1mlv

Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase

Method: X-RAY DIFFRACTION

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

Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase

Pisum sativum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	S-ADENOSYL-L-HOMOCYSTEINE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	S-ADENOSYL-L-HOMOCYSTEINE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	S-ADENOSYL-L-HOMOCYSTEINE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	S-ADENOSYL-L-HOMOCYSTEINE × 3 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 water × 3	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	S-ADENOSYL-L-HOMOCYSTEINE × 6 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBCMT_PEA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–438； UniProt 46–482 Author chain B； PDBConstruct 2–438； UniProt 46–482 Author chain C； PDBConstruct 2–438； UniProt 46–482

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	1mlv
Deposition date deposition_date	2002-08-30
Structure title title	Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase
Keywords keywords	SET Domain, Lysine N-Methylation, Photosynthesis, Post-translational Modification, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1mlv__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1mlv__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mlv__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	49.78 Å
Rg (electron density)	50.38 Å
Total Rg	50.28 Å
Atom count	10604
Residues	1302
Excluded volume	189290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mlv__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mlv__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1mlv__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1mlv__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1mlv__assembly_5__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
Molecular weight formula_weight	50629.2 kDa
EC 编号 ec_number	2.1.1.127
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	11270

MTEPSLSPAVQTFWKWLQEEGVITAKTPVKASVVTEGLGLVALKDISRNDVILQVPKRLWINPDAVAASEIGRVCSELKPWLSVILFLIRERSREDSVWKHYFGILPQETDSTIYWSEEELQELQGSQLLKTTVSVKEYVKNECLKLEQEIILPNKRLFPDPVTLDDFFWAFGILRSRAFSRLRNENLVVVPMADLINHSAGVTTEDHAYEVKGAAGLFSWDYLFSLKSPLSVKAGEQVYIQYDLNKSNAELALDYGFIEPNENRHAYTLTLEISESDPFFDDKLDVAESNGFAQTAYFDIFYNRTLPPGLLPYLRLVALGGTDAFLLESLFRDTIWGHLELSVSRDNEELLCKAVREACKSALAGYHTTIEQDRELKEGNLDSRLAIAVGIREGEKMVLQQIDGIFEQKELELDQLEYYQERRLKDLGLCGENGDILENLYFQ

Source Source

Source organism organism	Pisum sativum
Common name common_name	pea
NCBI taxonomy ID ncbi_taxonomy_id	3888
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	666

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1mlva1
Class class	a — All alpha proteins
Fold Fold fold	a.166 — RuBisCo LSMT C-terminal, substrate-binding domain
Superfamily Superfamily superfamily	a.166.1 — RuBisCo LSMT C-terminal, substrate-binding domain
Family Family family	a.166.1.1 — RuBisCo LSMT C-terminal, substrate-binding domain

Domain ID domain_id	d1mlva2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.3 — RuBisCo LSMT catalytic domain

Domain ID domain_id	d1mlva3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1mlvb1
Class class	a — All alpha proteins
Fold Fold fold	a.166 — RuBisCo LSMT C-terminal, substrate-binding domain
Superfamily Superfamily superfamily	a.166.1 — RuBisCo LSMT C-terminal, substrate-binding domain
Family Family family	a.166.1.1 — RuBisCo LSMT C-terminal, substrate-binding domain

Domain ID domain_id	d1mlvb2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.3 — RuBisCo LSMT catalytic domain

Domain ID domain_id	d1mlvb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1mlvc1
Class class	a — All alpha proteins
Fold Fold fold	a.166 — RuBisCo LSMT C-terminal, substrate-binding domain
Superfamily Superfamily superfamily	a.166.1 — RuBisCo LSMT C-terminal, substrate-binding domain
Family Family family	a.166.1.1 — RuBisCo LSMT C-terminal, substrate-binding domain

Domain ID domain_id	d1mlvc2
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.7 — SET domain
Family Family family	b.85.7.3 — RuBisCo LSMT catalytic domain

Domain ID domain_id	d1mlvc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1mlvA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	1mlvA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	1mlvB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	1mlvB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	1mlvC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	1mlvC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

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Unit-cell length a length_a	132.160 Å
Unit-cell length b length_b	156.680 Å
Unit-cell length c length_c	268.440 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.780 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2770

Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase

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

Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1mlv__assembly_4__model_1

1mlv__assembly_4__model_1 | I(q)

1mlv__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase

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

Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1mlv__assembly_4__model_1

1mlv__assembly_4__model_1 | I(q)

1mlv__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)