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- PDB-5u9p: Crystal structure of a gluconate 5-dehydrogenase from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 5u9p
TitleCrystal structure of a gluconate 5-dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP and tartrate
ComponentsGluconate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / structural genomics / Burkholderia cenocepacia / gluconate 5-dehydrogenase / dehydrogenase / NAD / tartrate / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


gluconate 5-dehydrogenase / gluconate 5-dehydrogenase activity / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L(+)-TARTARIC ACID / Gluconate 5-dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a gluconate 5-dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP and tartrate
Authors: Abendroth, J. / Edwards, T.E. / Lorimer, D.D.
History
DepositionDec 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gluconate 5-dehydrogenase
B: Gluconate 5-dehydrogenase
C: Gluconate 5-dehydrogenase
D: Gluconate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,53326
Polymers114,7384
Non-polymers4,79522
Water20,4831137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24650 Å2
ΔGint-90 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.380, 91.680, 121.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Gluconate 5-dehydrogenase /


Mass: 28684.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: idnO, BCAL3386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EEX4, gluconate 5-dehydrogenase
#2: 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
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1137 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, E10: 20% (w/V) PEG 3350, 200mM Ammonium tartrate: BuceA.00010.x.B1.PW37241 at 20.44mg/ml + 4mM NADP: cryo: 20% EG + 10mM NADP in 2 steps: tray 285582 e10, puck bdg3-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 29, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 116982 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.14 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.65-1.693.680.582.140.713192.4
1.69-1.744.330.4862.960.829199.4
1.74-1.794.80.423.690.882199.9
1.79-1.845.380.3265.210.941100
1.84-1.915.40.2536.680.9621100
1.91-1.975.390.2068.180.972199.9
1.97-2.055.390.15810.580.986199.9
2.05-2.135.410.13212.70.9891100
2.13-2.225.410.10415.70.9931100
2.22-2.335.130.09117.630.9941100
2.33-2.465.390.07919.890.9951100
2.46-2.615.420.06523.510.9971100
2.61-2.795.410.05726.490.998199.9
2.79-3.015.410.04631.990.9981100
3.01-3.35.380.03737.810.999199.9
3.3-3.695.360.0345.20.999199.9
3.69-4.265.340.02749.380.999199.9
2.46-5.225.280.02353.990.999199.9
5.22-7.385.160.02648.110.999199.9
7.38-504.670.02253.730.999196.5

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
XDSdata reduction
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ibo
Resolution: 1.65→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.83
RfactorNum. reflection% reflection
Rfree0.1639 1965 1.68 %
Rwork0.1355 --
obs0.136 116823 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.25 Å2 / Biso mean: 14.9941 Å2 / Biso min: 4.72 Å2
Refinement stepCycle: final / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7763 0 312 1160 9235
Biso mean--15.2 27.75 -
Num. residues----1031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098355
X-RAY DIFFRACTIONf_angle_d0.97111372
X-RAY DIFFRACTIONf_chiral_restr0.0651262
X-RAY DIFFRACTIONf_plane_restr0.0061588
X-RAY DIFFRACTIONf_dihedral_angle_d13.055001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69130.23451220.23287562768492
1.6913-1.7370.23171590.19448083824299
1.737-1.78810.23181620.176481558317100
1.7881-1.84580.18181500.152781508300100
1.8458-1.91180.18751590.144381748333100
1.9118-1.98830.19241140.152682138327100
1.9883-2.07880.16251190.130782328351100
2.0788-2.18840.1611510.124882128363100
2.1884-2.32550.13981310.123482168347100
2.3255-2.50510.16441430.127182688411100
2.5051-2.75710.14281570.127282718428100
2.7571-3.15590.15281200.126683128432100
3.1559-3.97560.14141550.119983828537100
3.9756-41.12320.15681230.12898628875199
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)
12.12131.8771-0.19913.3154-1.03040.7877-0.34340.1380.7787-0.3162-0.05750.0292-0.56910.19480.14050.204-0.0187-0.0570.14690.03290.2705-40.500615.95689.9179
21.62830.14160.58683.7958-0.66182.2156-0.0016-0.22810.07050.13590.00150.1486-0.0366-0.05340.06060.0418-0.00140.01330.0888-0.01220.0964-46.12490.587719.0807
32.4736-0.8128-0.4661.6564-0.12410.98210.0149-0.17-0.09990.0741-0.01180.285-0.0125-0.10520.00190.0668-0.0031-0.00590.1133-0.00160.0978-53.8828-2.503618.043
40.9353-0.40860.48990.9627-0.54071.12090.043-0.0571-0.1263-0.07410.03140.22950.0848-0.1278-0.07560.0626-0.0179-0.01060.0824-0.00040.1081-44.1724-11.729913.7446
51.4589-1.19811.50461.86-1.69072.90540.08970.0052-0.1612-0.1044-0.01130.19780.16450.0119-0.10290.0713-0.0039-0.00240.0667-0.01090.1047-40.2648-14.379810.8625
60.6513-0.18530.28470.7467-0.08450.4291-0.0238-0.10760.00440.06990.01220.0214-0.016-0.01720.01180.0579-0.00520.00540.0734-0.00410.0543-31.0676-3.395420.4472
72.06230.27231.25770.38670.64941.45380.1072-0.1036-0.30920.0883-0.2354-0.8205-0.05960.64150.06340.19780.0139-0.05070.30230.06290.37726.392-29.208220.6105
82.9572-0.60791.07721.2522-0.42292.08670.11350.1703-0.1368-0.1847-0.0692-0.04140.16170.097-0.03880.10440.016-0.00110.0537-0.00760.1034-12.7493-34.10338.7272
94.7986-1.54380.5330.8482-0.04681.1260.0080.2222-0.286-0.1337-0.08380.28540.1698-0.00730.04980.1378-0.0029-0.01150.0530.00730.1257-15.6381-42.81537.8513
105.2531-2.3006-0.4491.43410.18580.7769-0.1011-0.0539-0.2828-0.01660.0470.18490.0950.00170.0690.111-0.0093-0.00490.07640.00910.1269-18.9737-40.140611.8536
111.2061-0.59460.5961.443-0.49031.15590.0268-0.0432-0.1718-0.0675-0.00880.07890.1346-0.0292-0.06050.0841-0.00800.0528-0.01270.0904-25.6205-31.192612.5899
120.9018-0.51820.48411.0986-0.55531.3509-0.0049-0.0454-0.0508-0.00160.00550.03530.0309-0.0046-0.0010.0587-0.00010.01140.0474-0.0060.0645-23.9505-22.58515.8751
131.3308-0.04410.37071.0473-0.02461.53710.17850.3251-0.1455-0.32460.03150.11940.38240.1148-0.14360.16880.0224-0.03910.1102-0.03310.1183-16.3845-22.00442.5718
143.93490.88271.40722.70511.74072.4441-0.15920.4380.1115-0.54720.02240.1717-0.13890.14750.12230.17640.0059-0.00360.1577-0.01260.0887-12.55-13.1965-6.2625
150.4048-0.18670.10560.4611-0.6041.2177-0.00930.0199-0.0351-0.0047-0.0117-0.05120.05120.02250.01620.0815-0.0014-0.00620.0934-0.0140.1056-9.0844-18.813212.3943
162.0281.1570.28152.9530.7361.3735-0.0690.1409-0.3523-0.14070.0806-0.12530.16120.07010.01960.0760.02560.01470.0937-0.01510.13288.6517-18.960813.2462
171.96961.13510.15563.0210.72021.16390.0103-0.1178-0.12560.0825-0.0266-0.11590.07020.03270.01310.04880.0072-0.00010.08480.00750.077312.0006-12.045920.9205
181.4218-1.14790.54064.6792-1.23720.93240.0139-0.0559-0.0016-0.0351-0.0669-0.10420.05330.08410.06080.0609-0.00570.01350.10790.01820.077219.6606-9.042121.3651
191.6222-0.5768-0.62090.86360.47661.13470.0052-0.02320.0741-0.00690.0088-0.0948-0.04910.1239-0.03180.0548-0.0094-0.01260.07410.0030.06188.55040.761617.1585
201.6832-0.9797-1.351.54891.31822.46660.05350.00530.1544-0.0188-0.0203-0.098-0.110.0355-0.11990.062-0.0034-0.00910.07110.0130.07765.32183.530113.6135
211.0333-0.5377-0.75810.86830.64741.5277-0.01780.0544-0.0106-0.005-0.02420.01070.0124-0.08020.09140.0536-0.0111-0.00470.064-0.0090.0684-4.1414-2.74714.5229
221.48830.1796-0.51711.39660.25792.77840.0327-0.2720.01060.24550.0079-0.08450.06140.114-0.03580.07030.0128-0.01620.09220.00280.0875-0.6428-7.589927.9623
231.62610.0580.23121.34450.4011.53920.0105-0.42620.05080.2188-0.01790.03280.07760.0140.02320.1272-0.00990.00510.15320.00030.0776-9.5022-11.926935.9196
241.293-0.0845-0.46880.5910.17071.3847-0.01610.0282-0.1046-0.0247-0.0064-0.01350.01890.01260.01550.0562-0.0092-0.00610.0439-0.00780.067-4.9584-14.857817.1893
253.32281.85891.06782.05790.85762.1759-0.0717-0.4210.38310.1913-0.34820.92680.1013-0.62810.28260.17640.00750.04080.2035-0.0730.2503-36.890918.593521.2442
263.62120.2803-1.34832.09020.56832.7471-00.15770.1525-0.2120.02460.0488-0.1193-0.0687-0.0160.09830.0058-0.01540.04020.00830.0766-22.252223.380211.363
271.7434-0.2847-0.81531.6806-0.32230.87670.01290.09290.3651-0.12320.0426-0.0527-0.1935-0.0728-0.05320.13840.0086-0.00710.0727-0.01030.1431-18.180431.142912.8179
286.8901-4.0454-2.47424.11412.93052.17190.0257-0.06160.3205-0.02350.0326-0.1907-0.15680.0369-0.06080.1369-0.0238-0.0070.0691-0.00980.126-11.15228.512625.4713
291.3203-1.2099-1.17431.94311.23181.76920.0490.00660.057-0.1206-0.0452-0.0836-0.08010.0276-0.02170.0709-0.01540.00020.0719-00.0693-9.119314.966110.4382
304.2123-2.512-4.55851.6213.02626.00940.0012-0.16930.1336-0.02630.0974-0.1169-0.04190.1954-0.13130.0814-0.0047-0.01090.0542-0.0020.0945-7.656416.500219.7451
311.048-0.4389-0.56770.60510.29510.7287-0.0392-0.00790.01130.0141-0.01050.02560.0322-0.02350.05510.0811-0.0081-0.00310.0621-0.01330.0756-14.23317.589517.1582
321.1354-0.1387-0.55661.09060.46121.94150.02840.19240.13-0.248-0.0317-0.0399-0.2279-0.0501-0.02070.1150.0029-0.00270.07640.01520.0931-17.591812.26184.4956
331.83970.0126-0.61021.14490.06981.80690.05460.1576-0.0007-0.2544-0.0764-0.0424-0.094-0.00570.06120.15890.0086-0.00030.1285-0.00340.0699-21.05114.4623-5.5121
340.6386-0.2038-0.17030.50460.27151.1042-0.0028-0.01080.03770.0058-0.04380.033-0.0315-0.00150.0490.0836-0.0121-0.00120.0846-0.00450.0853-26.00517.899113.2174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 13 )A0 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 34 )A14 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 72 )A35 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 109 )A73 - 109
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 138 )A110 - 138
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 257 )A139 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid -3 through 13 )B-3 - 13
8X-RAY DIFFRACTION8chain 'B' and (resid 14 through 34 )B14 - 34
9X-RAY DIFFRACTION9chain 'B' and (resid 35 through 58 )B35 - 58
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 72 )B59 - 72
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 109 )B73 - 109
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 182 )B110 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 205 )B183 - 205
14X-RAY DIFFRACTION14chain 'B' and (resid 206 through 223 )B206 - 223
15X-RAY DIFFRACTION15chain 'B' and (resid 224 through 257 )B224 - 257
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 22 )C3 - 22
17X-RAY DIFFRACTION17chain 'C' and (resid 23 through 45 )C23 - 45
18X-RAY DIFFRACTION18chain 'C' and (resid 46 through 72 )C46 - 72
19X-RAY DIFFRACTION19chain 'C' and (resid 73 through 109 )C73 - 109
20X-RAY DIFFRACTION20chain 'C' and (resid 110 through 138 )C110 - 138
21X-RAY DIFFRACTION21chain 'C' and (resid 139 through 182 )C139 - 182
22X-RAY DIFFRACTION22chain 'C' and (resid 183 through 205 )C183 - 205
23X-RAY DIFFRACTION23chain 'C' and (resid 206 through 223 )C206 - 223
24X-RAY DIFFRACTION24chain 'C' and (resid 224 through 257 )C224 - 257
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 13 )D1 - 13
26X-RAY DIFFRACTION26chain 'D' and (resid 14 through 34 )D14 - 34
27X-RAY DIFFRACTION27chain 'D' and (resid 35 through 72 )D35 - 72
28X-RAY DIFFRACTION28chain 'D' and (resid 73 through 86 )D73 - 86
29X-RAY DIFFRACTION29chain 'D' and (resid 87 through 109 )D87 - 109
30X-RAY DIFFRACTION30chain 'D' and (resid 110 through 138 )D110 - 138
31X-RAY DIFFRACTION31chain 'D' and (resid 139 through 182 )D139 - 182
32X-RAY DIFFRACTION32chain 'D' and (resid 183 through 205 )D183 - 205
33X-RAY DIFFRACTION33chain 'D' and (resid 206 through 223 )D206 - 223
34X-RAY DIFFRACTION34chain 'D' and (resid 224 through 257 )D224 - 257

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