2nvv

Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16.

Method: X-RAY DIFFRACTION

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

Acetyl-CoA hydrolase/transferase family protein

Porphyromonas gingivalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MVN7_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–498； UniProt 1–498 Author chain B； PDBConstruct 1–498； UniProt 1–498 Author chain C； PDBConstruct 1–498； UniProt 1–498 Author chain D； PDBConstruct 1–498； UniProt 1–498 Author chain E； PDBConstruct 1–498； UniProt 1–498 Author chain F； PDBConstruct 1–498； UniProt 1–498

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	2nvv
Deposition date deposition_date	2006-11-13
Structure title title	Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16.
Keywords keywords	;alpha beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

2nvv__assembly_1__model_1

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

Download this curve (.dat)

2nvv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nvv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.14 Å
Rg (electron density)	28.37 Å
Total Rg	29.09 Å
Atom count	7658
Residues	968
Excluded volume	136470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nvv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nvv__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nvv__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Description description	Acetyl-CoA hydrolase/transferase family protein
Molecular weight formula_weight	56424.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23178

MALRFITAEEAAEFVHHNDNVGFSGFTPAGNPKVVPAAIAKRAIAAHEKGNPFKIGMFTGASTGARLDGVLAQADAVKFRTPYQSNKDLRNLINNGSTSYFDLHLSTLAQDLRYGFYGKVDVAIIEVADVTEDGKILPTTGVGILPTICRLADRIIVELNDKHPKEIMGMHDLCEPLDPPARRELPVYTPSDRIGKPYVQVDPAKIVGVVRTSEPNDESDFAPLDPVTQAIGDNVAAFLVSEMKAGRIPKDFLPLQSGVGNVANAVLGALGDNPDIPAFNMYTEVIQDAVIALMKKGRIKFASGCSLSVSRSVIQDIYANLDFFKDKILLRPQEYSNNPEIVRRLGVITINTALEADIFGNINSTHVSGTRMMNGIGGSGDFTRNSYVSIFTTPSVMKDGKISSFVPMVAHHDHSEHSVKVIISEWGVADLRGKNPRERAHEIIDKCVHPDYRPLLRQYLELGVKGQTPQNLDCCFAFHQELAKSGDMRNVRWEDYMKLEHHHHHH

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	242619
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2nvva1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvva2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvve1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvve2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

Domain ID domain_id	d2nvvf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.0 — automated matches

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Unit-cell length a length_a	131.051 Å
Unit-cell length b length_b	131.051 Å
Unit-cell length c length_c	162.093 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2870
R_work r_work	0.2870
R_free r_free	0.2900

Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16.

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

Acetyl-CoA hydrolase/transferase family protein

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

2nvv__assembly_1__model_1

2nvv__assembly_1__model_1 | I(q)

2nvv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)

Crystal Structure of the Putative Acetyl-CoA hydrolase/transferase PG1013 from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR16.

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

Acetyl-CoA hydrolase/transferase family protein

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

2nvv__assembly_1__model_1

2nvv__assembly_1__model_1 | I(q)

2nvv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

7. Citations (1)