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- PDB-5wqn: Crystal structure of a carbonyl reductase from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 5wqn
TitleCrystal structure of a carbonyl reductase from Pseudomonas aeruginosa PAO1 (condition II)
ComponentsProbable dehydrogenase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase
Function / homology
Function and homology information


carbonyl reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, S. / Wang, Y. / Bartlam, M.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
National Key Basic Research Development Program2014CB560709 China
Tianjin Municipal Science and Technology Commission13JCYBJC20800 China
CitationJournal: FEBS Lett. / Year: 2017
Title: Structure and characterization of a NAD(P)H-dependent carbonyl reductase from Pseudomonas aeruginosa PAO1.
Authors: Li, S. / Teng, X. / Su, L. / Mao, G. / Xu, Y. / Li, T. / Liu, R. / Zhang, Q. / Wang, Y. / Bartlam, M.
History
DepositionNov 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable dehydrogenase
B: Probable dehydrogenase
C: Probable dehydrogenase
D: Probable dehydrogenase


Theoretical massNumber of molelcules
Total (without water)97,3634
Polymers97,3634
Non-polymers00
Water7,242402
1
A: Probable dehydrogenase
D: Probable dehydrogenase


Theoretical massNumber of molelcules
Total (without water)48,6812
Polymers48,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-28 kcal/mol
Surface area17950 Å2
MethodPISA
2
B: Probable dehydrogenase
C: Probable dehydrogenase


Theoretical massNumber of molelcules
Total (without water)48,6812
Polymers48,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-28 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.191, 131.180, 143.552
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 1 - 229 / Label seq-ID: 1 - 229

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Probable dehydrogenase / Carbonyl reductase


Mass: 24340.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4079 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HWU9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.9 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51221 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 18.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQM

5wqm


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.616 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24153 2000 3.9 %RANDOM
Rwork0.1913 ---
obs0.19325 49111 99.68 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 0 402 6985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196685
X-RAY DIFFRACTIONr_bond_other_d0.0020.026528
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.979058
X-RAY DIFFRACTIONr_angle_other_deg1.01314878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9155873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59323.333300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.279151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5471569
X-RAY DIFFRACTIONr_chiral_restr0.1020.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021567
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_it3.5411.4873516
X-RAY DIFFRACTIONr_mcbond_other3.5411.4873515
X-RAY DIFFRACTIONr_mcangle_it4.7532.2024381
X-RAY DIFFRACTIONr_mcangle_other4.7532.2024382
X-RAY DIFFRACTIONr_scbond_it5.7852.1273169
X-RAY DIFFRACTIONr_scbond_other5.7852.1273169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8712.9594677
X-RAY DIFFRACTIONr_long_range_B_refined9.47719.6877350
X-RAY DIFFRACTIONr_long_range_B_other9.4819.2377262
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129160.08
12B129160.08
21A127320.09
22C127320.09
31A127840.08
32D127840.08
41B128320.09
42C128320.09
51B127740.09
52D127740.09
61C130020.09
62D130020.09
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 144 -
Rwork0.227 3525 -
obs--97.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.26250.39880.24132.56610.28940.52230.0096-0.0181-0.16270.0381-0.02790.07790.1417-0.05850.01830.1391-0.0228-0.00850.00730.00060.05729.27-22.061-30.049
21.0258-0.36860.1053.2011-0.76511.5632-0.0168-0.0425-0.0601-0.0147-0.0007-0.1310.16950.0190.01750.1409-0.02570.01490.00940.00350.0599-5.505-18.176-61.364
31.0612-0.1339-0.23053.2425-0.32171.4585-0.03780.09410.1683-0.1291-0.0322-0.2157-0.28520.05960.06990.2167-0.01810.00080.0290.02020.1127-6.68614.434-70.278
41.14210.67470.0622.93250.31511.10020.0002-0.0970.19610.14210.0170.0261-0.1413-0.0272-0.01720.11010.0076-0.00830.0114-0.02120.079418.50710.227-24.763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 229
2X-RAY DIFFRACTION2B1 - 229
3X-RAY DIFFRACTION3C1 - 229
4X-RAY DIFFRACTION4D1 - 229

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