2zci

Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum

Method: X-RAY DIFFRACTION

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

Phosphoenolpyruvate carboxykinase [GTP]

OrganismNot specified

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCK_CORGL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–610； UniProt 1–610 Author chain B； PDBConstruct 1–610； UniProt 1–610 Author chain C； PDBConstruct 1–610； UniProt 1–610 Author chain D； PDBConstruct 1–610； UniProt 1–610

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	2zci
Deposition date deposition_date	2007-11-09
Structure title title	Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum
Keywords keywords	GTP-dependent, carboxykinase, SIGNALING PROTEIN, LYASE; SIGNALING PROTEIN, LYASE
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.

2zci__assembly_1__model_1

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

Download this curve (.dat)

2zci__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zci__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.70 Å
Rg (electron density)	30.74 Å
Total Rg	31.44 Å
Atom count	9074
Residues	1172
Excluded volume	160180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zci__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zci__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 (2)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2zcia1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d2zcia2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

Domain ID domain_id	d2zcib1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d2zcib2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

Domain ID domain_id	d2zcic1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d2zcic2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

Domain ID domain_id	d2zcid1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d2zcid2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2zciA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	2zciA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	2zciA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2zciB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	2zciB02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	2zciB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2zciC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	2zciC02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	2zciC03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2zciD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	2zciD02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	2zciD03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	70.336 Å
Unit-cell length b length_b	118.055 Å
Unit-cell length c length_c	152.931 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	24.830 Å
R factor r_factor	0.1923
R_work r_work	0.1877
R_free r_free	0.2788

Description description	Phosphoenolpyruvate carboxykinase [GTP]
Molecular weight formula_weight	66937.1 kDa
EC 编号 ec_number	4.1.1.32
Source method src_method	nat
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	18407

Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum

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

Phosphoenolpyruvate carboxykinase [GTP]

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

2zci__assembly_1__model_1

2zci__assembly_1__model_1 | I(q)

2zci__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

Structure of a GTP-dependent bacterial PEP-carboxykinase from Corynebacterium glutamicum

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

Phosphoenolpyruvate carboxykinase [GTP]

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

2zci__assembly_1__model_1

2zci__assembly_1__model_1 | I(q)

2zci__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)