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- PDB-4exa: Crystal structure of the PA4992, the putative aldo-keto reductase... -

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Basic information

Entry
Database: PDB / ID: 4exa
TitleCrystal structure of the PA4992, the putative aldo-keto reductase from Pseudomona aeruginosa
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / 8(a/b) barrel / aldo-keto reductase / NADP-binding
Function / homology
Function and homology information


nucleotide binding / cytosol
Similarity search - Function
NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent oxidoreductase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSandalova, T. / Schnell, R. / Schneider, G.
CitationJournal: 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. / ...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. / Naismith, J.H. / Schneider, G.
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Mar 20, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_measured_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,71014
Polymers189,7736
Non-polymers4,9378
Water2,090116
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9835
Polymers63,2582
Non-polymers1,7253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-8 kcal/mol
Surface area21680 Å2
MethodPISA
2
C: Putative uncharacterized protein
F: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9835
Polymers63,2582
Non-polymers1,7253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-11 kcal/mol
Surface area22110 Å2
MethodPISA
3
D: Putative uncharacterized protein
E: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7444
Polymers63,2582
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-12 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.170, 120.277, 151.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A4 - 30
2111B4 - 30
3111C4 - 30
4111D4 - 30
5111E4 - 30
6111F4 - 30
1121A43 - 219
2121B43 - 219
3121C43 - 219
4121D43 - 219
5121E43 - 219
6121F43 - 219
1131A227 - 268
2131B227 - 268
3131C227 - 268
4131D227 - 268
5131E227 - 268
6131F227 - 268

NCS ensembles :
ID
1
2
3

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Components

#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 PAO1 (bacteria) / Strain: PAO1 / Gene: PA4992 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HUH3
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10mM NADP+ 25.5% of polyacrylic acid 0.1M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2009
RadiationMonochromator: Silicon 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.8→94.11 Å / Num. obs: 41558 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 24625 / % possible all: 98.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YNP

1ynp


Resolution: 2.8→94.11 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.859 / SU B: 15.498 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27237 2102 5.1 %RANDOM
Rwork0.22723 ---
obs0.22949 39433 96.63 %-
all-39433 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.901 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→94.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11626 0 216 116 11958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02112023
X-RAY DIFFRACTIONr_bond_other_d0.0020.028127
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.99916305
X-RAY DIFFRACTIONr_angle_other_deg0.942319735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5451505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37323.165534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.773151997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.89815120
X-RAY DIFFRACTIONr_chiral_restr0.0680.21866
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022373
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.57525
X-RAY DIFFRACTIONr_mcbond_other0.0891.53121
X-RAY DIFFRACTIONr_mcangle_it1.107211980
X-RAY DIFFRACTIONr_scbond_it1.42834498
X-RAY DIFFRACTIONr_scangle_it2.6374.54325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A332TIGHT POSITIONAL0.030.05
12B332TIGHT POSITIONAL0.030.05
13C332TIGHT POSITIONAL0.030.05
14D332TIGHT POSITIONAL0.030.05
15E332TIGHT POSITIONAL0.040.05
16F332TIGHT POSITIONAL0.030.05
11A332TIGHT THERMAL0.080.5
12B332TIGHT THERMAL0.060.5
13C332TIGHT THERMAL0.070.5
14D332TIGHT THERMAL0.070.5
15E332TIGHT THERMAL0.090.5
16F332TIGHT THERMAL0.080.5
21A2233TIGHT POSITIONAL0.030.05
22B2233TIGHT POSITIONAL0.040.05
23C2233TIGHT POSITIONAL0.040.05
24D2233TIGHT POSITIONAL0.040.05
25E2233TIGHT POSITIONAL0.040.05
26F2233TIGHT POSITIONAL0.040.05
21A2233TIGHT THERMAL0.070.5
22B2233TIGHT THERMAL0.070.5
23C2233TIGHT THERMAL0.070.5
24D2233TIGHT THERMAL0.070.5
25E2233TIGHT THERMAL0.070.5
26F2233TIGHT THERMAL0.080.5
31A504TIGHT POSITIONAL0.030.05
32B504TIGHT POSITIONAL0.030.05
33C504TIGHT POSITIONAL0.030.05
34D504TIGHT POSITIONAL0.030.05
35E504TIGHT POSITIONAL0.030.05
36F504TIGHT POSITIONAL0.030.05
31A504TIGHT THERMAL0.070.5
32B504TIGHT THERMAL0.060.5
33C504TIGHT THERMAL0.060.5
34D504TIGHT THERMAL0.060.5
35E504TIGHT THERMAL0.060.5
36F504TIGHT THERMAL0.060.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 146 -
Rwork0.335 2945 -
obs--98.03 %

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