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- PDB-7rbx: Crystal structure of isocitrate lyase and phosphorylmutase:isocit... -

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Basic information

Entry
Database: PDB / ID: 7rbx
TitleCrystal structure of isocitrate lyase and phosphorylmutase:isocitrate lyase from Brucella melitensis biovar Abortus 2308 bound to itaconic acid
ComponentsIsocitrase
KeywordsLYASE/LYASE INHIBITOR / structural genomics / NIAID / brucellosis / Brucellaceae / covalent inhibitor / ITN / substrate analog / ICL / glyoxylate cycle / isocitrate / succinate / TCA cycle bypass / Seattle Structural Genomics Center for Infectious Disease / SSGCID / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
2-methylidenebutanedioic acid / Isocitrate lyase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos Pathog. / Year: 2021
Title: Aconitate decarboxylase 1 participates in the control of pulmonary Brucella infection in mice.
Authors: Demars, A. / Vitali, A. / Comein, A. / Carlier, E. / Azouz, A. / Goriely, S. / Smout, J. / Flamand, V. / Van Gysel, M. / Wouters, J. / Abendroth, J. / Edwards, T.E. / Machelart, A. / ...Authors: Demars, A. / Vitali, A. / Comein, A. / Carlier, E. / Azouz, A. / Goriely, S. / Smout, J. / Flamand, V. / Van Gysel, M. / Wouters, J. / Abendroth, J. / Edwards, T.E. / Machelart, A. / Hoffmann, E. / Brodin, P. / De Bolle, X. / Muraille, E.
History
DepositionJul 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Isocitrase
B: Isocitrase
C: Isocitrase
D: Isocitrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,73920
Polymers196,5574
Non-polymers1,18216
Water28,6441590
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33640 Å2
ΔGint-209 kcal/mol
Surface area47320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.750, 136.270, 181.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrase / Isocitratase / Isocitrate lyase


Mass: 49139.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB1_1631 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YQA0, isocitrate lyase

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Non-polymers , 5 types, 1606 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1590 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BrabA.00014.a.A1.PW38950 at 25.5 mg/mL with 2.5 mM itaconic acid and 2.5 mM MgCl2 against MCSG1 screen condition G8: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with ...Details: BrabA.00014.a.A1.PW38950 at 25.5 mg/mL with 2.5 mM itaconic acid and 2.5 mM MgCl2 against MCSG1 screen condition G8: 0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant; crystal tracking ID 321126g8, unique puck ID qrt6-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→47.59 Å / Num. obs: 175674 / % possible obs: 99.4 % / Redundancy: 6.833 % / Biso Wilson estimate: 25.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Χ2: 0.937 / Net I/σ(I): 14.83 / Num. measured all: 1200309
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
1.8-1.857.050.5393.369093412950128990.9230.58199.6
1.85-1.97.0240.4264.28831012607125730.9510.4699.7
1.9-1.956.9760.3525.028574712315122920.9670.38199.8
1.95-2.016.9270.286.168258311946119220.9750.30399.8
2.01-2.086.8420.2157.827895511562115390.9850.23299.8
2.08-2.156.7560.1739.327525911179111400.9890.18799.7
2.15-2.236.4290.14610.666880110845107020.990.15998.7
2.23-2.326.2430.12312.246371810440102060.9920.13497.8
2.32-2.437.2170.11114.787217310028100000.9940.1299.7
2.43-2.557.1760.116.568191953995020.9950.10899.6
2.55-2.687.1210.08519.0864612912490740.9950.09299.5
2.68-2.857.0410.07821.0161021870286670.9960.08599.6
2.85-3.046.9160.06923.5955850810380750.9960.07599.7
3.04-3.296.7980.06225.5851530759175800.9970.06799.9
3.29-3.66.5110.05627.7845706703370200.9970.06199.8
3.6-4.026.0820.05328.8338502638863300.9970.05799.1
4.02-4.656.1170.04930.1432916562453810.9980.05395.7
4.65-5.697.1320.04633.0434441483448290.9980.0599.9
5.69-8.057.1070.0443326807377737720.9980.04899.9
8.05-47.596.5650.0433.2414253220421710.9980.04398.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev-4274refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eol
Resolution: 1.8→47.59 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1663 1913 1.09 %
Rwork0.1427 173702 -
obs0.143 175615 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.8 Å2 / Biso mean: 31.1116 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 1.8→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12970 0 74 1592 14636
Biso mean--37.12 38.1 -
Num. residues----1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613513
X-RAY DIFFRACTIONf_angle_d0.78118328
X-RAY DIFFRACTIONf_dihedral_angle_d13.3944932
X-RAY DIFFRACTIONf_chiral_restr0.051967
X-RAY DIFFRACTIONf_plane_restr0.0082436
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 (%)
1.8-1.850.21561310.19821228512416100
1.85-1.890.22431430.18191233912482100
1.89-1.950.2021300.17651234512475100
1.95-2.010.19961260.16811236712493100
2.01-2.090.21921380.15881237312511100
2.09-2.170.21491340.15311232812462100
2.17-2.270.16891470.1479121171226498
2.27-2.390.1731200.1436123571247799
2.39-2.540.14961290.14181240612535100
2.54-2.730.15811430.14261244112584100
2.73-3.010.1641340.14521244612580100
3.01-3.440.15731780.14321250612684100
3.44-4.340.1461260.1248123721249898
4.34-47.590.15271340.13141302013154100
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)
10.9587-0.41820.34541.5071-0.04751.23070.00770.04850.14550.013-0.0275-0.2808-0.20730.24590.03420.1999-0.05620.020.22520.00650.22-4.876529.8006-30.717
20.98090.4177-0.77721.5965-0.96992.6748-0.0212-0.00990.01940.0091-0.05770.033-0.0822-0.1040.0770.15620.0027-0.01830.1586-0.01320.1804-21.595723.4927-35.111
30.5083-0.1463-0.15060.96130.13852.8384-0.025-0.07530.04250.12290.03840.0404-0.0446-0.0965-0.0150.2001-0.0286-0.00970.174-0.00070.211-14.68126.9671-21.1674
41.54210.3655-0.58572.8676-0.93962.15040.0476-0.28440.04370.54710.06020.1314-0.3888-0.0796-0.13020.39980.0286-0.00370.2704-0.03470.2264-18.466333.779-3.1846
52.19370.09460.90472.06130.59842.50370.0028-0.12570.27470.1036-0.07110.1331-0.4684-0.23670.07750.31390.02330.01450.1582-0.02380.2112-21.468644.3396-22.28
60.50270.08450.74541.0050.19142.84970.02140.00440.0552-0.2299-0.11320.2752-0.3621-0.51780.08110.27280.1226-0.05190.2916-0.03490.3039-40.372731.4015-45.519
74.1518-2.2748-1.3234.14261.60941.70560.18740.5427-0.2368-0.6383-0.32360.4214-0.1846-0.38840.1120.39520.0225-0.03680.29640.02870.1927-23.068121.7442-60.7956
81.1676-0.50770.30571.1450.04110.91770.1201-0.0062-0.27330.1434-0.16530.48090.3394-0.50680.03830.3692-0.18130.03010.4374-0.08780.4062-45.904-9.8603-42.2896
90.91890.16980.65332.20080.10140.71630.03680.0410.00340.0383-0.16280.57880.0588-0.55530.10660.1702-0.0099-0.00450.4088-0.08320.3125-47.11113.9432-40.7299
101.5914-0.5242-0.64661.35290.28221.86750.04630.1631-0.022-0.078-0.09540.0911-0.0616-0.1920.05130.1845-0.0023-0.03140.2078-0.01250.1858-29.882415.2145-46.0578
110.1318-0.2283-0.15941.521.10592.2123-0.0290.0244-0.04830.0308-0.09840.25540.097-0.35840.12610.1385-0.0412-0.00360.2828-0.02770.247-38.52479.8086-36.5065
120.3806-0.3547-0.46380.52320.04332.00960.0450.08370.0045-0.1441-0.08560.15850.0819-0.33030.04770.2183-0.0269-0.05080.2921-0.0550.2571-35.3393.0236-56.6848
133.1427-0.4323-1.28750.87630.42511.3960.18160.3167-0.0176-0.3555-0.15490.1828-0.0166-0.3426-0.01370.37770.03-0.11710.3872-0.05420.2411-35.20032.2436-70.477
140.6961-0.21180.22361.08190.59341.37090.00510.1753-0.0087-0.3607-0.11950.3175-0.2127-0.4240.13120.29840.0635-0.1310.504-0.05510.3721-47.623417.0329-59.2191
151.09260.1470.5121.21240.93441.5863-0.03710.03440.2726-0.1568-0.08990.2037-0.4032-0.31150.12850.26520.0994-0.03290.2480.00740.2772-33.42937.7446-38.6045
161.1708-0.04870.04355.0119-3.67674.4697-0.0145-0.27550.18470.7734-0.09580.0329-0.7328-0.17310.06970.33520.02590.05790.3921-0.06860.2982-38.14426.3473-16.7648
172.0156-0.80971.1342.3246-0.16632.58980.03330.2720.2674-0.5203-0.0609-0.5514-0.22910.52520.00910.2614-0.03180.11510.32250.020.33624.086313.0768-57.2512
180.8208-0.5120.02572.4023-0.49531.67860.0410.03320.0855-0.0423-0.0079-0.3364-0.0050.319-0.00960.1684-0.00890.00920.2256-0.02810.21890.88656.3957-43.3872
192.957-0.69760.43021.10810.14851.29370.06330.0683-0.10820.0389-0.02920.0970.2794-0.0628-0.03550.266-0.00370.00520.1662-0.00060.174-14.5979-4.0914-40.2176
206.86834.68165.34823.45823.79224.2492-0.1072-0.20370.13150.1264-0.0079-0.0256-0.0701-0.02080.11050.16580.03420.01180.1999-0.00970.1865-3.80316.4249-29.7654
210.50430.27430.36840.82720.69671.61980.0280.0666-0.036-0.1320.0133-0.04050.15130.0244-0.04660.24020.02030.02520.20810.00640.1875-10.348-2.3798-56.5402
221.3922-0.3366-0.50292.1458-0.01832.4776-0.03720.038-0.15950.02340.0629-0.19760.37980.1767-0.00390.25920.07420.00570.2062-0.03250.22691.3351-14.7438-51.475
230.7018-0.47180.29480.9939-0.53413.0819-0.0828-0.1267-0.15910.34210.1013-0.040.67270.1763-0.00980.51940.0946-0.00140.20220.01230.2286-8.9488-16.8595-20.6845
240.6103-0.3467-0.49325.90151.12652.089-0.1092-0.0566-0.04260.42550.1984-0.17220.28430.291-0.09090.25970.0419-0.05850.28490.00450.2144-1.55065.1717-16.3787
252.15650.0663-0.29476.2545-0.21612.1366-0.0736-0.4085-0.06841.16430.278-0.54170.16420.6097-0.20210.52320.0303-0.10340.4693-0.01450.3163-1.72935.5712-6.6375
260.6905-0.3296-0.06981.1243-0.14930.98780.0097-0.14-0.08190.2871-0.02960.45890.1829-0.58650.05910.3334-0.13090.11910.4752-0.04020.3433-44.7013.371-13.0251
270.9453-0.3345-0.07040.75550.27321.1612-0.0038-0.0668-0.17470.2274-0.06610.07020.3716-0.1260.07030.3347-0.04320.03020.18620.00920.1663-22.2288-6.2119-19.684
281.8391.59392.12335.15255.67286.3985-0.03520.0095-0.1037-0.1061-0.14830.18660.3061-0.29740.17690.2966-0.07280.03890.20310.01610.1947-27.399-8.3661-31.8061
290.34990.19380.2240.75470.56351.3716-0.0346-0.0702-0.02240.20280.00320.03910.1987-0.06340.040.3041-0.03370.04630.2340.01270.1762-23.77445.2796-6.9468
300.25610.2433-0.17051.1002-0.19041.2859-0.0432-0.2967-0.11120.4523-0.0147-0.06790.60260.10910.06010.66280.00090.02530.31160.06060.23-18.2163-11.2022-2.6646
310.5313-0.0136-0.60631.87280.76732.6651-0.0635-0.1033-0.16730.14610.0759-0.1340.6180.2621-0.00540.4090.1061-0.03330.21210.02680.2181-3.5198-16.7077-30.8981
323.3004-1.30710.84621.6606-1.28631.6130.14480.4519-0.2763-0.2325-0.18660.0640.67680.0589-0.01620.5106-0.06960.01990.2562-0.05390.2941-22.6626-18.3114-46.2074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 75 )A3 - 75
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 131 )A76 - 131
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 236 )A132 - 236
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 274 )A237 - 274
5X-RAY DIFFRACTION5chain 'A' and (resid 275 through 344 )A275 - 344
6X-RAY DIFFRACTION6chain 'A' and (resid 345 through 382 )A345 - 382
7X-RAY DIFFRACTION7chain 'A' and (resid 383 through 426 )A383 - 426
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 39 )B2 - 39
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 75 )B40 - 75
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 108 )B76 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 168 )B109 - 168
12X-RAY DIFFRACTION12chain 'B' and (resid 169 through 236 )B169 - 236
13X-RAY DIFFRACTION13chain 'B' and (resid 237 through 274 )B237 - 274
14X-RAY DIFFRACTION14chain 'B' and (resid 275 through 344 )B275 - 344
15X-RAY DIFFRACTION15chain 'B' and (resid 345 through 382 )B345 - 382
16X-RAY DIFFRACTION16chain 'B' and (resid 383 through 425 )B383 - 425
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 24 )C2 - 24
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 75 )C25 - 75
19X-RAY DIFFRACTION19chain 'C' and (resid 76 through 108 )C76 - 108
20X-RAY DIFFRACTION20chain 'C' and (resid 109 through 131 )C109 - 131
21X-RAY DIFFRACTION21chain 'C' and (resid 132 through 274 )C132 - 274
22X-RAY DIFFRACTION22chain 'C' and (resid 275 through 344 )C275 - 344
23X-RAY DIFFRACTION23chain 'C' and (resid 345 through 382 )C345 - 382
24X-RAY DIFFRACTION24chain 'C' and (resid 383 through 405 )C383 - 405
25X-RAY DIFFRACTION25chain 'C' and (resid 406 through 426 )C406 - 426
26X-RAY DIFFRACTION26chain 'D' and (resid 2 through 39 )D2 - 39
27X-RAY DIFFRACTION27chain 'D' and (resid 40 through 108 )D40 - 108
28X-RAY DIFFRACTION28chain 'D' and (resid 109 through 131 )D109 - 131
29X-RAY DIFFRACTION29chain 'D' and (resid 132 through 274 )D132 - 274
30X-RAY DIFFRACTION30chain 'D' and (resid 275 through 344 )D275 - 344
31X-RAY DIFFRACTION31chain 'D' and (resid 345 through 382 )D345 - 382
32X-RAY DIFFRACTION32chain 'D' and (resid 383 through 426 )D383 - 426

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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