SAXSdb — 2ze9

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

Phospholipase D

Streptomyces antibioticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 (2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLD_STRAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–509； UniProt 48–556

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	2ze9
Deposition date deposition_date	2007-12-06
Structure title title	Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine
Keywords keywords	ALPHA-BETA-BETA-ALPHA SANDWICH, Hydrolase, Lipid degradation, Secreted; 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.

2ze9__assembly_1__model_1

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

Download this curve (.dat)

2ze9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ze9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.76 Å
Rg (electron density)	21.45 Å
Total Rg	22.40 Å
Atom count	3796
Residues	504
Excluded volume	66752 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ze9__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	Phospholipase D
Molecular weight formula_weight	53969.0 kDa
EC 编号 ec_number	3.1.4.4
Mutation mutation	H168A
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	4161

ADTPPTPHLDAIERSLRDTSPGLEGSVWQRTDGNRLDAPDGDPAGWLLQTPGCWGDAGCKDRAGTRRLLDKMTRNIADARHTVDISSLAPFPNGGFEDAVVDGLKASVAAGHSPRVRILVGAAPIYHLNVVPSRYRDELIGKLGAAAGKVTLNVASMTTSKTSLSWNASKLLVVDGKTAITGGINGWKDDYLDTAHPVSDVDMALSGPAARSAGKYLDTLWDWTCRNASDPAKVWLATSNGASCMPSMEQDEAGSAPAEPTGDVPVIAVGGLGVGIKESDPSSGYHPDLPTAPDTKCTVGLHDNTNADRDYDTVNPEENALRSLIASARSHVEISQQDLNATCPPLPRYDIRTYDTLAGKLAAGVKVRIVVSDPANRGAVGSGGYSQIKSLDEISDTLRTRLVALTGDNEKASRALCGNLQLASFRSSDAAKWADGKPYALHHKLVSVDDSAFYIGSKNLYPAWLQDFGYIVESPAAAQQLKTELLDPEWKYSQQAAATPAGCPARQAG

Source Source

Source organism organism	Streptomyces antibioticus
NCBI taxonomy ID ncbi_taxonomy_id	1890
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 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	1

Entity 3 Entity 3 non-polymer

Description description	(2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate
Molecular weight formula_weight	396.4 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	365

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ze9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	2ze9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

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Unit-cell length a length_a	60.868 Å
Unit-cell length b length_b	78.232 Å
Unit-cell length c length_c	98.603 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	2.300 Å
Low-resolution limit resolution_low	48.040 Å
R factor r_factor	0.1745
R_work r_work	0.1703
R_free r_free	0.2514

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine

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

Phospholipase D

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

2ze9__assembly_1__model_1

2ze9__assembly_1__model_1 | I(q)

2ze9__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (3)

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine

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

Phospholipase D

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

2ze9__assembly_1__model_1

2ze9__assembly_1__model_1 | I(q)

2ze9__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (3)