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- PDB-6c0e: Crystal Structure of Isocitrate Dehydrogenase from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 6c0e
TitleCrystal Structure of Isocitrate Dehydrogenase from Legionella pneumophila with bound NADPH with an alpha-ketoglutarate adduct
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Isocitrate dehydrogenase / 2-oxoglutarate / ketoglutarate / NADPH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EE1 / GLYCINE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Isocitrate Dehydrogenase from Legionella pneumophila with bound NADPH with an ??-ketoglutarate adduct
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: 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

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Assembly

Deposited unit
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2878
Polymers92,2482
Non-polymers2,0406
Water14,808822
1
A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2746
Polymers46,1241
Non-polymers1,1505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0132
Polymers46,1241
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules

A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,57516
Polymers184,4964
Non-polymers4,07912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18300 Å2
ΔGint-107 kcal/mol
Surface area57230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.960, 62.290, 144.820
Angle α, β, γ (deg.)90.000, 98.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-505-

CL

21A-776-

HOH

31A-1002-

HOH

41A-1033-

HOH

51A-1094-

HOH

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Components

#1: Protein Isocitrate dehydrogenase /


Mass: 46123.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icd, lpg0816 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5ZXB6, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-EE1 / (3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid / NADPH with ketoglutarate adduct


Mass: 889.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H34N7O22P3
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: LepnA.00092.a.B1.PW38312 at 23.72 mg/ml, protein was incubated with 3 mM NADP and ??-ketoglutarate, then mixed 1:1 with Morpheus(h1): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M ...Details: LepnA.00092.a.B1.PW38312 at 23.72 mg/ml, protein was incubated with 3 mM NADP and ??-ketoglutarate, then mixed 1:1 with Morpheus(h1): 10% (w/v) PEG-20,000, 20% (v/v) PEG MME 550, 0.1 M MES/imidazole, pH = 6.5, 0.02 M each sodium L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine. Tray: 294280h1. Puck: tcq3-8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→35.959 Å / Num. obs: 88456 / % possible obs: 98.1 % / Redundancy: 4.096 % / Biso Wilson estimate: 20.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Χ2: 1.049 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.1220.452.7164740.8550.51597.3
1.74-1.794.2750.3723.4262760.9040.42497.6
1.79-1.844.2750.2914.5460830.9410.33297.5
1.84-1.94.2480.2345.7160160.9610.26797.7
1.9-1.964.2090.1757.857520.9770.297.8
1.96-2.034.1940.1399.7256270.9850.15997.9
2.03-2.114.1430.1112.2154240.9890.12698.2
2.11-2.194.1030.08814.9652310.9930.10198.3
2.19-2.294.0540.07417.5750190.9940.08598.1
2.29-2.44.0410.06220.3448070.9950.07198.2
2.4-2.534.0050.05422.6146230.9960.06298.7
2.53-2.693.9770.04825.0343500.9970.05698.6
2.69-2.873.9530.04228.5640460.9970.04998.6
2.87-3.13.8720.03631.9638650.9980.04298.6
3.1-3.43.8850.03235.734820.9980.03798.7
3.4-3.83.9220.02938.7531980.9980.03399
3.8-4.394.0190.02541.1728460.9990.02999
4.39-5.384.0670.02242.4824020.9990.02699.3
5.38-7.64.0620.02241.7818890.9990.02699.4
7.6-35.9593.8380.02242.510460.9990.02596.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2947refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PB1

1pb1


Resolution: 1.7→35.959 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 2034 2.3 %
Rwork0.1704 86405 -
obs0.1712 88439 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.45 Å2 / Biso mean: 29.0052 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: final / Resolution: 1.7→35.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6349 0 248 828 7425
Biso mean--25.72 36.06 -
Num. residues----833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73950.30071350.23985675581097
1.7395-1.7830.24091430.22565635577897
1.783-1.83130.27891180.20935734585297
1.8313-1.88510.26231470.20825660580798
1.8851-1.9460.24171270.20525732585998
1.946-2.01550.23861300.19575733586398
2.0155-2.09620.24411350.1865717585298
2.0962-2.19160.20961510.17675740589198
2.1916-2.30710.1941220.1755770589298
2.3071-2.45160.22251230.17385806592999
2.4516-2.64090.20881390.17925757589698
2.6409-2.90650.22491520.17875792594499
2.9065-3.32690.18631300.16575828595899
3.3269-4.19050.17921510.14145847599899
4.1905-35.96730.15691310.14895979611099
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)
11.1501-0.5371-0.21841.92630.19850.7293-0.0661-0.10610.01580.12120.08840.0460.06030.0034-0.02520.09860.0007-0.00650.13290.0080.128522.5111-6.592871.863
21.2113-0.05840.06131.653-0.51890.93230.00930.0010.0346-0.05920.07110.10560.1076-0.0786-0.0850.086-0.0174-0.00360.10210.01050.090119.9004-10.780555.2175
31.63680.91130.04212.7506-0.54781.0507-0.12170.20920.4112-0.08840.18650.3788-0.2591-0.0129-0.08930.2001-0.02260.00320.17730.05140.229318.558511.554948.404
41.5912-1.209-0.62931.74320.44291.34640.04190.1799-0.0246-0.18870.02740.13080.1707-0.2052-0.04570.1937-0.0708-0.03850.20020.0340.17168.909-13.565442.1531
53.2569-1.01810.59941.6440.06150.5923-0.01420.26290.1537-0.11810.00170.2157-0.1212-0.1237-0.00850.2291-0.0039-0.00850.22350.07150.20436.37984.951542.8882
61.2271-0.07320.06111.20990.15390.8447-0.0040.04820.2118-0.0650.0745-0.0548-0.09270.0242-0.06070.1004-0.00830.01420.09450.01090.169126.27367.421460.7698
78.0489-0.5051-3.33880.8571-0.08312.4570.14730.6929-0.3171-0.33940.02030.092-0.2345-0.1095-0.16880.66460.0421-0.0240.4378-0.03240.281916.7917-6.44212.2525
80.9018-0.05060.68590.9160.2491.73310.09990.23910.0117-0.3639-0.10240.13880.0382-0.1098-0.00150.44640.04170.02570.32490.01370.253616.7184-1.611416.5248
90.9710.2213-0.46560.6965-0.12951.38520.01050.1364-0.0841-0.1584-0.0145-0.040.19920.01820.0090.26510.0107-0.00650.16790.01010.124926.9284-14.125635.5808
101.1528-0.30090.62771.1972-0.17851.09470.05190.16560.157-0.3624-0.06120.1162-0.2044-0.02680.00820.44250.02320.03130.31720.0120.248520.97917.46120.7844
112.02371.9832.01572.01312.06342.119-0.77338.1384-0.5553-1.66640.2437-2.47591.9521.37140.52540.437-0.0423-0.01950.55610.01280.49765.5964-8.637667.8461
122.82212.00031.87142.13511.9462.40080.5145-0.02976.70481.55221.425610.5576-4.6874-1.2967-1.94520.74380.0294-0.04980.67390.05570.831917.411920.6158.6108
134.01480.8646-3.66712.55910.59994.1632-0.4506-5.8072-0.21296.73651.66320.7254-5.7638-2.2134-1.20360.86590.16590.20340.9069-0.00380.9584.1650.97976.8776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 106 )A4 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 137 )A107 - 137
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 160 )A138 - 160
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 259 )A161 - 259
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 323 )A260 - 323
6X-RAY DIFFRACTION6chain 'A' and (resid 324 through 422 )A324 - 422
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 41 )B5 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 160 )B42 - 160
9X-RAY DIFFRACTION9chain 'B' and (resid 161 through 297 )B161 - 297
10X-RAY DIFFRACTION10chain 'B' and (resid 298 through 422 )B298 - 422
11X-RAY DIFFRACTION11chain 'A' and (resid 502 through 502 )A502
12X-RAY DIFFRACTION12chain 'A' and (resid 503 through 503 )A503
13X-RAY DIFFRACTION13chain 'A' and (resid 504 through 504 )A504

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