SAXSdb — 3d02

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

Putative LACI-type transcriptional regulator

Klebsiella pneumoniae subsp. pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 3 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6THR5_KLEP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–303； UniProt 26–327

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	3d02
Deposition date deposition_date	2008-04-30
Structure title title	Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution
Keywords keywords	;YP_001338366.1, periplasmic sugar-binding protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, TRANSCRIPTION, SUGAR BINDING PROTEIN ;; SUGAR BINDING PROTEIN
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.

3d02__assembly_1__model_1

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

Download this curve (.dat)

3d02__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d02__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.02 Å
Rg (electron density)	19.17 Å
Total Rg	20.01 Å
Atom count	2272
Residues	291
Excluded volume	40693 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d02__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Putative LACI-type transcriptional regulator
Molecular weight formula_weight	33460.7 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	2925

GAAEKTVVNISKVDGMPWFNRMGEGVVQAGKEFNLNASQVGPSSTDAPQQVKIIEDLIARKVDAITIVPNDANVLEPVFKKARDAGIVVLTNESPGQPSANWDVEIIDNEKFAAEYVEHMAKRMGGKGGYVIYVGSLTVPQHNLWADLLVKYQKEHYPDMHEVTRRMPVAESVDDSRRTTLDLMKTYPDLKAVVSFGSNGPIGAGRAVKEKRAKNKVAVYGMMIPSQAASLIKSGDITEGITYDPATAGYALAAVASTLLNGKTIEPGFELKELGKAEVDSDKHIIRFHKVLLVNKDNIDSLY

Source Source

Source organism organism	Klebsiella pneumoniae subsp. pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	272620
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	313

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3d02a_
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.93.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3d02A01
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	3d02A02
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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Unit-cell length a length_a	66.240 Å
Unit-cell length b length_b	76.960 Å
Unit-cell length c length_c	113.980 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	28.630 Å
R factor r_factor	0.1580
R_work r_work	0.1570
R_free r_free	0.1720

Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution

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

Putative LACI-type transcriptional regulator

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

3d02__assembly_1__model_1

3d02__assembly_1__model_1 | I(q)

3d02__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution

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

Putative LACI-type transcriptional regulator

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

3d02__assembly_1__model_1

3d02__assembly_1__model_1 | I(q)

3d02__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)