SAXSdb — 3o7w

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

Leucine carboxyl methyltransferase 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 23–334	Fragment：UNP residues 23-334 with deletion of residues 233-258	GOL GLYCEROL × 1 SAM S-ADENOSYLMETHIONINE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.05 M Ammonium Sulfate, 0.05M Bis Tris (pH6.5), 30% Pentaerythritol Ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.00 Å R-free 0.265

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 3O7W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3IEI Crystal structure of human leucine carboxylmethyltransferase-1 in complex with S-adenosyl homocysteine Deposited 2009-07-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；Protein solution (10 mg/ml LCMT-1, 5 mM SAH) was mixed with an equal volume of reservoir solution containing 17-19% v/v PEG MME 2000, 150 mM Triethylamine N-oxide, 5 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.232
3P71 Crystal structure of the complex of LCMT-1 and PP2A Deposited 2010-10-11	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 T 1–334（334 aa）	Mutation：C19M, A21E, D22N, P115S	PEG DI(HYDROXYETHYL)ETHER × 1 AN6 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine × 1 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；291 K；PROTEIN COMPLEX (~5 MG/ML), 100MM TRIS-HCL, 22-26% V/V PEG 4000, 200 MM SODIUM ACETATE, 5 MM DTT, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.70 Å R-free 0.249

2 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LCMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–294； UniProt 23–334

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	3o7w
Deposition date deposition_date	2010-08-01
Structure title title	The Crystal Structure of Human Leucine Carboxyl Methyltransferase 1
Keywords keywords	Modified Rossmann fold, Transferase, PP2A; TRANSFERASE
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	19.78 Å
Radius of gyration Rg (electron density) rg_electron	18.41 Å
Forward intensity I(0) i0	19002600.00
Molecular weight molecular_weight	33066.0 kDa
Excluded volume excluded_volume	41377 Å³
Envelope volume envelope_volume	47094 Å³
Hydration-shell volume shell_volume	20872 Å³
Envelope diameter envelope_diameter	64.5 Å
Shell Rg shell_rg	25.31 Å
Envelope Rg envelope_rg	18.70 Å
Shape Rg shape_rg	18.39 Å
Total Rg total_rg	19.41 Å
Total atoms total_atoms	2315
Residues n_residues	282
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	63.2 Å
Rg (real space) rg_real	19.63 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.9000e+07
I(0) uncertainty (real space) i0_real_error	2.3620e+05
Rg (reciprocal space) rg_reciprocal	19.65 Å
I(0) (reciprocal space) i0_reciprocal	19000000.0000
Solution quality estimate total_estimate	0.8892
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5615000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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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	Leucine carboxyl methyltransferase 1
Molecular weight formula_weight	33910.9 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2453

GAMDENDEGVRGTCEDASLCKRFAVSIGYWHDPYIQHFVRLSKERKAPEINRGYFARVHGVSQLIKAFLRKTECHCQIVNLGAGMDTTFWRLKDEDLLPSKYFEVDFPMIVTRKLHSIKCKPPLSSPILELHSEDTLQMDGHILDSKRYAVIGADLRDLSELEEKLKKCNMNTQLPTLLIAECVLVYMTPEQSANLLKWAANSFERAMFINYEQVNEGKSLESQKERLLSNGWETASAVDMMELYNRLPRAEVSRIESLEFLDEMELLEQLMRHYCLCWATKGGNELGLKEITY

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

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	138

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3o7wA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. Citations (1)

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Unit-cell length a length_a	49.086 Å
Unit-cell length b length_b	63.296 Å
Unit-cell length c length_c	81.770 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	17.530 Å
R factor r_factor	0.2078
R_work r_work	0.2048
R_free r_free	0.2650

fit	/app/data/saxs_computation/o7/3o7w/3o7w.fit
pddf	/app/data/pr_computation/o7/3o7w/3o7w.pr.out
profile	/app/data/saxs_computation/o7/3o7w/3o7w.dat

The Crystal Structure of Human Leucine Carboxyl Methyltransferase 1

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

Leucine carboxyl methyltransferase 1

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