3c5y

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

Method: X-RAY DIFFRACTION

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

Ribose/galactose isomerase

Novosphingobium aromaticivorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 18 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 24 NITRATE ION × 6 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 11 NITRATE ION × 1 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	1,2-ETHANEDIOL × 8 NITRATE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4XEL3_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–231； UniProt 1–212 Author chain B； PDBConstruct 20–231； UniProt 1–212 Author chain C； PDBConstruct 20–231； UniProt 1–212 Author chain D； PDBConstruct 20–231； UniProt 1–212 Author chain E； PDBConstruct 20–231； UniProt 1–212 Author chain F； PDBConstruct 20–231； UniProt 1–212 Author chain G； PDBConstruct 20–231； UniProt 1–212 Author chain H； PDBConstruct 20–231； UniProt 1–212 Author chain I； PDBConstruct 20–231； UniProt 1–212 Author chain J； PDBConstruct 20–231； UniProt 1–212 Author chain K； PDBConstruct 20–231； UniProt 1–212 Author chain L； PDBConstruct 20–231； UniProt 1–212 Author chain M； PDBConstruct 20–231； UniProt 1–212 Author chain N； PDBConstruct 20–231； UniProt 1–212 Author chain O； PDBConstruct 20–231； UniProt 1–212 Author chain P； PDBConstruct 20–231； UniProt 1–212

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	3c5y
Deposition date deposition_date	2008-02-01
Structure title title	Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, isomerase; 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.

3c5y__assembly_1__model_1

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

Download this curve (.dat)

3c5y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c5y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.11 Å
Rg (electron density)	28.42 Å
Total Rg	28.93 Å
Atom count	6444
Residues	806
Excluded volume	115950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c5y__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c5y__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3c5y__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3c5y__assembly_4__model_1`	tetrameric （4）	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	Ribose/galactose isomerase
Molecular weight formula_weight	25823.9 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	28863

MGSDKIHHHHHHENLYFQGMKIALIIENSQAAKNAVVHEALTTVAEPLGHKVFNYGMYTAEDKASLTYVMNGLLAGILLNSGAADFVVTGCGTGMGSMLAANAMPGVFCGLVIDPTDAFLFGQINDGNAISMPYSKGFGWAAELNLQDVYRKLFDGERGLGYPRERAEIMRKNRGILRELKDASCRDMLTVLKTVDQDLLRAAIAGEKFAELFYPNCKDDAIANYLRSLDA

Source Source

Source organism organism	Novosphingobium aromaticivorans
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	61

Entity 3 Entity 3 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2655

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3c5yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yO00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

Domain ID domain_id	3c5yP00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1400 — Ribose 5-phosphate Isomerase B; Chain: A,
Homologous superfamily homologous superfamily	10 — Sugar-phosphate isomerase, RpiB/LacA/LacB

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Unit-cell length a length_a	106.754 Å
Unit-cell length b length_b	109.462 Å
Unit-cell length c length_c	167.569 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

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

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	49.147 Å
R factor r_factor	0.1730
R_work r_work	0.1700
R_free r_free	0.2200

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

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

Ribose/galactose isomerase

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

3c5y__assembly_1__model_1

3c5y__assembly_1__model_1 | I(q)

3c5y__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 (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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

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

Ribose/galactose isomerase

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

3c5y__assembly_1__model_1

3c5y__assembly_1__model_1 | I(q)

3c5y__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 (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) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)