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- PDB-4ia5: Hydratase from Lactobacillus acidophilus - SeMet derivative (apo LAH) -

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Basic information

Entry
Database: PDB / ID: 4ia5
TitleHydratase from Lactobacillus acidophilus - SeMet derivative (apo LAH)
ComponentsMyosin-crossreactive antigen
KeywordsIMMUNE SYSTEM / conjugated linoleic acid / CLA / MCRA / Rossmann fold / FAD binding / hydratase / Fatty acid
Function / homology
Function and homology information


oleate hydratase activity / FAD binding / fatty acid metabolic process
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #80 / Oleate hydratase / MCRA family / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Myosin-crossreactive antigen
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsKhoshnevis, S. / Neumann, P. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Crystal structure analysis of a fatty acid double-bond hydratase from Lactobacillus acidophilus
Authors: Volkov, A. / Khoshnevis, S. / Neumann, P. / Herrfurth, C. / Wohlwend, D. / Ficner, R. / Feussner, I.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-crossreactive antigen
B: Myosin-crossreactive antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,53516
Polymers137,0812
Non-polymers1,45414
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-99 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.750, 78.970, 108.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myosin-crossreactive antigen / Hydratase


Mass: 68540.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: LBA0649 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5FL96

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Non-polymers , 7 types, 487 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 37% MPD, 0.1M Hepes/KOH, 10mM Phenol, 3.6mM linoleic acid, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionNumber: 374947 / Rmerge(I) obs: 0.051 / D res high: 2.22 Å / Num. obs: 122719 / % possible obs: 88.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.5944.79507995.510.037
4.696.59920797.210.039
3.834.691196397.910.039
3.323.831416698.110.046
2.973.321610298.210.064
2.722.971780398.610.096
2.512.721844093.710.119
2.352.511699880.510.152
2.222.351296157.810.193
ReflectionResolution: 2.22→50 Å / Num. obs: 122663 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 3.05 % / Biso Wilson estimate: 39.164 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.22-2.320.940.1873.9151591715695360.25255.6
2.32-2.420.9540.1564.951874414455105870.20673.2
2.42-2.620.9780.1187.434415022687199410.14987.9
2.62-3.40.9960.06916.4716112745803448900.0898
3.4-3.790.9970.03928.083872910776105590.04698
3.79-4.180.9980.03531.5825376711369650.04197.9
4.18-4.570.9980.03333.7317160486047630.03998
4.57-140.9980.03333.895264715373148950.03996.9
14-170.9980.02937.48442592480.03495.8
17-500.9980.02936.719382982790.03493.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.22→44.791 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7713 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 29.48 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 6159 5.02 %RANDOM
Rwork0.2138 ---
obs0.2161 122595 88.38 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.92 Å2 / Biso mean: 64.7363 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: LAST / Resolution: 2.22→44.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 0 90 473 9930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079692
X-RAY DIFFRACTIONf_angle_d1.19413130
X-RAY DIFFRACTIONf_chiral_restr0.081389
X-RAY DIFFRACTIONf_plane_restr0.0061684
X-RAY DIFFRACTIONf_dihedral_angle_d16.1853603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.24530.36561140.31782089220348
2.2453-2.27170.40891300.3212411254155
2.2717-2.29940.42541420.30472547268959
2.2994-2.32850.33061510.30232858300965
2.3285-2.35910.3031560.30333059321570
2.3591-2.39140.34011710.30023238340974
2.3914-2.42560.36011830.30333492367580
2.4256-2.46180.34291900.29223587377781
2.4618-2.50030.33581980.27933720391886
2.5003-2.54130.3352130.28143984419789
2.5413-2.58510.33252100.27323987419791
2.5851-2.63210.31542130.26734188440194
2.6321-2.68270.35372200.26424149436996
2.6827-2.73740.28632340.27224320455498
2.7374-2.7970.25192270.2544315454299
2.797-2.8620.32092260.25494357458399
2.862-2.93360.32392260.25154319454599
2.9336-3.01290.33262330.24674328456199
3.0129-3.10150.30132290.24224270449998
3.1015-3.20160.26982280.22574325455398
3.2016-3.3160.29272340.21734309454398
3.316-3.44870.23292290.21224360458998
3.4487-3.60560.2352300.19014282451298
3.6056-3.79560.23782270.1874274450198
3.7956-4.03330.19192260.17164314454098
4.0333-4.34440.19812270.15924320454798
4.3444-4.78120.21662280.15634280450898
4.7812-5.4720.21262200.16724273449397
5.472-6.89010.20122290.18694250447997
6.8901-44.79990.20662150.17924231444696
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)
12.5147-0.7601-0.24252.1163-0.17551.2999-0.12040.8854-0.5033-0.06770.0040.49610.2109-0.38980.10020.3746-0.12610.03290.5785-0.14180.3333-53.53755.8017-31.0062
20.2947-0.0427-0.04751.11910.21510.97210.080.349-0.3256-0.32140.0981-0.0470.3242-0.1305-0.09020.7508-0.38310.17180.7992-0.85881.7361-60.1296-16.4395-34.5728
31.72750.0012-0.04230.6516-0.15011.0157-0.3308-1.40310.10440.41180.2340.2870.0476-0.04840.08050.53730.1190.14570.853-0.07670.2392-53.165210.9805-4.4553
42.2595-0.0922-0.25521.8848-0.20691.4859-0.1883-0.44460.31770.2990.13070.40750.0558-0.46830.06270.39870.02540.16420.6641-0.09020.5971-75.725416.1292-12.8656
51.2402-1.6202-0.26362.30480.30351.0801-0.32570.1853-0.82460.09380.09510.18160.1952-0.01350.21430.5972-0.12860.250.4055-0.02821.2397-60.3074-12.5727-20.1868
60.4470.170.21031.20051.39891.6569-0.1651-1.02640.59050.86750.0142-0.1266-0.01690.11590.01420.80550.1491-0.14010.9347-0.59440.5405-36.985322.0448-1.0639
72.76450.153-0.04090.8617-0.16470.51630.06451.60562.4623-0.03-0.0767-0.2899-0.06880.05320.01460.4297-0.0637-0.01040.39740.97210.8814-31.645528.3458-37.6861
81.1862-0.5911-0.10582.18220.24830.48070.14160.3420.414-0.3605-0.2891-0.03-0.30860.0313-0.01220.79260.0027-0.10310.75660.76171.9993-28.302351.1962-41.1759
93.7508-0.6820.31871.6293-0.12910.347-0.2386-0.3841.42620.25610.0893-0.4117-0.115-0.0040.12020.4239-0.0203-0.08420.2704-0.08180.5596-14.562819.2326-18.6018
101.5825-0.48780.19360.9529-0.36310.41420.14042.01651.7458-0.1053-0.4396-0.5757-0.06890.04850.15070.37790.01850.08911.0630.77040.6379-3.63916.5918-40.6501
111.0741-1.2675-0.31581.84680.53380.16560.19080.12090.4356-0.00960.08580.2066-0.0788-0.1041-0.2250.5934-0.3139-0.27310.56340.46642.0803-18.531945.501-31.1231
121.545-0.7630.22211.6535-1.12721.0376-0.1896-1.2019-0.06190.51660.1310.03410.00860.11770.06020.55380.05660.04610.66020.02230.2913-25.10376.2231-7.262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )A1 - 121
2X-RAY DIFFRACTION1CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )A218 - 245
3X-RAY DIFFRACTION1CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )A282 - 289
4X-RAY DIFFRACTION1CHAIN A AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )A471 - 535
5X-RAY DIFFRACTION2CHAIN A AND (RESID 246:281 )A246 - 281
6X-RAY DIFFRACTION3CHAIN A AND (RESID 135:217 )A135 - 217
7X-RAY DIFFRACTION4CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )A290 - 311
8X-RAY DIFFRACTION4CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )A336 - 470
9X-RAY DIFFRACTION4CHAIN A AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )A122 - 134
10X-RAY DIFFRACTION5CHAIN A AND (RESID 312:335)A312 - 335
11X-RAY DIFFRACTION6CHAIN A AND (RESID 536:591 )A536 - 591
12X-RAY DIFFRACTION7CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )B1 - 121
13X-RAY DIFFRACTION7CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )B218 - 245
14X-RAY DIFFRACTION7CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )B282 - 289
15X-RAY DIFFRACTION7CHAIN B AND (RESID 1:121 OR RESID 218:245 OR RESID 282:289 OR RESID 471:535 )B471 - 535
16X-RAY DIFFRACTION8CHAIN B AND (RESID 246:281 )B246 - 281
17X-RAY DIFFRACTION9CHAIN B AND (RESID 135:217 )B135 - 217
18X-RAY DIFFRACTION10CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )B290 - 311
19X-RAY DIFFRACTION10CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )B336 - 470
20X-RAY DIFFRACTION10CHAIN B AND (RESID 290:311 OR RESID 336:470 OR RESID 122:134 )B122 - 134
21X-RAY DIFFRACTION11CHAIN B AND (RESID 312:335)B312 - 335
22X-RAY DIFFRACTION12CHAIN B AND (RESID 536:591 )B536 - 591

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