SAXSdb — 8abp

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

L-ARABINOSE-BINDING PROTEIN

Escherichia coli

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 24–329	Not recorded	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.49 Å

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.

Other PDB	Difference from Current Entry 8ABP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ABE NOVEL STEREOSPECIFICITY OF THE L-ARABINOSE-BINDING PROTEIN Deposited 1992-04-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1ABF SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES Deposited 1992-04-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1APB A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES Deposited 1991-11-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.76 Å
1BAP A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES Deposited 1991-11-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.75 Å
2WRZ Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state Deposited 2009-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；20% PEG 3350, 0.2M (NH4)CITRATE, 2UMOL/ML SEROTONIN, pH 8.0	Resolution 2.20 Å R-free 0.272
2WRZ Crystal structure of an arabinose binding protein with designed serotonin binding site in open, ligand-free state Deposited 2009-09-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–329（306 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；20% PEG 3350, 0.2M (NH4)CITRATE, 2UMOL/ML SEROTONIN, pH 8.0	Resolution 2.20 Å R-free 0.272
5ABP SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES Deposited 1990-12-26	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
6ABP SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY Deposited 1991-04-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	ARA alpha-L-arabinopyranose × 1 ARB beta-L-arabinopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.67 Å
7ABP SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY Deposited 1991-04-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	FCA alpha-D-fucopyranose × 1 FCB beta-D-fucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.67 Å
9ABP A PRO TO GLY MUTATION IN THE HINGE OF THE ARABINOSE-BINDING PROTEIN ENHANCES BINDING AND ALTERS SPECIFICITY: SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES Deposited 1991-11-15	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–329（306 aa）	Not recorded	GLA alpha-D-galactopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.97 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARAF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 24–329

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	8abp
Deposition date deposition_date	1991-04-25
Structure title title	SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY
Keywords keywords	BINDING PROTEINS; BINDING PROTEINS
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	20.83 Å
Radius of gyration Rg (electron density) rg_electron	20.09 Å
Forward intensity I(0) i0	18349700.00
Molecular weight molecular_weight	33092.0 kDa
Excluded volume excluded_volume	41696 Å³
Envelope volume envelope_volume	47170 Å³
Hydration-shell volume shell_volume	20001 Å³
Envelope diameter envelope_diameter	71.0 Å
Shell Rg shell_rg	26.14 Å
Envelope Rg envelope_rg	20.34 Å
Shape Rg shape_rg	20.09 Å
Total Rg total_rg	20.90 Å
Total atoms total_atoms	2328
Residues n_residues	305
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	68.5 Å
Rg (real space) rg_real	20.85 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.8350e+07
I(0) uncertainty (real space) i0_real_error	2.5240e+05
Rg (reciprocal space) rg_reciprocal	20.85 Å
I(0) (reciprocal space) i0_reciprocal	18350000.0000
Solution quality estimate total_estimate	0.7985
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.426
Kurtosis Kurtosis kurtosis	-0.258
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7579000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	L-ARABINOSE-BINDING PROTEIN
Molecular weight formula_weight	33233.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2547

ENLKLGFLVKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSLAASGAKGFVICTPDPKLGSAIVAKARGYDMKVIAVDDQFVNAKGKPMDTVPLVMLAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGFPEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAADIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKDVEPPKFTEVTDVVLITRDNFKEELEKKGLGGK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562

Entity 2 Entity 2 non-polymer

Description description	alpha-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	man
Copy count entity_count	207

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d8abpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamily	c.93.1 — Periplasmic binding protein-like I
Family Family family	c.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id	8abpA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	8abpA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (11)

;Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity. ;

Biochemistry (1991)

PMID: 2069949 · DOI: 10.1021/bi00242a009 PRIMARY

Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules

Nature (1989)

Novel Stereospecificity of the L-Arabinose-Binding Protein

Nature (1984)

;Hinge-Bending in L-Arabinose-Binding Protein. The "Venus'S-Flytrap" Model ;

J.Biol.Chem. (1982)

Structure of the L-Arabinose-Binding Protein from Escherichia Coli at 2.4 Angstroms Resolution

J.Mol.Biol. (1981)

L-Arabinose-Binding Protein-Sugar Complex at 2.4 Angstroms Resolution. Stereochemistry and Evidence for a Structural Change

J.Biol.Chem. (1981)

The Radius of Gyration of L-Arabinose-Binding Protein Decreases Upon Binding of Ligand

J.Biol.Chem. (1981)

The Thiol Group of the L-Arabinose-Binding Protein. Chromophoric Labeling and Chemical Identification of the Sugar-Binding Site

J.Biol.Chem. (1979)

;Location of the Sugar-Binding Site of L-Arabinose-Binding Protein. Sugar Derivative Syntheses, Sugar Binding Specificity, and Difference Fourier Analyses ;

J.Biol.Chem. (1979)

The 2.8-Angstroms Resolution Structure of the L-Arabinose-Binding Protein from Escherichia Coli

J.Biol.Chem. (1977)

Structure of L-Arabinose-Binding Protein from Escherichia Coli at 5 Angstroms Resolution and Preliminary Results at 3.5 Angstroms

Proc.Natl.Acad.Sci.USA (1976)

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Unit-cell length a length_a	55.620 Å
Unit-cell length b length_b	71.930 Å
Unit-cell length c length_c	78.090 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	4

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

Resolution resolution	1.490 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1750
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ab/8abp/8abp.fit
pddf	/app/data/pr_computation/ab/8abp/8abp.pr.out
profile	/app/data/saxs_computation/ab/8abp/8abp.dat

SUGAR-BINDING AND CRYSTALLOGRAPHIC STUDIES OF AN ARABINOSE-BINDING PROTEIN MUTANT (MET108LEU) WHICH EXHIBITS ENHANCED AFFINITY AND ALTERED SPECIFICITY