PDB-4v6h: Crystal structure of succinate-semialdehyde dehydrogenase from Bu...

ID or keywords:

Entry

Database: PDB / ID: 4v6h

Title

Crystal structure of succinate-semialdehyde dehydrogenase from Burkholderia pseudomallei

Components

Succinate-semialdehyde dehydrogenase (NADP+)

Keywords

OXIDOREDUCTASE / NIAID /

.Infectious Disease / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Non-crystallographic symmetry / NCS

Function / homology

Function and homology information

succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase [NAD(P)+] activity / gamma-aminobutyric acid catabolic process
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of succinate-semialdehyde dehydrogenase from Burkholderia pseudomallei
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Jul 24, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Supersession	Dec 10, 2014	ID: 3IFH, 3IFG
Revision 1.1	Dec 10, 2014	Group: Other
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4v6h.cif.gz	2.6 MB	Display	PDBx/mmCIF format
PDB format	pdb4v6h.ent.gz		Display	PDB format
PDBx/mmJSON format	4v6h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v6/4v6h ftp://data.pdbj.org/pub/pdb/validation_reports/v6/4v6h	HTTPS FTP

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Related structure data

Related structure data	3ek1S S: Starting model for refinement
Similar structure data	4qf6-2 4qf6-3 4qet-d 5gt6-d 1bpw-d 5dib-d 2onm-3 2w8r-2 1zum-1 4kwg-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: BupsA.00020.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Succinate-semialdehyde dehydrogenase (NADP+)

B: Succinate-semialdehyde dehydrogenase (NADP+)

C: Succinate-semialdehyde dehydrogenase (NADP+)

D: Succinate-semialdehyde dehydrogenase (NADP+)

E: Succinate-semialdehyde dehydrogenase (NADP+)

F: Succinate-semialdehyde dehydrogenase (NADP+)

G: Succinate-semialdehyde dehydrogenase (NADP+)

H: Succinate-semialdehyde dehydrogenase (NADP+)

I: Succinate-semialdehyde dehydrogenase (NADP+)

J: Succinate-semialdehyde dehydrogenase (NADP+)

K: Succinate-semialdehyde dehydrogenase (NADP+)

L: Succinate-semialdehyde dehydrogenase (NADP+)

M: Succinate-semialdehyde dehydrogenase (NADP+)

N: Succinate-semialdehyde dehydrogenase (NADP+)

O: Succinate-semialdehyde dehydrogenase (NADP+)

P: Succinate-semialdehyde dehydrogenase (NADP+)

Q: Succinate-semialdehyde dehydrogenase (NADP+)

R: Succinate-semialdehyde dehydrogenase (NADP+)

S: Succinate-semialdehyde dehydrogenase (NADP+)

T: Succinate-semialdehyde dehydrogenase (NADP+)

U: Succinate-semialdehyde dehydrogenase (NADP+)

V: Succinate-semialdehyde dehydrogenase (NADP+)

W: Succinate-semialdehyde dehydrogenase (NADP+)

X: Succinate-semialdehyde dehydrogenase (NADP+)

Y: Succinate-semialdehyde dehydrogenase (NADP+)

Z: Succinate-semialdehyde dehydrogenase (NADP+)

1: Succinate-semialdehyde dehydrogenase (NADP+)

2: Succinate-semialdehyde dehydrogenase (NADP+)

3: Succinate-semialdehyde dehydrogenase (NADP+)

4: Succinate-semialdehyde dehydrogenase (NADP+)

5: Succinate-semialdehyde dehydrogenase (NADP+)

6: Succinate-semialdehyde dehydrogenase (NADP+)

1.64 MDa, 32 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Succinate-semialdehyde dehydrogenase (NADP+)

B: Succinate-semialdehyde dehydrogenase (NADP+)

C: Succinate-semialdehyde dehydrogenase (NADP+)

D: Succinate-semialdehyde dehydrogenase (NADP+)

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

2

E: Succinate-semialdehyde dehydrogenase (NADP+)

F: Succinate-semialdehyde dehydrogenase (NADP+)

G: Succinate-semialdehyde dehydrogenase (NADP+)

H: Succinate-semialdehyde dehydrogenase (NADP+)

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

3

I: Succinate-semialdehyde dehydrogenase (NADP+)

J: Succinate-semialdehyde dehydrogenase (NADP+)

K: Succinate-semialdehyde dehydrogenase (NADP+)

L: Succinate-semialdehyde dehydrogenase (NADP+)

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

4

M: Succinate-semialdehyde dehydrogenase (NADP+)

N: Succinate-semialdehyde dehydrogenase (NADP+)

O: Succinate-semialdehyde dehydrogenase (NADP+)

P: Succinate-semialdehyde dehydrogenase (NADP+)

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

5

Q: Succinate-semialdehyde dehydrogenase (NADP+)

R: Succinate-semialdehyde dehydrogenase (NADP+)

S: Succinate-semialdehyde dehydrogenase (NADP+)

T: Succinate-semialdehyde dehydrogenase (NADP+)

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

6

U: Succinate-semialdehyde dehydrogenase (NADP+)

V: Succinate-semialdehyde dehydrogenase (NADP+)

W: Succinate-semialdehyde dehydrogenase (NADP+)

X: Succinate-semialdehyde dehydrogenase (NADP+)

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

7

Y: Succinate-semialdehyde dehydrogenase (NADP+)

Z: Succinate-semialdehyde dehydrogenase (NADP+)

1: Succinate-semialdehyde dehydrogenase (NADP+)

2: Succinate-semialdehyde dehydrogenase (NADP+)

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

8

3: Succinate-semialdehyde dehydrogenase (NADP+)

4: Succinate-semialdehyde dehydrogenase (NADP+)

5: Succinate-semialdehyde dehydrogenase (NADP+)

6: Succinate-semialdehyde dehydrogenase (NADP+)

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

Unit cell

Length a, b, c (Å)	185.656, 164.873, 278.901
Angle α, β, γ (deg.)	90.00, 92.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 3 - 484 / Label seq-ID: 3 - 484

#1: Protein	... Succinate-semialdehyde dehydrogenase (NADP+) / Succinate-semialdehyde dehydrogenase (NADP+) Mass: 51284.555 Da / Num. of mol.: 32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gabD, BURPS1710b_2207 / Production host: Escherichia coli (E. coli) References: UniProt: Q3JS51, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1404 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

...
Succinate-semialdehyde dehydrogenase (NADP+) /

Succinate-semialdehyde dehydrogenase (NADP+)

Mass: 51284.555 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gabD, BURPS1710b_2207 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q3JS51, succinate-semialdehyde dehydrogenase [NAD(P)+]

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1404 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.68 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2 mg/mL protein, crystal tracking ID 108914b8, PACT screen B8, 0.1 M MES pH 6.1, 20% PEG 6000, 0.2 M ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
Detector	Date: Apr 3, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03317 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 453409 / % possible obs: 98.6 % / Redundancy: 2.9 % / R_merge(I) obs: 0.104 / Χ²: 1.031 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.692 / Mean I/σ(I) obs: 1.6 / Num. unique all: 44884 / Χ²: 1.046 / % possible all: 98.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3EK1

3ek1

Resolution: 2.7→49.47 Å / Cor.coef. F_o:F_c: 0.932 / Cor.coef. F_o:F_c free: 0.903 / WR_factor R_free: 0.272 / WR_factor R_work: 0.226 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.743 / SU B: 15.61 / SU ML: 0.319 / SU R_free: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.282	22748	5 %	RANDOM
R_work	0.236	-	-	-
obs	0.238	453148	98.29 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 70.39 Å² / B_iso mean: 40.767 Å² / B_iso min: 21.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.36 Å²	0 Å²	-0.55 Å²
2-	-	-0.25 Å²	0 Å²
3-	-	-	-1.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→49.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	56733	0	0	862	57595

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	115694
X-RAY DIFFRACTION	r_angle_refined_deg	1.096	1.959	157464
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.387	5	15392
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.482	23.664	4410
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.802	15	17497
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.75	15	694
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	18066
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	87993
X-RAY DIFFRACTION	r_mcbond_it	0.275	1.5	76384
X-RAY DIFFRACTION	r_mcangle_it	0.535	2	121312
X-RAY DIFFRACTION	r_scbond_it	0.822	3	39310
X-RAY DIFFRACTION	r_scangle_it	1.445	4.5	36152

Refine LS restraints NCS

Ens-ID: 1 / Number: 3444 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	LOOSE POSITIONAL	0.32	5
2	B	LOOSE POSITIONAL	0.27	5
3	C	LOOSE POSITIONAL	0.31	5
4	D	LOOSE POSITIONAL	0.33	5
5	E	LOOSE POSITIONAL	0.31	5
6	F	LOOSE POSITIONAL	0.29	5
7	G	LOOSE POSITIONAL	0.31	5
8	H	LOOSE POSITIONAL	0.35	5
9	I	LOOSE POSITIONAL	0.44	5
10	J	LOOSE POSITIONAL	0.36	5
11	K	LOOSE POSITIONAL	0.32	5
12	L	LOOSE POSITIONAL	0.31	5
13	M	LOOSE POSITIONAL	0.32	5
14	N	LOOSE POSITIONAL	0.33	5
15	O	LOOSE POSITIONAL	0.33	5
16	P	LOOSE POSITIONAL	0.31	5
17	Q	LOOSE POSITIONAL	0.37	5
18	R	LOOSE POSITIONAL	0.35	5
19	S	LOOSE POSITIONAL	0.36	5
20	T	LOOSE POSITIONAL	0.4	5
21	U	LOOSE POSITIONAL	0.48	5
22	V	LOOSE POSITIONAL	0.41	5
23	W	LOOSE POSITIONAL	0.39	5
24	X	LOOSE POSITIONAL	0.5	5
25	Y	LOOSE POSITIONAL	0.49	5
26	Z	LOOSE POSITIONAL	0.55	5
27	1	LOOSE POSITIONAL	0.48	5
28	2	LOOSE POSITIONAL	0.41	5
29	3	LOOSE POSITIONAL	0.36	5
30	4	LOOSE POSITIONAL	0.36	5
31	5	LOOSE POSITIONAL	0.32	5
32	6	LOOSE POSITIONAL	0.35	5
1	A	LOOSE THERMAL	4.71	10
2	B	LOOSE THERMAL	5.88	10
3	C	LOOSE THERMAL	5.76	10
4	D	LOOSE THERMAL	4.21	10
5	E	LOOSE THERMAL	7.77	10
6	F	LOOSE THERMAL	7.74	10
7	G	LOOSE THERMAL	5.57	10
8	H	LOOSE THERMAL	5.13	10
9	I	LOOSE THERMAL	6.37	10
10	J	LOOSE THERMAL	4.46	10
11	K	LOOSE THERMAL	4.99	10
12	L	LOOSE THERMAL	6.17	10
13	M	LOOSE THERMAL	1.84	10
14	N	LOOSE THERMAL	4.02	10
15	O	LOOSE THERMAL	3.86	10
16	P	LOOSE THERMAL	7.49	10
17	Q	LOOSE THERMAL	6.72	10
18	R	LOOSE THERMAL	3.81	10
19	S	LOOSE THERMAL	4.8	10
20	T	LOOSE THERMAL	7.73	10
21	U	LOOSE THERMAL	10.32	10
22	V	LOOSE THERMAL	5.7	10
23	W	LOOSE THERMAL	4.12	10
24	X	LOOSE THERMAL	10.59	10
25	Y	LOOSE THERMAL	4.96	10
26	Z	LOOSE THERMAL	8.97	10
27	1	LOOSE THERMAL	8.17	10
28	2	LOOSE THERMAL	3.66	10
29	3	LOOSE THERMAL	2.67	10
30	4	LOOSE THERMAL	2.69	10
31	5	LOOSE THERMAL	3.25	10
32	6	LOOSE THERMAL	6.01	10

LS refinement shell

Resolution: 2.7→2.767 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.399	1567	-
R_work	0.319	30438	-
all	-	32005	-
obs	-	-	94.15 %

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