1tez

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Method: X-RAY DIFFRACTION

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

Deoxyribodipyrimidine photo-lyase type I

Synechococcus elongatus PCC 6301

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(APTPCPGPGPCPT(TCP)PCPGPC)-3' × 1 5'-D(PCPGPAPAPGPCPCPGPA)-3' × 1 MAGNESIUM ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(APTPCPGPGPCPT(TCP)PCPGPC)-3' × 1 5'-D(PCPGPAPAPGPCPCPGPA)-3' × 1 MAGNESIUM ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPGPC)-3' × 1 5'-D(PGPCPCPGP*A)-3' × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE × 1 water × 3	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(TPCPGPC)-3' × 1 5'-D(PGPCPCPGP*A)-3' × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q31S25_SYNE7
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–474； UniProt 2–475 Author chain B； PDBConstruct 1–474； UniProt 2–475 Author chain C； PDBConstruct 1–474； UniProt 2–475 Author chain D； PDBConstruct 1–474； UniProt 2–475

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	1tez
Deposition date deposition_date	2004-05-26
Structure title title	COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS
Keywords keywords	PHOTOLYASE; DNA REPAIR; LIGHT-DRIVEN ELECTRON TRANSFER, LYASE-DNA COMPLEX; LYASE/DNA
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.

1tez__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1tez__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tez__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	24.53 Å
Rg (electron density)	23.68 Å
Total Rg	24.60 Å
Atom count	4032
Residues	483
Excluded volume	70532 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tez__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tez__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tez__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1tez__assembly_4__model_1`	trimeric （3）	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 (9)

Entity 1 Entity 1 polymer

Description description	5'-D(APTPCPGPGPCPT(TCP)PCPGP*C)-3'
Molecular weight formula_weight	3259.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,K
Atom count atom_count	18206

ATCGGCTTCGC

Entity 2 Entity 2 polymer

Description description	5'-D(PCPGPAPAPGPCPCPGP*A)-3'
Molecular weight formula_weight	2749.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,L

CGAAGCCGA

Entity 3 Entity 3 polymer

Description description	5'-D(TPCPGPC)-3'
Molecular weight formula_weight	1166.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,O

TCGC

Entity 4 Entity 4 polymer

Description description	5'-D(PGPCPCPGP*A)-3'
Molecular weight formula_weight	1505.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N,P

GCCGA

Entity 5 Entity 5 polymer

Description description	Deoxyribodipyrimidine photo-lyase type I
Molecular weight formula_weight	53474.4 kDa
EC 编号 ec_number	4.1.99.3
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

AAPILFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITPIERRGYPAPIVNHNLRQKQFKALYNQLKAAI

Source Source

Source organism organism	Synechococcus elongatus PCC 6301
NCBI taxonomy ID ncbi_taxonomy_id	269084
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
Molecular weight formula_weight	363.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1614

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1teza1
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

Domain ID domain_id	d1teza2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

Domain ID domain_id	d1tezb1
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

Domain ID domain_id	d1tezb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

Domain ID domain_id	d1tezc1
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

Domain ID domain_id	d1tezc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

Domain ID domain_id	d1tezd1
Class class	a — All alpha proteins
Fold Fold fold	a.99 — Cryptochrome/photolyase FAD-binding domain
Superfamily Superfamily superfamily	a.99.1 — Cryptochrome/photolyase FAD-binding domain
Family Family family	a.99.1.1 — Cryptochrome/photolyase FAD-binding domain

Domain ID domain_id	d1tezd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.28 — Cryptochrome/photolyase, N-terminal domain
Superfamily Superfamily superfamily	c.28.1 — Cryptochrome/photolyase, N-terminal domain
Family Family family	c.28.1.1 — Cryptochrome/photolyase, N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	1tezA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1tezA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1tezA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	1tezB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1tezB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1tezB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	1tezC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1tezC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1tezC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

Domain ID domain_id	1tezD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1tezD02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1tezD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	579 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3
Homologous superfamily homologous superfamily	10 — DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3

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Unit-cell length a length_a	173.815 Å
Unit-cell length b length_b	88.505 Å
Unit-cell length c length_c	161.622 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.920 Å
R factor r_factor	0.2051
R_work r_work	0.2050
R_free r_free	0.2260

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

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

Deoxyribodipyrimidine photo-lyase type I

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

1tez__assembly_3__model_1

1tez__assembly_3__model_1 | I(q)

1tez__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (2)

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

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

Deoxyribodipyrimidine photo-lyase type I

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

1tez__assembly_3__model_1

1tez__assembly_3__model_1 | I(q)

1tez__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (2)