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

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Basic information

Entry
Database: PDB / ID: 5wqm
TitleCrystal structure of a carbonyl reductase from Pseudomonas aeruginosa PAO1 (condition I)
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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, S. / Wang, Y. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 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 1.0Jul 4, 2018Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4096
Polymers97,3634
Non-polymers462
Water1,58588
1
A: Probable dehydrogenase
C: Probable dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7274
Polymers48,6812
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-40 kcal/mol
Surface area17550 Å2
MethodPISA
2
B: 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 area2890 Å2
ΔGint-30 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.150, 109.150, 142.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-301-

NA

21C-425-

HOH

31D-312-

HOH

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


Mass: 24340.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 27161 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rpim(I) all: 0.03 / Net I/σ(I): 24.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1291 / Rpim(I) all: 0.299 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXB

3wxb


Resolution: 2.6→43.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 24.383 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.327
RfactorNum. reflection% reflectionSelection details
Rfree0.23304 1981 7.5 %RANDOM
Rwork0.18992 ---
obs0.19317 24428 97.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 53.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 2.6→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6532 0 2 88 6622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0146636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176012
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.6388992
X-RAY DIFFRACTIONr_angle_other_deg0.8241.62314040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70620.87368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8471568
X-RAY DIFFRACTIONr_chiral_restr0.0550.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
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_it1.8952.0263480
X-RAY DIFFRACTIONr_mcbond_other1.8952.0263479
X-RAY DIFFRACTIONr_mcangle_it3.1113.0354336
X-RAY DIFFRACTIONr_mcangle_other3.1113.0354337
X-RAY DIFFRACTIONr_scbond_it2.212.3423156
X-RAY DIFFRACTIONr_scbond_other2.212.3423156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.583.4054656
X-RAY DIFFRACTIONr_long_range_B_refined6.00724.4016994
X-RAY DIFFRACTIONr_long_range_B_other624.386990
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)
11A64720.1
12B64720.1
21A65200.09
22C65200.09
31A65460.09
32D65460.09
41B65060.09
42C65060.09
51B65110.09
52D65110.09
61C65830.09
62D65830.09
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 130 -
Rwork0.263 1595 -
obs--88.28 %
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)
12.92390.5146-0.04134.1159-0.01521.3056-0.0001-0.03570.7366-0.37620.1842-0.6349-0.28360.3897-0.18410.1255-0.09480.17320.2155-0.11570.511533.629-44.686-13.854
23.824-1.41130.74364.9374-1.50861.9464-0.0047-0.87240.78610.39020.3136-0.4708-0.3070.3023-0.30890.0783-0.06570.09160.4206-0.32030.449131.637-43.018-0.046
34.13750.85180.00714.1864-0.27862.09560.1127-0.68530.4990.04170.0067-0.7541-0.23250.3561-0.11940.229-0.07130.10950.2556-0.08060.410111.247-21.405-18.967
45.9675-1.06070.0133.674-1.16422.6441-0.10860.34690.4136-1.14760.073-0.83890.09940.24760.03560.4515-0.09220.24990.13330.04040.322414.391-23.147-32.561
53.59350.7352-1.16524.31080.571.8831-0.16880.118-0.4875-0.30670.08180.30850.3251-0.00950.0870.12630.0140.01360.07250.00660.259215.019-72.236-14.126
64.276-0.9672-1.15972.62320.91683.8092-0.1938-0.5641-0.58220.64960.12670.20520.58470.67820.06710.24570.1180.10590.2780.09930.211818.038-75.56-0.718
73.31011.66890.47933.35121.1511.75210.1674-0.5702-0.10010.1943-0.13530.57720.0403-0.3196-0.03220.24760.02050.01360.18610.14020.3273-16.428-39.734-21.515
85.72810.8016-0.28635.71172.41162.0033-0.00150.07420.0914-0.6484-0.1080.642-0.4729-0.05510.10950.37490.0094-0.08160.06710.07620.2283-18.546-36.303-35.149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION2A195 - 229
3X-RAY DIFFRACTION3B1 - 183
4X-RAY DIFFRACTION4B195 - 229
5X-RAY DIFFRACTION5C1 - 183
6X-RAY DIFFRACTION6C195 - 229
7X-RAY DIFFRACTION7D1 - 183
8X-RAY DIFFRACTION8D195 - 229

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