5dcx

Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation

Method: X-RAY DIFFRACTION

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

Protein Rep68

Adeno-associated virus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	REP68_AAV2S
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–227； UniProt 1–224 Author chain B； PDBConstruct 4–227； UniProt 1–224 Author chain C； PDBConstruct 4–227； UniProt 1–224 Author chain D； PDBConstruct 4–227； UniProt 1–224 Author chain E； PDBConstruct 4–227； UniProt 1–224 Author chain F； PDBConstruct 4–227； UniProt 1–224 Author chain G； PDBConstruct 4–227； UniProt 1–224 Author chain H； PDBConstruct 4–227； UniProt 1–224 Author chain I； PDBConstruct 4–227； UniProt 1–224 Author chain J； PDBConstruct 4–227； UniProt 1–224 Author chain K； PDBConstruct 4–227； UniProt 1–224

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	5dcx
Deposition date deposition_date	2015-08-24
Structure title title	Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation
Keywords keywords	Parvovirus, Adeno-Associated Virus, DNA replication, Small-angle X-ray scattering, DNA binding protein, Rep proteins; DNA BINDING PROTEIN
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.

5dcx__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5dcx__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dcx__assembly_9__model_1 | P(r) · Pending

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

Rg（Guinier）	17.85 Å
Rg (electron density)	16.38 Å
Total Rg	17.54 Å
Atom count	1542
Residues	189
Excluded volume	27608 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dcx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5dcx__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5dcx__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5dcx__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5dcx__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5dcx__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5dcx__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5dcx__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`5dcx__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`5dcx__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`5dcx__assembly_11__model_1`	monomeric （1）	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	Protein Rep68
Molecular weight formula_weight	26103.6 kDa
EC 编号 ec_number	3.6.4.12
Mutation mutation	C151S
Source method src_method	man
Copy count entity_count	11

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K
Atom count atom_count	17626

GSHMPGFYEIVIKVPSDLDGHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNYLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARY

Source Source

Source organism organism	Adeno-associated virus 2
Common name common_name	AAV-2
NCBI taxonomy ID ncbi_taxonomy_id	10804
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d5dcxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxa2
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	d5dcxb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxb2
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	d5dcxc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d5dcxk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

CATH v4.4 (11 domains)

Domain ID domain_id	5dcxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5dcxK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	75.644 Å
Unit-cell length b length_b	178.706 Å
Unit-cell length c length_c	130.358 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	22

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	29.814 Å
R factor r_factor	0.1928
R_work r_work	0.1905
R_free r_free	0.2375

Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation

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

Protein Rep68

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

5dcx__assembly_9__model_1

5dcx__assembly_9__model_1 | I(q)

5dcx__assembly_9__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) 24 domains

SCOP 2.08 (13 domains)

CATH v4.4 (11 domains)

7. Citations (1)

Structural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation

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

Protein Rep68

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

5dcx__assembly_9__model_1

5dcx__assembly_9__model_1 | I(q)

5dcx__assembly_9__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) 24 domains

SCOP 2.08 (13 domains)

CATH v4.4 (11 domains)

7. Citations (1)