SAXSdb — 1brw

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

PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–433 Chain B； UniProt 1–433	Not recorded	PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 URA URACIL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；0.1 M MES PH 6.0-6.2 25% PEG 6000 PSEUDOURIDINE AT 10X PROTEIN CONCENTRATION	Resolution 2.10 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PDP_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–433； UniProt 1–433 Author chain B； PDBConstruct 1–433； UniProt 1–433

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	1brw
Deposition date deposition_date	1998-08-25
Structure title title	THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
Keywords keywords	NUCLEOSIDE PHOSPHORYLASE, DOMAIN MOVEMENT, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.85 Å
Radius of gyration Rg (electron density) rg_electron	33.55 Å
Forward intensity I(0) i0	133171000.00
Molecular weight molecular_weight	92712.0 kDa
Excluded volume excluded_volume	116470 Å³
Envelope volume envelope_volume	145980 Å³
Hydration-shell volume shell_volume	37692 Å³
Envelope diameter envelope_diameter	110.9 Å
Shell Rg shell_rg	39.05 Å
Envelope Rg envelope_rg	33.32 Å
Shape Rg shape_rg	33.60 Å
Total Rg total_rg	33.80 Å
Total atoms total_atoms	6482
Residues n_residues	866
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	110.8 Å
Rg (real space) rg_real	34.00 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.3320e+08
I(0) uncertainty (real space) i0_real_error	2.2170e+06
Rg (reciprocal space) rg_reciprocal	33.91 Å
I(0) (reciprocal space) i0_reciprocal	133200000.0000
Solution quality estimate total_estimate	0.8498
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.609
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44820000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.837

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)
Molecular weight formula_weight	46063.2 kDa
EC 编号 ec_number	2.4.2.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6592

MRMVDLIAKKRDGKALTKEEIEWIVRGYTNGDIPDYQMSALAMAIYFRGMTEEETAALTMAMVQSGEMLDLSSIRGVKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDKLESVPGFHVEISKDEFIRLVNENGIAIIGQTGDLTPADKKLYALRDVTATVNSIPLIASSIMSKKIAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVGRRTMAVISDMSQPLGYAVGNALEVKEAIETLKGNGPHDLTELCLTLGSHMVYLAEKAPSLDEARRLLEEAIRSGAAIAAFKTFLAAQGGDASVVDDLDKLPKAAYTSTVTAAADGYVAEMAADDIGTAAMWLGAGRAKKEDVIDLAVGIVLHKKIGDRVQKGEALATIHSNRPDVLDVKEKIEAAIRLSPQPVARPPLIYETIV

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	URACIL
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1brwa1
Class class	a — All alpha proteins
Fold Fold fold	a.46 — Methionine synthase domain-like
Superfamily Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

Domain ID domain_id	d1brwa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Superfamily Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Family Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	d1brwa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
Family Family family	d.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain

Domain ID domain_id	d1brwb1
Class class	a — All alpha proteins
Fold Fold fold	a.46 — Methionine synthase domain-like
Superfamily Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

Domain ID domain_id	d1brwb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Superfamily Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
Family Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	d1brwb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.3 — Pyrimidine nucleoside phosphorylase C-terminal domain
Family Family family	d.41.3.1 — Pyrimidine nucleoside phosphorylase C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1brwA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

Domain ID domain_id	1brwA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	1brwA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

Domain ID domain_id	1brwB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	30 — Pyrimidine nucleoside phosphorylase-like, C-terminal domain

Domain ID domain_id	1brwB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Domain ID domain_id	1brwB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

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8. Citations (1)

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Unit-cell length a length_a	53.570 Å
Unit-cell length b length_b	70.450 Å
Unit-cell length c length_c	122.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2760

fit	/app/data/saxs_computation/br/1brw/1brw.fit
pddf	/app/data/pr_computation/br/1brw/1brw.pr.out
profile	/app/data/saxs_computation/br/1brw/1brw.dat

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

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

PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction