1k1e

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Method: X-RAY DIFFRACTION

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

deoxy-D-mannose-octulosonate 8-phosphate phosphatase

Haemophilus influenzae Rd

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 4 MERCURY (II) ION × 4 SULFATE ION × 6 GLYCEROL × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 4 MERCURY (II) ION × 4 SULFATE ION × 6 GLYCEROL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	COBALT (II) ION × 4 MERCURY (II) ION × 4 SULFATE ION × 6 GLYCEROL × 3 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 8	COBALT (II) ION × 8 MERCURY (II) ION × 8 SULFATE ION × 12 GLYCEROL × 6 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 water × 8	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 8	COBALT (II) ION × 8 MERCURY (II) ION × 8 SULFATE ION × 12 GLYCEROL × 3 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDOP_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 1–180 Author chain B； PDBConstruct 1–180； UniProt 1–180 Author chain C； PDBConstruct 1–180； UniProt 1–180 Author chain D； PDBConstruct 1–180； UniProt 1–180 Author chain E； PDBConstruct 1–180； UniProt 1–180 Author chain F； PDBConstruct 1–180； UniProt 1–180 Author chain G； PDBConstruct 1–180； UniProt 1–180 Author chain H； PDBConstruct 1–180； UniProt 1–180 Author chain I； PDBConstruct 1–180； UniProt 1–180 Author chain J； PDBConstruct 1–180； UniProt 1–180 Author chain K； PDBConstruct 1–180； UniProt 1–180 Author chain L； PDBConstruct 1–180； UniProt 1–180

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	1k1e
Deposition date deposition_date	2001-09-25
Structure title title	Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)
Keywords keywords	HI1679, structural genomics, KDO 8-P phosphatase, Structure 2 Function Project, S2F, 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.

1k1e__assembly_1__model_1

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

Download this curve (.dat)

1k1e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k1e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.88 Å
Rg (electron density)	26.04 Å
Total Rg	26.98 Å
Atom count	5334
Residues	698
Excluded volume	95355 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k1e__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k1e__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1k1e__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1k1e__assembly_4__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1k1e__assembly_5__model_1`	octameric （8）	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	deoxy-D-mannose-octulosonate 8-phosphate phosphatase
Molecular weight formula_weight	19455.3 kDa
EC 编号 ec_number	3.1.3.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	17393

MQQKLENIKFVITDVDGVLTDGQLHYDANGEAIKSFHVRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFFLGKLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACGTSFAVADAPIYVKNAVDHVLSTHGGKGAFREMSDMILQAQGKSSVFDTAQGFLKSVKSMGQ

Source Source

Source organism organism	Haemophilus influenzae Rd
NCBI taxonomy ID ncbi_taxonomy_id	71421
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 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	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1414

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1k1ea_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1eb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ec_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ed_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ee_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ef_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1eg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1eh_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ei_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ej_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1ek_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

Domain ID domain_id	d1k1el_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.108 — HAD-like
Superfamily Superfamily superfamily	c.108.1 — HAD-like
Family Family family	c.108.1.5 — Probable phosphatase YrbI

CATH v4.4 (12 domains)

Domain ID domain_id	1k1eA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eK00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	1k1eL00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

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Unit-cell length a length_a	109.300 Å
Unit-cell length b length_b	109.100 Å
Unit-cell length c length_c	179.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.2250

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

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

deoxy-D-mannose-octulosonate 8-phosphate 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

1k1e__assembly_1__model_1

1k1e__assembly_1__model_1 | I(q)

1k1e__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 (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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

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

deoxy-D-mannose-octulosonate 8-phosphate 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

1k1e__assembly_1__model_1

1k1e__assembly_1__model_1 | I(q)

1k1e__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 (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

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)