7w1g

Crystal structure of YfiH with C107A mutation in complex with UDP-MurNAc-L-Serine

Method: X-RAY DIFFRACTION

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

Purine nucleoside phosphorylase YfiH

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	;(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid ; × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid ; × 1 SULFATE ION × 1 ACETATE ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 ;(2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;(2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PURNU_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 1–243 Author chain B； PDBConstruct 1–243； UniProt 1–243 Author chain C； PDBConstruct 1–243； UniProt 1–243 Author chain D； PDBConstruct 1–243； UniProt 1–243

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	7w1g
Deposition date deposition_date	2021-11-19
Structure title title	Crystal structure of YfiH with C107A mutation in complex with UDP-MurNAc-L-Serine
Keywords keywords	hydrolase, DUF152, amidase; 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.

7w1g__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7w1g__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7w1g__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.31 Å
Rg (electron density)	17.15 Å
Total Rg	18.10 Å
Atom count	1900
Residues	243
Excluded volume	33499 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7w1g__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7w1g__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7w1g__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7w1g__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 (7)

Entity 1 Entity 1 polymer

Description description	Purine nucleoside phosphorylase YfiH
Molecular weight formula_weight	27407.0 kDa
EC 编号 ec_number	3.5.4.4
Mutation mutation	C107A
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	8095

MSKLIVPQWPQPKGVAACSSTRIGGVSLPPYDSLNLGAHCGDNPDHVEENRKRLFAAGNLPSKPVWLEQVHGKDVLKLTGEPYASKRADASYSNTPGTVCAVMTADALPVLFCNRAGTEVAAAHAGWRGLCAGVLEETVSCFADNPENILAWLGPAIGPRAFEVGGEVREAFMAVDAKASAAFIQHGDKYLADIYQLARQRLANVGVEQIFGGDRCTYTENETFFSYRRDKTTGRMASFIWLILEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid ;
Molecular weight formula_weight	679.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	;(2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid ;
Molecular weight formula_weight	766.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	442

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Unit-cell length a length_a	70.556 Å
Unit-cell length b length_b	99.236 Å
Unit-cell length c length_c	136.933 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	27.450 Å
R factor r_factor	0.2175
R_work r_work	0.2149
R_free r_free	0.2661

Crystal structure of YfiH with C107A mutation in complex with UDP-MurNAc-L-Serine

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

Purine nucleoside phosphorylase YfiH

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

7w1g__assembly_4__model_1

7w1g__assembly_4__model_1 | I(q)

7w1g__assembly_4__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)

Crystal structure of YfiH with C107A mutation in complex with UDP-MurNAc-L-Serine

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

Purine nucleoside phosphorylase YfiH

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

7w1g__assembly_4__model_1

7w1g__assembly_4__model_1 | I(q)

7w1g__assembly_4__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (2)