SAXSdb — 1f75

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

UNDECAPRENYL PYROPHOSPHATE SYNTHETASE

Micrococcus luteus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UPPS_MICLU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–249； UniProt 1–249 Author chain B； PDBConstruct 1–249； UniProt 1–249

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	1f75
Deposition date deposition_date	2000-06-26
Structure title title	CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26
Keywords keywords	PARALLEL BETA SHEET, new fold for Isoprenoid Synthase, PEPTIDOGLYCAN SYNTHESIS, TRANSFERASE; TRANSFERASE
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.

1f75__assembly_1__model_1

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

Download this curve (.dat)

1f75__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1f75__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.87 Å
Rg (electron density)	23.79 Å
Total Rg	24.78 Å
Atom count	3514
Residues	429
Excluded volume	62960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1f75__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
Molecular weight formula_weight	28945.2 kDa
EC 编号 ec_number	2.5.1.31
Mutation mutation	K54R
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	3552

MFPIKKRKAIKNNNINAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNRHRRFGGL

Source Source

Source organism organism	Micrococcus luteus
NCBI taxonomy ID ncbi_taxonomy_id	1270
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1f75a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.101 — Undecaprenyl diphosphate synthase
Superfamily Superfamily superfamily	c.101.1 — Undecaprenyl diphosphate synthase
Family Family family	c.101.1.1 — Undecaprenyl diphosphate synthase

Domain ID domain_id	d1f75b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.101 — Undecaprenyl diphosphate synthase
Superfamily Superfamily superfamily	c.101.1 — Undecaprenyl diphosphate synthase
Family Family family	c.101.1.1 — Undecaprenyl diphosphate synthase

CATH v4.4 (2 domains)

Domain ID domain_id	1f75A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1180 — Undecaprenyl pyrophosphate synthetase
Homologous superfamily homologous superfamily	10 — Decaprenyl diphosphate synthase-like

Domain ID domain_id	1f75B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1180 — Undecaprenyl pyrophosphate synthetase
Homologous superfamily homologous superfamily	10 — Decaprenyl diphosphate synthase-like

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Unit-cell length a length_a	127.197 Å
Unit-cell length b length_b	60.161 Å
Unit-cell length c length_c	75.703 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1900
R_free r_free	0.2460

CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26

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

UNDECAPRENYL PYROPHOSPHATE SYNTHETASE

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

1f75__assembly_1__model_1

1f75__assembly_1__model_1 | I(q)

1f75__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26

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

UNDECAPRENYL PYROPHOSPHATE SYNTHETASE

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

1f75__assembly_1__model_1

1f75__assembly_1__model_1 | I(q)

1f75__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)