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- PDB-8bcj: Crystal structure of short-chain dehydrogenase PA3128 from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 8bcj
TitleCrystal structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1 in complex with NADP+
ComponentsProbable short-chain dehydrogenase
KeywordsUNKNOWN FUNCTION / PA3128 / P. aeruginosa / NADP+ / SDR
Function / homologyShort-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L(+)-TARTARIC ACID / Probable short-chain dehydrogenase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsPopp, M.A. / Vit, A. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)BL587/5-1 Germany
CitationJournal: To Be Published
Title: The structure of short-chain dehydrogenase PA3128 from Pseudomonas aeruginosa PAO1
Authors: Popp, M.A. / Vit, A. / Blankenfeldt, W.
History
DepositionOct 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable short-chain dehydrogenase
B: Probable short-chain dehydrogenase
C: Probable short-chain dehydrogenase
D: Probable short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,57315
Polymers105,7914
Non-polymers3,78111
Water23,3291295
1
A: Probable short-chain dehydrogenase
B: Probable short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8218
Polymers52,8962
Non-polymers1,9256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-20 kcal/mol
Surface area17990 Å2
MethodPISA
2
C: Probable short-chain dehydrogenase
D: Probable short-chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7527
Polymers52,8962
Non-polymers1,8565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-19 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.689, 143.000, 72.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-647-

HOH

21D-703-

HOH

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Components

#1: Protein
Probable short-chain dehydrogenase


Mass: 26447.836 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: PA3128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HZ96
#2: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1 M imidazol, pH 8.2, 1.1 M K/Na tartrate, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.15→44.62 Å / Num. obs: 337928 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 9.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.038 / Rrim(I) all: 0.082 / Net I/σ(I): 10.3 / Num. measured all: 1486813
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.15-1.170.6271596166090.7350.3350.7072.299.9
6.3-44.620.033987422850.9980.0180.03833.999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.1.29data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BCI
Resolution: 1.15→34.12 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1491 17043 5.05 %
Rwork0.1351 320767 -
obs0.1358 337810 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.27 Å2 / Biso mean: 14.1588 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: final / Resolution: 1.15→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7311 0 580 1305 9196
Biso mean--10.41 25.77 -
Num. residues----995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.160.215460.21831062711173100
1.16-1.180.21675660.21111059811164100
1.18-1.190.20935580.20521057211130100
1.19-1.210.19625770.19881063311210100
1.21-1.220.20446370.19091054011177100
1.22-1.240.19265710.19061054811119100
1.24-1.260.21065490.18881066611215100
1.26-1.280.19555860.18331058511171100
1.28-1.30.18565490.17791060511154100
1.3-1.320.18515630.17011062911192100
1.32-1.340.19225700.16981060511175100
1.34-1.360.17535160.16241065711173100
1.36-1.390.17765550.15741071211267100
1.39-1.420.16765490.14961064011189100
1.42-1.450.1625460.14581067711223100
1.45-1.480.15966330.13731060411237100
1.48-1.520.13645540.12631067611230100
1.52-1.560.14175620.12231065311215100
1.56-1.610.13145460.12191071411260100
1.61-1.660.13555870.12051067011257100
1.66-1.720.13275570.1181069111248100
1.72-1.790.14385640.12171071411278100
1.79-1.870.14075680.12241077711345100
1.87-1.970.13535590.12011069711256100
1.97-2.090.13465670.11961075211319100
2.09-2.250.1295960.1151070411300100
2.25-2.480.12985690.1151079711366100
2.48-2.840.13315730.12411086611439100
2.84-3.570.14295980.12541090811506100
3.57-34.120.14035720.1289112501182299
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.03730.0188-0.0310.02550.01560.0398-0.0158-0.09140.0360.09490.02560.03250.02430.02370.00190.10150.0218-0.00480.1095-0.01050.0739-164.654174.6114238.271
20.0760.0311-0.01230.02150.02090.0366-0.0345-0.12640.02670.07950.08110.0183-0.027-0.05530.00210.12510.0377-0.00310.1378-0.00840.0801-169.1112181.0473242.2032
30.05630.0072-0.01480.01530.01440.016-0.0171-0.10440.06490.0230.0435-0.0624-0.02760.0743-00.15680.0221-0.00170.1249-0.02310.092-164.1635183.9223238.8604
40.0722-0.04820.02910.0323-0.01260.0178-0.0039-0.07220.23930.15530.0313-0.1094-0.06050.1947-0.00030.1677-0.007-0.02080.1386-0.0410.1397-157.2754189.5919236.0195
50.099-0.022-0.13520.07550.03150.1388-0.015-0.01760.02610.02610.05030.0087-0.0739-0.03610.01630.07330.0132-0.00060.08410.00070.0789-169.5986181.2457221.6208
60.0112-0.0182-0.04090.17870.00030.0986-0.0038-0.01420.09450.02910.0182-0.0662-0.07460.01250.00690.08190.0028-0.00270.0812-0.01180.1016-156.8651184.3735224.9617
70.0507-0.0044-0.08950.1228-0.02770.1824-0.01010.00880.01090.01180.01650.0123-0.0125-0.0040.0090.05660.0075-0.00040.0723-0.00240.0718-165.3834174.084220.4595
80.0273-0.0144-0.02380.0160.00440.00850.0405-0.0075-0.1061-0.0257-0.03040.08890.0047-0.0594-0.00010.08450.0141-0.00350.0998-0.01940.1261-181.3013163.7691222.4779
90.04580.0191-0.00540.0966-0.00480.0477-0.0047-0.0165-0.00250.01650.02230.01170.00980.00340.00380.07130.01040.00040.0802-0.00610.0904-161.5506164.6298227.7976
100.0493-0.0348-0.04150.03820.01180.02370.00790.0998-0.0135-0.09670.0011-0.0496-0.094-0.0435-00.10940.0027-0.00860.11780.00660.0768-167.5765186.516186.399
110.1435-0.015-0.09180.05-0.05580.08460.01270.0420.0334-0.07940.004-0.0173-0.08450.0260.00190.1138-0.0028-0.01050.09250.00450.0802-160.9695187.3942188.3742
120.06130.00420.04340.01930.02320.0728-0.16970.02120.0051-0.12620.0716-0.0879-0.07530.0015-0.00380.205-0.05130.03810.16280.02450.1373-157.769195.2098184.2747
130.08110.0680.00150.0430.00380.0053-0.06770.02010.0513-0.04330.0757-0.0175-0.0271-0.0384-00.1458-0.00910.00040.09010.0090.0831-164.8771193.5578191.2507
140.05290.00470.04690.01520.01250.04510.0521-0.03960.1318-0.1371-0.03330.1022-0.0796-0.1412-0.00180.15160.0194-0.02470.1180.01460.1102-173.0828195.3144195.3782
150.1004-0.1123-0.120.26520.03240.1374-0.01980.01360.0292-0.00980.01750.0114-0.0715-0.01530.01360.06810.0054-0.00810.07270.00240.0708-166.0252186.3889205.0364
160.0433-0.03510.01630.0527-0.00410.2447-0.0035-0.008-0.0116-0.0020.0136-0.0012-0.00590.00330.01060.0578-0.0019-0.00460.0735-0.00090.0782-160.0244178.18204.1158
170.02260.0136-0.02380.00760.00120.0150.00530.0042-0.05020.00310.0075-0.09260.02060.0036-00.0756-0.0036-0.01010.1002-0.00430.1204-142.611174.2963199.3853
180.0478-0.0461-0.00640.0443-0.00960.01780.01020.0028-0.0105-0.01960.01730.02110.02770.01830.00250.0725-0.0045-0.00560.0847-0.00090.0882-161.2625172.2169192.9801
190.06990.0580.03770.0694-0.05610.1018-0.0254-0.0576-0.02830.09270.0212-0.02760.02650.01370.00120.11710.02640.01490.09070.0080.0733-155.7226143.2798231.9469
200.0179-0.01630.00080.00720.00330.0099-0.0688-0.0926-0.01330.1576-0.0601-0.02480.190.083900.1820.0344-0.0150.13190.00570.1164-148.5597137.605237.0877
210.09310.0508-0.00670.028-0.00560.0066-0.0569-0.03570.01090.05440.0239-0.00560.09660.054800.15530.02250.00640.0853-0.00190.083-155.6084136.1076228.5375
220.1118-0.1059-0.00710.2906-0.04970.1801-0.0197-0.0083-0.01840.03450.02480.02660.05140.00680.02640.07690.00760.01150.06160.00160.0691-157.7395143.1947215.8503
230.0394-0.0778-0.01110.22290.0130.0722-0.0092-0.00410.0190.01820.02310.00390.01690.00370.01290.06520.00830.00560.0753-0.00230.0757-157.2349151.3256216.4401
240.048-0.1184-0.00340.29590.0191-0.024-0.0119-0.01260.01010.02640.0286-0.0333-0.00580.00950.01260.07860.01170.00160.0844-0.00520.0957-153.2898158.8275224.4802
250.0335-0.02880.00750.02320.00720.02010.04880.1288-0.0049-0.1873-0.02120.03680.1085-0.02570.0010.15780.0006-0.00440.11570.00250.0763-162.0919154.5929181.1722
260.030.01640.00550.0270.01860.00340.04910.1383-0.0057-0.4096-0.02430.01540.2142-0.019-0.02660.2946-0.0015-0.03870.1327-0.0050.0719-163.9279148.2683176.9042
270.22390.00420.06180.0599-0.11830.2663-0.0060.0998-0.0852-0.22240.00340.00530.04360.0194-0.0010.28080.0188-0.02050.1267-0.01610.06-159.539146.5045179.851
280.18110.099-0.0440.1113-0.06380.06040.06840.0357-0.1439-0.2292-0.0691-0.06020.04590.12530.00550.22950.04370.02980.1525-0.02120.0905-150.1339142.535182.8879
290.054-0.09070.00660.23160.10070.0812-0.03250.0342-0.0318-0.08350.04320.0420.1298-0.02860.00170.0998-0.0107-0.00280.0771-0.00180.0833-164.4565144.0067200.5903
300.0672-0.03620.00340.0561-0.03190.03510.11770.0082-0.0568-0.167-0.0793-0.09210.11290.06280.01070.11870.02790.0510.1029-0.00140.0964-145.3519151.0348190.5693
310.0348-0.05070.07440.2962-0.11610.16940.00450.0015-0.0017-0.04030.01750.03660.0414-0.00810.01470.0657-0.0055-0.00250.0687-0.00030.0721-162.6423154.3901199.329
320.01280.00130.01080.01520.00480.0020.01140.0105-0.00680.0152-0.02050.22950.0697-0.055700.1019-0.01660.00390.11020.00650.1865-180.9625159.2526197.6267
330.0534-0.03750.02880.0804-0.06530.04750.00880.0112-0.0163-0.0330.02470.01410.01180.002800.0788-0.0014-0.00270.0822-0.00070.0894-162.2659164.4539191.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 49 )A25 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 63 )A50 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 78 )A64 - 78
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 101 )A79 - 101
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 135 )A102 - 135
7X-RAY DIFFRACTION7chain 'A' and (resid 136 through 202 )A136 - 202
8X-RAY DIFFRACTION8chain 'A' and (resid 203 through 218 )A203 - 218
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 248 )A219 - 248
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 12 )B-1 - 12
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 36 )B13 - 36
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 49 )B37 - 49
13X-RAY DIFFRACTION13chain 'B' and (resid 50 through 63 )B50 - 63
14X-RAY DIFFRACTION14chain 'B' and (resid 64 through 78 )B64 - 78
15X-RAY DIFFRACTION15chain 'B' and (resid 79 through 135 )B79 - 135
16X-RAY DIFFRACTION16chain 'B' and (resid 136 through 202 )B136 - 202
17X-RAY DIFFRACTION17chain 'B' and (resid 203 through 218 )B203 - 218
18X-RAY DIFFRACTION18chain 'B' and (resid 219 through 248 )B219 - 248
19X-RAY DIFFRACTION19chain 'C' and (resid 0 through 36 )C0 - 36
20X-RAY DIFFRACTION20chain 'C' and (resid 37 through 49 )C37 - 49
21X-RAY DIFFRACTION21chain 'C' and (resid 50 through 63 )C50 - 63
22X-RAY DIFFRACTION22chain 'C' and (resid 64 through 154 )C64 - 154
23X-RAY DIFFRACTION23chain 'C' and (resid 155 through 202 )C155 - 202
24X-RAY DIFFRACTION24chain 'C' and (resid 203 through 248 )C203 - 248
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 24 )D1 - 24
26X-RAY DIFFRACTION26chain 'D' and (resid 25 through 49 )D25 - 49
27X-RAY DIFFRACTION27chain 'D' and (resid 50 through 63 )D50 - 63
28X-RAY DIFFRACTION28chain 'D' and (resid 64 through 78 )D64 - 78
29X-RAY DIFFRACTION29chain 'D' and (resid 79 through 113 )D79 - 113
30X-RAY DIFFRACTION30chain 'D' and (resid 114 through 135 )D114 - 135
31X-RAY DIFFRACTION31chain 'D' and (resid 136 through 202 )D136 - 202
32X-RAY DIFFRACTION32chain 'D' and (resid 203 through 218 )D203 - 218
33X-RAY DIFFRACTION33chain 'D' and (resid 219 through 248 )D219 - 248

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