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- PDB-6y4d: Crystal structure of a short-chain dehydrogenase/reductase (SDR) ... -

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Basic information

Entry
Database: PDB / ID: 6y4d
TitleCrystal structure of a short-chain dehydrogenase/reductase (SDR) from Zephyranthes treatiae in complex with NADP+
Componentsshort-chain dehydrogenase/reductase (SDR)
KeywordsOXIDOREDUCTASE / asymmetric reduction / biocatalysis / imine reduction / mutagenesis / rational design / short-chain dehydrogenase/reductase / Zephyranthes treatiae / complex
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesZephyranthes treatiae (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSautner, V. / Steimle, S. / Roth, S. / Mueller, M. / Tittmann, K.
CitationJournal: Chembiochem / Year: 2020
Title: Crossing the Border: From Keto- to Imine Reduction in Short-Chain Dehydrogenases/Reductases.
Authors: Roth, S. / Stockinger, P. / Steff, J. / Steimle, S. / Sautner, V. / Tittmann, K. / Pleiss, J. / Muller, M.
History
DepositionFeb 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: short-chain dehydrogenase/reductase (SDR)
B: short-chain dehydrogenase/reductase (SDR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9327
Polymers62,1682
Non-polymers1,7635
Water2,342130
1
A: short-chain dehydrogenase/reductase (SDR)
B: short-chain dehydrogenase/reductase (SDR)
hetero molecules

A: short-chain dehydrogenase/reductase (SDR)
B: short-chain dehydrogenase/reductase (SDR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,86314
Polymers124,3374
Non-polymers3,52610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area20620 Å2
ΔGint-129 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.900, 95.900, 136.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein short-chain dehydrogenase/reductase (SDR)


Mass: 31084.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zephyranthes treatiae (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: pentaerythritol propoxylate, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→60.715 Å / Num. obs: 37479 / % possible obs: 99.1 % / Redundancy: 6.745 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.141 / Χ2: 1.01 / Net I/σ(I): 10.75 / Num. measured all: 252798 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.26.8592.5621.1532581482347500.5842.7798.5
2.2-2.36.8021.8191.5927140403439900.6981.96898.9
2.3-2.56.861.1492.342510628461970.8641.24398.6
2.5-36.8180.4335.1563465937693080.9730.46999.3
3-3.56.6580.13512.4831751480547690.9960.14799.3
3.5-46.6690.06622.9818233274127340.9990.07299.7
4-4.56.7380.04331.7611091165016460.9990.04799.8
4.5-56.6060.04133.867115108010770.9990.04599.7
5-66.410.04530.757929123912370.9990.04999.8
6-106.3870.02941.0886481370135410.03198.8
10-205.7590.0258.08207936536110.02298.9
20-504.6480.01656.4251625410.01887.1
50-60.7152.50.05230.845520.06440

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEU

5feu


Resolution: 2.1→60.715 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.52
RfactorNum. reflection% reflection
Rfree0.247 1859 4.98 %
Rwork0.2072 --
obs0.2092 37328 98.67 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 110 Å2 / Biso mean: 50.0881 Å2 / Biso min: 25.34 Å2
Refinement stepCycle: final / Resolution: 2.1→60.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 138 132 4120
Biso mean--46 50.52 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15680.45651390.3723265298
2.1568-2.22030.38081410.3436266398
2.2203-2.2920.37851400.3139268899
2.292-2.37390.35071390.3026266998
2.3739-2.46890.33211390.2812267498
2.4689-2.58130.33431370.2712267798
2.5813-2.71740.30941420.2575270399
2.7174-2.88760.26041440.2334271999
2.8876-3.11060.26861430.2198272399
3.1106-3.42360.23251450.2078276199
3.4236-3.91890.20921460.1723275699
3.9189-4.93710.17621470.15542818100
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)
12.45250.1935-0.24153.4248-0.3373.5305-0.01810.18940.4752-0.15890.08670.1144-0.7929-0.3447-0.06040.5061-0.04070.01740.36180.06330.3488-45.682827.7202-1.3753
25.03576.43442.63428.34113.67192.4745-0.33970.7255-0.1562-0.25890.505-0.1692-0.04160.1941-0.15030.5953-0.0966-0.00390.74470.04230.3718-38.45618.8609-13.5577
30.79120.45310.43461.05880.52281.48860.0137-0.0339-0.04060.04710.02610.0171-0.0821-0.1072-0.04220.4231-0.02930.00320.48140.01290.3195-46.58428.8222-1.3106
41.70370.1871-0.97921.6833-0.47563.73490.00060.19270.2013-0.02720.18630.2383-0.2266-0.4838-0.1810.4128-0.0141-0.03210.34720.01940.3009-53.214.99319.5851
50.66460.73880.22091.9141-0.28524.82910.02930.06370.2550.19720.11080.1529-0.98490.2137-0.08470.6172-0.03860.050.3838-0.01850.3884-43.913727.154225.7174
64.37481.0075-0.41183.0002-0.78433.99770.1369-0.45920.54980.0773-0.1105-0.2283-0.92240.7199-0.08810.7319-0.0762-0.0090.4768-0.10720.3993-38.348426.920639.4518
71.2404-2.52580.6788.3608-3.90073.1838-0.0744-0.5130.11750.86420.22230.1524-0.5890.0421-0.10770.88480.12770.02960.6797-0.03850.3863-50.511920.644945.3886
80.9323-0.66260.47341.357-0.56351.818-0.057-0.0498-0.01680.09350.13590.0528-0.184-0.0453-0.0750.43390.00210.01920.4298-0.00280.3053-47.41999.708832.1235
96.8347-1.85581.41126.6152-0.28877.52790.33280.0661-0.19970.8940.3975-1.14810.77031.8758-0.46880.62120.0104-0.14860.8078-0.0910.5442-26.121510.760729.6386
103.68-1.8069-1.32934.3021.14183.25870.0383-0.13780.07770.07430.1852-0.4957-0.09620.5898-0.22140.4078-0.1138-0.03260.5266-0.06890.3623-31.54112.306720.542
112.2277-0.5643-0.35071.64730.3942.1343-0.0570.0602-0.16950.14110.12810.00150.08820.1045-0.14510.4855-0.0115-0.04910.47610.00110.3716-44.672511.671117.3083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 105 )A35 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 119 )A106 - 119
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 212 )A120 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 291 )A213 - 291
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 68 )B35 - 68
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 105 )B69 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 119 )B106 - 119
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 225 )B120 - 225
9X-RAY DIFFRACTION9chain 'B' and (resid 226 through 239 )B226 - 239
10X-RAY DIFFRACTION10chain 'B' and (resid 240 through 269 )B240 - 269
11X-RAY DIFFRACTION11chain 'B' and (resid 270 through 291 )B270 - 291

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