PDB-4pv6: Crystal Structure Analysis of Ard1 from Thermoplasma volcanium

Basic information

• Entry: Database: PDB / ID: 4pv6
• Title: Crystal Structure Analysis of Ard1 from Thermoplasma volcanium
• Components: N-terminal acetyltransferase complex subunit [ARD1]Peptide alpha-N-acetyltransferase
• Keywords: TRANSFERASE / N-terminal acetyltransferase

Function / homology

Function:

N-terminal protein amino acid acetylation / N-acetyltransferase activity

Domain/homology:

N-acetyltransferase RimI/Ard1 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETYL COENZYME *A / COENZYME A / N-terminal acetyltransferase complex subunit [ARD1]

• Biological species: Thermoplasma volcanium (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
• Authors: Ma, C. / Lee, S.J. / Lee, B.J.
• Citation: Journal: Biochim.Biophys.Acta / Year: 2014; Title: Structure of Thermoplasma volcanium Ard1 belongs to N-acetyltransferase family member suggesting multiple ligand binding modes with acetyl coenzyme A and coenzyme A.; Authors: Ma, C. / Pathak, C. / Jang, S. / Lee, S.J. / Nam, M. / Kim, S.J. / Im, H. / Lee, B.J.

History

Deposition	Mar 15, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

C: N-terminal acetyltransferase complex subunit [ARD1]

D: N-terminal acetyltransferase complex subunit [ARD1]

G: N-terminal acetyltransferase complex subunit [ARD1]

I: N-terminal acetyltransferase complex subunit [ARD1]

K: N-terminal acetyltransferase complex subunit [ARD1]

M: N-terminal acetyltransferase complex subunit [ARD1]

F: N-terminal acetyltransferase complex subunit [ARD1]

N: N-terminal acetyltransferase complex subunit [ARD1]

A: N-terminal acetyltransferase complex subunit [ARD1]

B: N-terminal acetyltransferase complex subunit [ARD1]

H: N-terminal acetyltransferase complex subunit [ARD1]

J: N-terminal acetyltransferase complex subunit [ARD1]

L: N-terminal acetyltransferase complex subunit [ARD1]

O: N-terminal acetyltransferase complex subunit [ARD1]

E: N-terminal acetyltransferase complex subunit [ARD1]

P: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• 308 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	308,364	24
Polymers	301,930	16
Non-polymers	6,435	8
Water	919	51

1

C: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

2

D: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

3

G: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

4

I: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

5

K: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

6

M: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

7

F: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

8

N: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

9

A: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.6 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,638	2
Polymers	18,871	1
Non-polymers	768	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

10

B: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

11

H: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

12

J: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

13

L: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

14

O: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

15

E: N-terminal acetyltransferase complex subunit [ARD1]

hetero molecules

Summary:

• defined by author&software
• 19.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,680	2
Polymers	18,871	1
Non-polymers	810	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

16

P: N-terminal acetyltransferase complex subunit [ARD1]

Summary:

• defined by author&software
• 18.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	18,871	1
Polymers	18,871	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

Unit cell

Length a, b, c (Å)	102.240, 129.935, 158.576
Angle α, β, γ (deg.)	90.00, 93.94, 90.00
Int Tables number	4
Space group name H-M	P1211

Components

#1: Protein

C D G I K M F N A B H J L O E P
N-terminal acetyltransferase complex subunit [ARD1] / Peptide alpha-N-acetyltransferase

Details:

Mass: 18870.615 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: TV0014, TvArd1, TVG0012647 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q97CT7

#2: Chemical

C-200 G-200 I-200 F-200 H-200 J-200 E-200
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA

Details:

Mass: 809.571 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S

#3: Chemical

A-201 ChemComp-COA / COENZYME A / Coenzyme A

Details:

Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.48 ų/Da / Density % sol: 64.66 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 ; Details: Tris, HCl, potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
• Detector: Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2012 / Details: Mirror
• Radiation: Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 3.3→50 Å / Num. all: 60855 / Num. obs: 57796
• Reflection shell: Resolution: 3.3→3.36 Å

Processing

Software

Name	Version	Classification
HKL-2000		data collection
CCP4		model building
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
CCP4		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7B

2x7b

Resolution: 3.32→49.59 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.888 / SU B: 20.418 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2462	3078	5.1 %	RANDOM
Rwork	0.20522	-	-	-
obs	0.20729	57758	99.13 %	-
all	-	60855	-	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 86.965 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-5.51 Å2	-0 Å2	1.41 Å2
2-	-	2.92 Å2	0 Å2
3-	-	-	2.48 Å2

Refinement step

Cycle: LAST / Resolution: 3.32→49.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19559	0	405	51	20015

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	20398
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19139
X-RAY DIFFRACTION	r_angle_refined_deg	1.575	1.972	27644
X-RAY DIFFRACTION	r_angle_other_deg	0.833	3	43708
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.233	5	2386
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.041	22.029	966
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.942	15	3434
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.969	15	208
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	3045
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	22586
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	5094
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	5.848	8.535	9599
X-RAY DIFFRACTION	r_mcbond_other	5.847	8.535	9598
X-RAY DIFFRACTION	r_mcangle_it	9.123	12.785	11962
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.058	8.976	10799
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.319→3.405 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.316	214	-
Rwork	0.273	4027	-
obs	-	-	94.35 %