SAXSdb — 6rmr

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

Glucose-1-phosphatase

Escherichia coli (strain K12)

UniProt P19926

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PENTAETHYLENE GLYCOL × 1 ACETATE ION × 16 ZINC ION × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–391； UniProt 23–413 Author chain B； PDBConstruct 1–391； UniProt 23–413

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	6rmr
Deposition date deposition_date	2019-05-07
Structure title title	Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D mutant
Keywords keywords	H18D Mutant of AGP, HYDROLASE; 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.

6rmr__assembly_1__model_1

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

Download this curve (.dat)

6rmr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rmr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.68 Å
Rg (electron density)	28.70 Å
Total Rg	29.35 Å
Atom count	5816
Residues	774
Excluded volume	102320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rmr__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 (6)

Entity 1 Entity 1 polymer

Description description	Glucose-1-phosphatase
Molecular weight formula_weight	43581.1 kDa
EC 编号 ec_number	3.1.3.10
Mutation mutation	H18D
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	5912

QTVPEGYQLQQVLMMSRDNLRAPLANNGSVLEQSTPNKWPEWDVPGGQLTTKGGVLEVYMGHYMREWLAEQGMVKSGECPPPYTVYAYANSLQRTVATAQFFITGAFPGCDIPVHHQEKMGTMDPTFNPVITDDSAAFSEQAVAAMEKELSKLQLTDSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSGPLKVGNSLVDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSNIASLLTALDFKPYQLHDQNERTPIGGKIVFQRWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCPIDADGFCPMDKFDSVLNEAVK

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6rmra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

Domain ID domain_id	d6rmrb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.2 — Histidine acid phosphatase

CATH v4.4 (4 domains)

Domain ID domain_id	6rmrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	6rmrA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	6rmrB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	6rmrB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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Unit-cell length a length_a	64.035 Å
Unit-cell length b length_b	101.651 Å
Unit-cell length c length_c	114.929 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	42.768 Å
R factor r_factor	0.2289
R_work r_work	0.2247
R_free r_free	0.2661

Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D mutant

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

Glucose-1-phosphatase

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

6rmr__assembly_1__model_1

6rmr__assembly_1__model_1 | I(q)

6rmr__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Escherichia coli periplasmic glucose-1-phosphatase H18D mutant

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

Glucose-1-phosphatase

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

6rmr__assembly_1__model_1

6rmr__assembly_1__model_1 | I(q)

6rmr__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)