4beb

MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

Method: X-RAY DIFFRACTION

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

TYPE I RESTRICTION ENZYME HSDR

ESCHERICHIA COLI

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 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q304R3_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1038； UniProt 1–1038 Author chain B； PDBConstruct 1–1038； UniProt 1–1038 Author chain C； PDBConstruct 1–1038； UniProt 1–1038 Author chain D； PDBConstruct 1–1038； UniProt 1–1038

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	4beb
Deposition date deposition_date	2013-03-07
Structure title title	MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP
Keywords keywords	HYDROLASE, DNA MODIFICATION; HYDROLASE
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.

4beb__assembly_2__model_1

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

Download this curve (.dat)

4beb__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4beb__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.22 Å
Rg (electron density)	29.15 Å
Total Rg	29.91 Å
Atom count	6878
Residues	842
Excluded volume	121840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4beb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4beb__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4beb__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4beb__assembly_4__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	TYPE I RESTRICTION ENZYME HSDR
Molecular weight formula_weight	120278.8 kDa
EC 编号 ec_number	3.1.21.3
Mutation mutation	YES
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	27369

MTHQTHTIAESNNFIVLDKYIKAEPTGDSYQSESDLERELIQDLRNQGYEFISVKSQSAMLANVREQLQNLNGVVFNDSEWRRFTEQYLDNPSDGILDKTRKIHIDYICDFIFDDERLENIYLIDKKNLMRNKVQIIQQFEQAGSHANRYDVTILVNGLPLVQIELKKRGVAIREAFNQIHRYSKESFNSENSLFKYLQLFVISNGTDTRYFANTTKRDENSFDFTMNWAKSDNTLIKDLKDFTATCFQKHTLLNVLVNYSVFDSSQTLLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDLDYQTMKEYQRFSPDSVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFGEAQKNLKKKFKRYYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETETDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVGMFLTGFDAPTLNTLFVDKNLRYHGLMQAFSRTNRIYDATKTFGNIVTFRDLERSTIDAITLFGDKNTKNVVLEKSYTEYMEGFTDAATGEAKRGFMTVVSELEQRFPDPTSIESEKEKKDFVKLFGEYLRAENILQNYDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIRLPADRKIQDYRSAYNDIRDWQRREKEAEKKEKSTTDWDDVVFEVDLLKSQEINLDYILGLIFEHNRQNKGKGEMIEEVKRLIRSSLGNRAKEGLVVDFIQQTNLDDLPDKASIIDAFFTFAQREQQREAEALIKEENLNEDAAKRYIRTSLKREYATENGTELNETLPKLSPLNPQYKTKKQAVFQKIVSFIEKFKGVGGKI

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

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	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4bebA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1570 — tt1808, chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1570 — tt1808, chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1570 — tt1808, chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebC04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1570 — tt1808, chain A
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4bebD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4bebD04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	127.112 Å
Unit-cell length b length_b	123.112 Å
Unit-cell length c length_c	160.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.48 °
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	2.989 Å
Low-resolution limit resolution_low	19.885 Å
R factor r_factor	0.2555
R_work r_work	0.2550
R_free r_free	0.2965

MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

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

TYPE I RESTRICTION ENZYME HSDR

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

4beb__assembly_2__model_1

4beb__assembly_2__model_1 | I(q)

4beb__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 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP

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

TYPE I RESTRICTION ENZYME HSDR

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

4beb__assembly_2__model_1

4beb__assembly_2__model_1 | I(q)

4beb__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 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)