PDB-4exb: Putative aldo-keto reductase from Pseudomona aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 4exb

Title

Putative aldo-keto reductase from Pseudomona aeruginosa

Components

Putative uncharacterized protein

Keywords

OXIDOREDUCTASE / Pseudomona / aldo-keto reductase / NADP+ binding

Function / homology

Function and homology information

nucleotide binding / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Schnell, R. / Schneider, G. / Sandalova, T.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.
Authors: Moynie, L. / Schnell, R. / McMahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...

History

Deposition	Apr 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Sep 13, 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_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4exb.cif.gz	289.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4exb.ent.gz	234.6 KB	Display	PDB format
PDBx/mmJSON format	4exb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4exb_validation.pdf.gz	480.6 KB	Display	wwPDB validaton report
Full document	4exb_full_validation.pdf.gz	493.8 KB	Display
Data in XML	4exb_validation.xml.gz	50.8 KB	Display
Data in CIF	4exb_validation.cif.gz	69.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/4exb ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exb	HTTPS FTP

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Related structure data

Related structure data	2xu8C 4avfC 4avrC 4avyC 4b79C 4b7cC 4b7xC 4b9aC 4b9eC 4es6C 4etrC 4exaC 1ynpS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xu1-d 4nu0-d 3l2z-d 4exa-1 4exa-2 4xtw-d 7d6m-d 3rux-d 1t8n-d 4h18-6 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#92 - Aug 2007 Anabolic Steroids similarity (3)

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

D: Putative uncharacterized protein

E: Putative uncharacterized protein

F: Putative uncharacterized protein

190 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

B: Putative uncharacterized protein

defined by author&software
63.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative uncharacterized protein

F: Putative uncharacterized protein

defined by author&software
63.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Putative uncharacterized protein

E: Putative uncharacterized protein

defined by author&software
63.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.331, 119.036, 150.854
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	4 - 30
2	1	1	2	B	4 - 30
3	1	1	2	C	4 - 30
4	1	1	2	D	4 - 30
5	1	1	2	E	4 - 30
6	1	1	2	F	4 - 30
1	1	2	2	A	43 - 219
2	1	2	2	B	43 - 219
3	1	2	2	C	43 - 219
4	1	2	2	D	43 - 219
5	1	2	2	E	43 - 219
6	1	2	2	F	43 - 219
1	1	3	2	A	227 - 268
2	1	3	2	B	227 - 268
3	1	3	2	C	227 - 268
4	1	3	2	D	227 - 268
5	1	3	2	E	227 - 268
6	1	3	2	F	227 - 268

NCS ensembles :

ID
1
2
3

#1: Protein	Putative uncharacterized protein Mass: 31628.807 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4992 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HUH3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative uncharacterized protein

Mass: 31628.807 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4992 / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HUH3

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.23 Å³/Da / Density % sol: 44.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: 0.1M of bis-Tris-methane pH 6.35, 0.1 M sodium malonate and 16 % (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.999 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2009
Radiation	Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2.75→42.1 Å / Num. all: 44634 / Num. obs: 44634 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / R_merge(I) obs: 0.103 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.75→2.9 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / Num. unique all: 6293 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YNP

1ynp

Resolution: 2.75→41.87 Å / Cor.coef. F_o:F_c: 0.905 / Cor.coef. F_o:F_c free: 0.879 / SU B: 16.428 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27396	2250	5 %	RANDOM
R_work	0.24263	-	-	-
all	0.24421	42346	-	-
obs	0.24421	42346	99.45 %	-

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 mean: 34.037 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.35 Å²	0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→41.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11574	0	0	107	11681

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	11741
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	8011
X-RAY DIFFRACTION	r_angle_refined_deg	1.261	1.977	15877
X-RAY DIFFRACTION	r_angle_other_deg	0.935	3	19436
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.438	5	1498
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.892	23.139	532
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.492	15	1988
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.024	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	1833
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	13169
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2365
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	0.577	1.5	7490
X-RAY DIFFRACTION	r_mcbond_other	0.069	1.5	3111
X-RAY DIFFRACTION	r_mcangle_it	1.126	2	11920
X-RAY DIFFRACTION	r_scbond_it	1.423	3	4251
X-RAY DIFFRACTION	r_scangle_it	2.627	4.5	3957
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	156	TIGHT POSITIONAL	0.03	0.05
1	2	B	156	TIGHT POSITIONAL	0.03	0.05
1	3	C	156	TIGHT POSITIONAL	0.03	0.05
1	4	D	156	TIGHT POSITIONAL	0.03	0.05
1	5	E	156	TIGHT POSITIONAL	0.03	0.05
1	6	F	156	TIGHT POSITIONAL	0.03	0.05
1	1	A	176	MEDIUM POSITIONAL	0.03	0.5
1	2	B	176	MEDIUM POSITIONAL	0.03	0.5
1	3	C	176	MEDIUM POSITIONAL	0.02	0.5
1	4	D	176	MEDIUM POSITIONAL	0.03	0.5
1	5	E	176	MEDIUM POSITIONAL	0.03	0.5
1	6	F	176	MEDIUM POSITIONAL	0.02	0.5
1	1	A	156	TIGHT THERMAL	0.05	0.5
1	2	B	156	TIGHT THERMAL	0.06	0.5
1	3	C	156	TIGHT THERMAL	0.06	0.5
1	4	D	156	TIGHT THERMAL	0.06	0.5
1	5	E	156	TIGHT THERMAL	0.06	0.5
1	6	F	156	TIGHT THERMAL	0.06	0.5
1	1	A	176	MEDIUM THERMAL	0.05	2
1	2	B	176	MEDIUM THERMAL	0.05	2
1	3	C	176	MEDIUM THERMAL	0.06	2
1	4	D	176	MEDIUM THERMAL	0.06	2
1	5	E	176	MEDIUM THERMAL	0.05	2
1	6	F	176	MEDIUM THERMAL	0.06	2
2	1	A	1004	TIGHT POSITIONAL	0.03	0.05
2	2	B	1004	TIGHT POSITIONAL	0.03	0.05
2	3	C	1004	TIGHT POSITIONAL	0.03	0.05
2	4	D	1004	TIGHT POSITIONAL	0.03	0.05
2	5	E	1004	TIGHT POSITIONAL	0.03	0.05
2	6	F	1004	TIGHT POSITIONAL	0.03	0.05
2	1	A	1242	MEDIUM POSITIONAL	0.03	0.5
2	2	B	1242	MEDIUM POSITIONAL	0.03	0.5
2	3	C	1242	MEDIUM POSITIONAL	0.03	0.5
2	4	D	1242	MEDIUM POSITIONAL	0.03	0.5
2	5	E	1242	MEDIUM POSITIONAL	0.03	0.5
2	6	F	1242	MEDIUM POSITIONAL	0.03	0.5
2	1	A	1004	TIGHT THERMAL	0.05	0.5
2	2	B	1004	TIGHT THERMAL	0.06	0.5
2	3	C	1004	TIGHT THERMAL	0.05	0.5
2	4	D	1004	TIGHT THERMAL	0.05	0.5
2	5	E	1004	TIGHT THERMAL	0.05	0.5
2	6	F	1004	TIGHT THERMAL	0.06	0.5
2	1	A	1242	MEDIUM THERMAL	0.05	2
2	2	B	1242	MEDIUM THERMAL	0.05	2
2	3	C	1242	MEDIUM THERMAL	0.05	2
2	4	D	1242	MEDIUM THERMAL	0.05	2
2	5	E	1242	MEDIUM THERMAL	0.06	2
2	6	F	1242	MEDIUM THERMAL	0.05	2
3	1	A	241	TIGHT POSITIONAL	0.02	0.05
3	2	B	241	TIGHT POSITIONAL	0.02	0.05
3	3	C	241	TIGHT POSITIONAL	0.03	0.05
3	4	D	241	TIGHT POSITIONAL	0.02	0.05
3	5	E	241	TIGHT POSITIONAL	0.02	0.05
3	6	F	241	TIGHT POSITIONAL	0.02	0.05
3	1	A	248	MEDIUM POSITIONAL	0.02	0.5
3	2	B	248	MEDIUM POSITIONAL	0.02	0.5
3	3	C	248	MEDIUM POSITIONAL	0.03	0.5
3	4	D	248	MEDIUM POSITIONAL	0.03	0.5
3	5	E	248	MEDIUM POSITIONAL	0.03	0.5
3	6	F	248	MEDIUM POSITIONAL	0.02	0.5
3	1	A	241	TIGHT THERMAL	0.04	0.5
3	2	B	241	TIGHT THERMAL	0.05	0.5
3	3	C	241	TIGHT THERMAL	0.04	0.5
3	4	D	241	TIGHT THERMAL	0.05	0.5
3	5	E	241	TIGHT THERMAL	0.05	0.5
3	6	F	241	TIGHT THERMAL	0.04	0.5
3	1	A	248	MEDIUM THERMAL	0.05	2
3	2	B	248	MEDIUM THERMAL	0.04	2
3	3	C	248	MEDIUM THERMAL	0.04	2
3	4	D	248	MEDIUM THERMAL	0.05	2
3	5	E	248	MEDIUM THERMAL	0.04	2
3	6	F	248	MEDIUM THERMAL	0.04	2

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	157	-
R_work	0.366	2941	-
obs	-	-	95.35 %

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