited 2002-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 8000, Ca acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.243
1MHT COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE Deposited 1994-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；289 K；BIS-TRIS-PROPANE_HCL, NACL, EDTA, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K
Resolution 2.60 Å
1SKM HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site Deposited 2004-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.221
1SVU Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions Deposited 2004-03-30 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 1–327（327 aa）
Mutation：Q237W SO4 SULFATE ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289 K；ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.66 Å R-free 0.266
1SVU Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions Deposited 2004-03-30 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 1–327（327 aa）
Mutation：Q237W SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289 K；ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.66 Å R-free 0.266
2C7O HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH Deposited 2005-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5 % GLUCOSE.
Resolution 1.90 Å R-free 0.215
2C7P HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH Deposited 2005-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.4 M AMMONIUM SULFATE
Resolution 1.70 Å R-free 0.220
2C7Q HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH Deposited 2005-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 3 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE
Resolution 1.85 Å R-free 0.210
2C7R HhaI DNA methyltransferase (T250G mutant) complex with oligonucleotide containing 2-aminopurine as a target base (GPGC:GMGC) and SAH Deposited 2005-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：YES SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 7 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.7 M AMMONIUM SULFATE, 5 % GLUCOSE
Resolution 1.90 Å R-free 0.217
2HMY BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DNA OLIGONUCLEOTIDE Deposited 1999-02-08 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 B 1–327（327 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；2.2M AMMONIUM SULFATE 50 MMSODIUM CITRATE PH 6.0
Resolution 2.61 Å
2HR1 Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy Deposited 2006-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；Ammonium Sulfate 15%, Sodium Citrate 100 mM, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.96 Å R-free 0.269
2I9K Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI Deposited 2006-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：F124A SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；290 K；20% Ammonium Sulfate, 100mM Sodium Citrate buffer, pH 6.0, hanging drop, temperature 290K
Resolution 2.65 Å R-free 0.262
2UYC HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH Deposited 2007-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：YES SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 6 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE, 5% GLUCOSE
Resolution 2.00 Å R-free 0.227
2UYH HhaI DNA methyltransferase S87Q-Q237S mutant complex with 13mer GCGC- GMGC oligonucleotide and SAH Deposited 2007-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：YES SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5% GLUCOSE
Resolution 2.63 Å R-free 0.258
2UZ4 HhaI DNA methyltransferase R165N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH Deposited 2007-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：YES SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE
Resolution 2.10 Å R-free 0.235
2Z6A S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation Deposited 2007-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：C81A SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；2.0M Ammonium Sulfate, 50mM Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.88 Å R-free 0.280
2Z6Q Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy Deposited 2007-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–327（327 aa）
Mutation：R165A DCZ 2'-DEOXYCYTIDINE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100 mM sodium citrate (pH 6.0), ammonium sulfate 1.2M, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.79 Å R-free 0.269
2Z6U Ternary structure of the Glu119Ala M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy Deposited 2007-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：E119A SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100mM sodium citrate buffer, 45%-55% 3.5M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.72 Å R-free 0.267
2ZCJ Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy Deposited 2007-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Mutation：E119Q SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100 mM Sodium Citrate, 1.6-2.1 Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.75 Å R-free 0.266
3EEO M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation. Deposited 2008-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.94 Å R-free 0.275
3MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DNA AND ADOHCY Deposited 1996-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
4MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DNA AND ADOHCY Deposited 1996-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
5CIY Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain Deposited 2015-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；AMMONIUM SULFATE 1.8 M, CITRATE 50mM
Resolution 1.59 Å R-free 0.188
5MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DNA AND ADOHCY Deposited 1996-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；10% PEG 8000, 50 MM CA-ACETATE, 50 MM SODIUM CACODYLATE PH 6.5
Resolution 2.70 Å
6MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET Deposited 1998-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；293 K；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6, temperature 293.0K
Resolution 2.05 Å R-free 0.231
7MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6
Resolution 2.87 Å
8MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6
Resolution 2.76 Å
9MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–327（327 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；10% (W/V) POLYETHYLENE GLYCOL 8000 50 MM CA-ACETATE 50 MM SODIUM CACODYLATE PH 5.6
Resolution 2.39 Å

30 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTH1_HAEPH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–327； UniProt 1–327 Author chain B； PDBConstruct 1–327； UniProt 1–327

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 5lod

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lod
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5lod
Deposition date deposition_date2016-08-09
Structure title titleCrystal structure of HhaI DNA methyltransferase in APO form
Keywords keywordsM.HhaI, C5-METHYLCYTOSINE, APO FORM, DNA methyltransferase, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.53 Å
Radius of gyration Rg (electron density) rg_electron29.03 Å
Forward intensity I(0) i085859200.00
Molecular weight molecular_weight73187.0 kDa
Excluded volume excluded_volume91599 ų
Envelope volume envelope_volume110640 ų
Hydration-shell volume shell_volume32893 ų
Envelope diameter envelope_diameter119.0 Å
Shell Rg shell_rg35.06 Å
Envelope Rg envelope_rg28.94 Å
Shape Rg shape_rg29.05 Å
Total Rg total_rg29.52 Å
Total atoms total_atoms5147
Residues n_residues642
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax107.5 Å
Rg (real space) rg_real29.65 Å
Rg uncertainty (real space) rg_real_error1.17 Å
I(0) (real space) i0_real8.5860e+07
I(0) uncertainty (real space) i0_real_error1.4020e+06
Rg (reciprocal space) rg_reciprocal29.60 Å
I(0) (reciprocal space) i0_reciprocal85860000.0000
Solution quality estimate total_estimate0.7574
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary29.9 Å
Skewness Skewness skewness0.491
Kurtosis Kurtosis kurtosis-0.197
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24820000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.653; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5loda_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.26 — C5 cytosine-specific DNA methylase, DCM
Domain ID domain_idd5lodb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.26 — C5 cytosine-specific DNA methylase, DCM

CATH v4.4 (4 domains)

Domain ID domain_id5lodA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id5lodA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Methylase, subunit A, domain 2
Domain ID domain_id5lodB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id5lodB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Methylase, subunit A, domain 2
▶

8. Citations (1)

▶

9. Files and Curves (10)