1z2i

CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

Method: X-RAY DIFFRACTION

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

malate dehydrogenase

Agrobacterium tumefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7CRW4_AGRT5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–358； UniProt 1–358 Author chain B； PDBConstruct 1–358； UniProt 1–358 Author chain C； PDBConstruct 1–358； UniProt 1–358 Author chain D； PDBConstruct 1–358； UniProt 1–358

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	1z2i
Deposition date deposition_date	2005-03-08
Structure title title	CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
Keywords keywords	;MALATE DEHYDROGENASE, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, New York SGX Research Center for Structural Genomics, NYSGXRC, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

1z2i__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1z2i__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z2i__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.59 Å
Rg (electron density)	25.55 Å
Total Rg	26.29 Å
Atom count	5350
Residues	700
Excluded volume	94127 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z2i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z2i__assembly_2__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	malate dehydrogenase
Molecular weight formula_weight	38298.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11399

MAHGNEKATVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH

Source Source

Source organism organism	Agrobacterium tumefaciens
NCBI taxonomy ID ncbi_taxonomy_id	358
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	699

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1z2ia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

Domain ID domain_id	d1z2ib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

Domain ID domain_id	d1z2ic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

Domain ID domain_id	d1z2id_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	1z2iA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1z2iA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1z2iA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1z2iB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1z2iB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1z2iB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1z2iC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1z2iC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1z2iC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1z2iD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1z2iD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1z2iD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

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Unit-cell length a length_a	98.220 Å
Unit-cell length b length_b	98.220 Å
Unit-cell length c length_c	146.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2650

CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

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

malate dehydrogenase

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

1z2i__assembly_2__model_1

1z2i__assembly_2__model_1 | I(q)

1z2i__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

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

malate dehydrogenase

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

1z2i__assembly_2__model_1

1z2i__assembly_2__model_1 | I(q)

1z2i__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (4 domains)

CATH v4.4 (12 domains)

7. Citations (1)