PDB-2jg7: Crystal structure of Seabream Antiquitin and Elucidation of its s...

ID or keywords:

Entry

Database: PDB / ID: 2jg7

Title

Crystal structure of Seabream Antiquitin and Elucidation of its substrate specificity

Components

ANTIQUITIN

Keywords

OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / nucleotide binding
Similarity search - Function

Biological species

ACANTHOPAGRUS SCHLEGELI (black porgy)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.83 Å

Authors

Tang, W.K. / Wong, K.B. / Cha, S.S. / Lee, H.S. / Cheng, C.H.K. / Fong, W.P.

Citation

Journal: FEBS Lett. / Year: 2008
Title: The Crystal Structure of Seabream Antiquitin Reveals the Structural Basis of its Substrate Specificity.
Authors: Tang, W.K. / Wong, K.B. / Lam, Y.M. / Cha, S.S. / Cheng, C.H.K. / Fong, W.P.

History

Deposition	Feb 9, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2008	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2jg7.cif.gz	734.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2jg7.ent.gz	616.1 KB	Display	PDB format
PDBx/mmJSON format	2jg7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2jg7_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	2jg7_full_validation.pdf.gz	2.8 MB	Display
Data in XML	2jg7_validation.xml.gz	129.3 KB	Display
Data in CIF	2jg7_validation.cif.gz	175 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jg/2jg7 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jg7	HTTPS FTP

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Related structure data

Related structure data	1bpwS S: Starting model for refinement
Similar structure data	6o4c-2 6v0z-2 4zuk-2 6o4k-2 6o4k-1 4x0t-d 6o4b-2 6o4h-2 6u2x-2 4zvw-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (6) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (6)

Deposited unit

A: ANTIQUITIN

B: ANTIQUITIN

C: ANTIQUITIN

D: ANTIQUITIN

E: ANTIQUITIN

F: ANTIQUITIN

G: ANTIQUITIN

H: ANTIQUITIN

hetero molecules

447 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ANTIQUITIN

B: ANTIQUITIN

C: ANTIQUITIN

D: ANTIQUITIN

hetero molecules

defined by author&software
224 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: ANTIQUITIN

F: ANTIQUITIN

G: ANTIQUITIN

H: ANTIQUITIN

hetero molecules

defined by author&software
224 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.160, 111.020, 113.640
Angle α, β, γ (deg.)	90.50, 98.10, 111.59
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
1	2	B
2	2	C
3	2	D
4	2	E
5	2	F
6	2	G
7	2	H

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	2 - 8
2	1	1	1	B	2 - 8
3	1	1	1	C	2 - 8
4	1	1	1	D	2 - 8
5	1	1	1	E	2 - 8
6	1	1	1	F	2 - 8
7	1	1	1	G	2 - 8
8	1	1	1	H	2 - 8
1	2	1	3	A	9
2	2	1	3	B	9
3	2	1	3	C	9
4	2	1	3	D	9
5	2	1	3	E	9
6	2	1	3	F	9
7	2	1	3	G	9
8	2	1	3	H	9
1	3	1	1	A	10 - 34
2	3	1	1	B	10 - 34
3	3	1	1	C	10 - 34
4	3	1	1	D	10 - 34
5	3	1	1	E	10 - 34
6	3	1	1	F	10 - 34
7	3	1	1	G	10 - 34
8	3	1	1	H	10 - 34
1	4	1	3	A	35
2	4	1	3	B	35
3	4	1	3	C	35
4	4	1	3	D	35
5	4	1	3	E	35
6	4	1	3	F	35
7	4	1	3	G	35
8	4	1	3	H	35
1	5	1	1	A	36 - 212
2	5	1	1	B	36 - 212
3	5	1	1	C	36 - 212
4	5	1	1	D	36 - 212
5	5	1	1	E	36 - 212
6	5	1	1	F	36 - 212
7	5	1	1	G	36 - 212
8	5	1	1	H	36 - 212
1	6	1	3	A	213
2	6	1	3	B	213
3	6	1	3	C	213
4	6	1	3	D	213
5	6	1	3	E	213
6	6	1	3	F	213
7	6	1	3	G	213
8	6	1	3	H	213
1	7	1	1	A	214 - 226
2	7	1	1	B	214 - 226
3	7	1	1	C	214 - 226
4	7	1	1	D	214 - 226
5	7	1	1	E	214 - 226
6	7	1	1	F	214 - 226
7	7	1	1	G	214 - 226
8	7	1	1	H	214 - 226
1	8	1	3	A	227
2	8	1	3	B	227
3	8	1	3	C	227
4	8	1	3	D	227
5	8	1	3	E	227
6	8	1	3	F	227
7	8	1	3	G	227
8	8	1	3	H	227
1	9	1	1	A	228 - 247
2	9	1	1	B	228 - 247
3	9	1	1	C	228 - 247
4	9	1	1	D	228 - 247
5	9	1	1	E	228 - 247
6	9	1	1	F	228 - 247
7	9	1	1	G	228 - 247
8	9	1	1	H	228 - 247
1	10	1	3	A	248
2	10	1	3	B	248
3	10	1	3	C	248
4	10	1	3	D	248
5	10	1	3	E	248
6	10	1	3	F	248
7	10	1	3	G	248
8	10	1	3	H	248
1	11	1	1	A	249 - 328
2	11	1	1	B	249 - 328
3	11	1	1	C	249 - 328
4	11	1	1	D	249 - 328
5	11	1	1	E	249 - 328
6	11	1	1	F	249 - 328
7	11	1	1	G	249 - 328
8	11	1	1	H	249 - 328
1	12	1	1	A	341 - 356
2	12	1	1	B	341 - 356
3	12	1	1	C	341 - 356
4	12	1	1	D	341 - 356
5	12	1	1	E	341 - 356
6	12	1	1	F	341 - 356
7	12	1	1	G	341 - 356
8	12	1	1	H	341 - 356
1	13	1	3	A	357
2	13	1	3	B	357
3	13	1	3	C	357
4	13	1	3	D	357
5	13	1	3	E	357
6	13	1	3	F	357
7	13	1	3	G	357
8	13	1	3	H	357
1	14	1	1	A	358 - 360
2	14	1	1	B	358 - 360
3	14	1	1	C	358 - 360
4	14	1	1	D	358 - 360
5	14	1	1	E	358 - 360
6	14	1	1	F	358 - 360
7	14	1	1	G	358 - 360
8	14	1	1	H	358 - 360
1	15	1	3	A	361
2	15	1	3	B	361
3	15	1	3	C	361
4	15	1	3	D	361
5	15	1	3	E	361
6	15	1	3	F	361
7	15	1	3	G	361
8	15	1	3	H	361
1	16	1	1	A	362 - 409
2	16	1	1	B	362 - 409
3	16	1	1	C	362 - 409
4	16	1	1	D	362 - 409
5	16	1	1	E	362 - 409
6	16	1	1	F	362 - 409
7	16	1	1	G	362 - 409
8	16	1	1	H	362 - 409
1	17	1	3	A	410
2	17	1	3	B	410
3	17	1	3	C	410
4	17	1	3	D	410
5	17	1	3	E	410
6	17	1	3	F	410
7	17	1	3	G	410
8	17	1	3	H	410
1	18	1	1	A	411 - 498
2	18	1	1	B	411 - 498
3	18	1	1	C	411 - 498
4	18	1	1	D	411 - 498
5	18	1	1	E	411 - 498
6	18	1	1	F	411 - 498
7	18	1	1	G	411 - 498
8	18	1	1	H	411 - 498
1	19	1	3	A	499 - 500
2	19	1	3	B	499 - 500
3	19	1	3	C	499 - 500
4	19	1	3	D	499 - 500
5	19	1	3	E	499 - 500
6	19	1	3	F	499 - 500
7	19	1	3	G	499 - 500
8	19	1	3	H	499 - 500
1	20	1	1	A	501 - 507
2	20	1	1	B	501 - 507
3	20	1	1	C	501 - 507
4	20	1	1	D	501 - 507
5	20	1	1	E	501 - 507
6	20	1	1	F	501 - 507
7	20	1	1	G	501 - 507
8	20	1	1	H	501 - 507
1	21	1	3	A	508 - 509
2	21	1	3	B	508 - 509
3	21	1	3	C	508 - 509
4	21	1	3	D	508 - 509
5	21	1	3	E	508 - 509
6	21	1	3	F	508 - 509
7	21	1	3	G	508 - 509
8	21	1	3	H	508 - 509
1	22	1	1	A	999
2	22	1	1	B	999
3	22	1	1	C	999
4	22	1	1	D	999
5	22	1	1	E	999
6	22	1	1	F	999
7	22	1	1	G	999
8	22	1	1	H	999
1	1	2	1	B	329 - 331
2	1	2	1	C	329 - 331
3	1	2	1	D	329 - 331
4	1	2	1	E	329 - 331
5	1	2	1	F	329 - 331
6	1	2	1	G	329 - 331
7	1	2	1	H	329 - 331
1	2	2	2	B	332 - 335
2	2	2	2	C	332 - 335
3	2	2	2	D	332 - 335
4	2	2	2	E	332 - 335
5	2	2	2	F	332 - 335
6	2	2	2	G	332 - 335
7	2	2	2	H	332 - 335
1	3	2	1	B	336 - 340
2	3	2	1	C	336 - 340
3	3	2	1	D	336 - 340
4	3	2	1	E	336 - 340
5	3	2	1	F	336 - 340
6	3	2	1	G	336 - 340
7	3	2	1	H	336 - 340

NCS ensembles :

ID
1
2

#1: Protein	ANTIQUITIN Mass: 55221.816 Da / Num. of mol.: 8 / Fragment: RESIDUES 2-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACANTHOPAGRUS SCHLEGELI (black porgy) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4KTQ7
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 46.53 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Type: PAL/PLS / Wavelength: 1.12714
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.12714 Å / Relative weight: 1
Reflection	Resolution: 2.8→30.2 Å / Num. obs: 86382 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.12 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 85

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Processing

Software

Name: REFMAC / Version: 5.2.0005 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BPW

1bpw

Resolution: 2.83→30.19 Å / Cor.coef. F_o:F_c: 0.884 / Cor.coef. F_o:F_c free: 0.865 / SU B: 16.132 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	4332	5 %	RANDOM
R_work	0.21	-	-	-
obs	0.211	82050	100 %	-

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: 21.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0.13 Å²	0.11 Å²
2-	-	-0.46 Å²	-0.46 Å²
3-	-	-	0.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.83→30.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30944	0	352	179	31475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	31984
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.062	1.971	43512
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.142	5	4064
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.999	24.472	1288
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.112	15	5240
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.101	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	4888
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	24008
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	14945
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	21919
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	1055
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	0.164	0.2	145
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.126	0.2	20
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	0.358	1.5	20599
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.618	2	32360
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.931	3	13092
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.637	4.5	11152
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3746	tight positional	0.02	0.05
1	2	B	3746	tight positional	0.02	0.05
1	3	C	3746	tight positional	0.03	0.05
1	4	D	3746	tight positional	0.02	0.05
1	5	E	3746	tight positional	0.02	0.05
1	6	F	3746	tight positional	0.02	0.05
1	7	G	3746	tight positional	0.03	0.05
1	8	H	3746	tight positional	0.02	0.05
2	1	B	79	tight positional	0.02	0.05
2	2	C	79	tight positional	0.02	0.05
2	3	D	79	tight positional	0.02	0.05
2	4	E	79	tight positional	0.02	0.05
2	5	F	79	tight positional	0.02	0.05
2	6	G	79	tight positional	0.03	0.05
2	7	H	79	tight positional	0.02	0.05
2	1	B	21	medium positional	0.67	0.5
2	2	C	21	medium positional	0.56	0.5
2	3	D	21	medium positional	0.72	0.5
2	4	E	21	medium positional	0.86	0.5
2	5	F	21	medium positional	0.55	0.5
2	6	G	21	medium positional	1.14	0.5
2	7	H	21	medium positional	0.93	0.5
1	1	A	60	loose positional	0.88	5
1	2	B	60	loose positional	0.98	5
1	3	C	60	loose positional	1.12	5
1	4	D	60	loose positional	1.01	5
1	5	E	60	loose positional	0.82	5
1	6	F	60	loose positional	1.07	5
1	7	G	60	loose positional	1.41	5
1	8	H	60	loose positional	1.15	5
1	1	A	3746	tight thermal	0.04	0.5
1	2	B	3746	tight thermal	0.04	0.5
1	3	C	3746	tight thermal	0.04	0.5
1	4	D	3746	tight thermal	0.04	0.5
1	5	E	3746	tight thermal	0.05	0.5
1	6	F	3746	tight thermal	0.04	0.5
1	7	G	3746	tight thermal	0.04	0.5
1	8	H	3746	tight thermal	0.05	0.5
2	1	B	79	tight thermal	0.03	0.5
2	2	C	79	tight thermal	0.05	0.5
2	3	D	79	tight thermal	0.05	0.5
2	4	E	79	tight thermal	0.05	0.5
2	5	F	79	tight thermal	0.03	0.5
2	6	G	79	tight thermal	0.05	0.5
2	7	H	79	tight thermal	0.05	0.5
2	1	B	21	medium thermal	0.22	2
2	2	C	21	medium thermal	0.19	2
2	3	D	21	medium thermal	0.43	2
2	4	E	21	medium thermal	0.17	2
2	5	F	21	medium thermal	0.23	2
2	6	G	21	medium thermal	0.33	2
2	7	H	21	medium thermal	0.25	2
1	1	A	60	loose thermal	1.51	10
1	2	B	60	loose thermal	1.34	10
1	3	C	60	loose thermal	1.79	10
1	4	D	60	loose thermal	0.96	10
1	5	E	60	loose thermal	1.09	10
1	6	F	60	loose thermal	1.54	10
1	7	G	60	loose thermal	1.36	10
1	8	H	60	loose thermal	0.96	10

LS refinement shell

Resolution: 2.83→2.9 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.355	265
R_work	0.313	4544

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi