SAXSdb — 2w4i

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

GLUTAMATE RACEMASE

HELICOBACTER PYLORI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	D-GLUTAMIC ACID × 2 1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	D-GLUTAMIC ACID × 2 1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MURI_HELPJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–255； UniProt 1–255 Author chain B； PDBConstruct 1–255； UniProt 1–255 Author chain E； PDBConstruct 1–255； UniProt 1–255 Author chain F； PDBConstruct 1–255； UniProt 1–255

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	2w4i
Deposition date deposition_date	2008-11-25
Structure title title	Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor
Keywords keywords	ISOMERASE, CELL SHAPE, GLUTAMATE RACEMASE, CELL WALL BIOGENESIS/DEGRADATION, PEPTIDOGLYCAN SYNTHESIS, PEPTIDOGLYCAN BIOSYNTHESIS; ISOMERASE
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.

2w4i__assembly_2__model_1

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

Download this curve (.dat)

2w4i__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w4i__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.47 Å
Rg (electron density)	24.43 Å
Total Rg	25.45 Å
Atom count	4053
Residues	508
Excluded volume	73670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w4i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2w4i__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 (4)

Entity 1 Entity 1 polymer

Description description	GLUTAMATE RACEMASE
Molecular weight formula_weight	28532.2 kDa
EC 编号 ec_number	5.1.1.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	9466

MKIGVFDSGVGGFSVLKSLLKARLFDEIIYYGDSARVPYGTKDPTTIKQFGLEALDFFKPHEIELLIVACNTASALALEEMQKYSKIPIVGVIEPSILAIKRQVEDKNAPILVLGTKATIQSNAYDNALKQQGYLNISHLATSLFVPLIEESILEGELLETCMHYYFTPLEILPEVIILGCTHFPLIAQKIEGYFMGHFALPTPPLLIHSGDAIVEYLQQKYALKNNACTFPKVEFHASGDVIWLERQAKEWLKL

Source Source

Source organism organism	HELICOBACTER PYLORI
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	D-GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL
Molecular weight formula_weight	373.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1351

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2w4iA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

Domain ID domain_id	2w4iF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1860 —

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Unit-cell length a length_a	59.074 Å
Unit-cell length b length_b	93.982 Å
Unit-cell length c length_c	101.295 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.46 °
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	1.870 Å
Low-resolution limit resolution_low	24.670 Å
R factor r_factor	0.1580
R_work r_work	0.1560
R_free r_free	0.2090

Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor

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

GLUTAMATE RACEMASE

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

2w4i__assembly_2__model_1

2w4i__assembly_2__model_1 | I(q)

2w4i__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor

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

GLUTAMATE RACEMASE

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

2w4i__assembly_2__model_1

2w4i__assembly_2__model_1 | I(q)

2w4i__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)