SAXSdb — 9p1b

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

Mandelate racemase

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	Tavaborole × 8 1,2-ETHANEDIOL × 20 MAGNESIUM ION × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MANR_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–383； UniProt 1–359 Author chain B； PDBConstruct 25–383； UniProt 1–359

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	9p1b
Deposition date deposition_date	2025-06-09
Structure title title	P. putida mandelate racemase co-crystallized with tavaborole
Keywords keywords	inhibitor, boronic acid, 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.

9p1b__assembly_1__model_1

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

Download this curve (.dat)

9p1b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p1b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.59 Å
Rg (electron density)	40.11 Å
Total Rg	40.58 Å
Atom count	21736
Residues	2856
Excluded volume	391320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p1b__assembly_1__model_1`	octameric （8）	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 (5)

Entity 1 Entity 1 polymer

Description description	Mandelate racemase
Molecular weight formula_weight	41304.6 kDa
EC 编号 ec_number	5.1.2.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6138

MASWSHPQFEKGALEVLFQGPGYHMSEVLITGLRTRAVNVPLAYPVHTAVGTVGTAPLVLIDLATSAGVVGHSYLFAYTPVALKSLKQLLDDMAAMIVNEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAGIDMAAWDALGKVHETPLVKLLGANARPVQAYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDDFGIMVDYNQSLDVPAAIKRSQALQQEGVTWIEEPTLQHDYEGHQRIQSKLNVPVQMGENWLGPEEMFKALSIGACRLAMPDAMKIGGVTGWIRASALAQQFGIPMSSHLFQEISAHLLAATPTAHWLERLDLAGSVIEPTLTFEGGNAVIPDLPGVGIIWREKEIGKYLV

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	Tavaborole
Molecular weight formula_weight	151.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	652

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Unit-cell length a length_a	150.646 Å
Unit-cell length b length_b	150.646 Å
Unit-cell length c length_c	177.551 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	tetragonal

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	57.440 Å
R factor r_factor	0.2018
R_work r_work	0.2000
R_free r_free	0.2348

P. putida mandelate racemase co-crystallized with tavaborole

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

Mandelate 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

9p1b__assembly_1__model_1

9p1b__assembly_1__model_1 | I(q)

9p1b__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

P. putida mandelate racemase co-crystallized with tavaborole

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

Mandelate 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

9p1b__assembly_1__model_1

9p1b__assembly_1__model_1 | I(q)

9p1b__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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)