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- PDB-4ia6: Hydratase from lactobacillus acidophilus in a ligand bound form (... -

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Basic information

Entry
Database: PDB / ID: 4ia6
TitleHydratase from lactobacillus acidophilus in a ligand bound form (LA 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
LINOLEIC ACID / : / NITRATE ION / PHOSPHATE ION / Myosin-crossreactive antigen
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)138,57732
Polymers135,3932
Non-polymers3,18430
Water25,0231389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-130 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.100, 77.740, 104.810
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: 67696.258 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 , 11 types, 1419 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EIC / LINOLEIC ACID / 9,12-LINOLEIC ACID / Linoleic acid


Mass: 280.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#11: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1389 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMRD A 601 AND MPD A 602 PLACE THE ALTERNATE POSITIONS.

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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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 37-38% MPD, 0.1M Hepes/KOH, 20mM NaBr, 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: 0.97977 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: 0.97977 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 122391 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 23.685 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.87
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
1.8-1.90.720.6522.366200418577156220.75184.1
1.9-20.8430.4523.66606615042150360.515100
2-2.20.940.2655.969926222542225280.30299.9
2.2-3.120.990.11213.0619656344541445260.128100
3.12-3.580.9980.04428.0835925820582000.05199.9
3.58-4.040.9980.03436.0921452493149220.03999.8
4.04-4.50.9990.02941.2513573312831240.03399.9
4.5-140.9990.02841.6834428815381310.03299.7
14-1710.01853.535171401380.02198.6
17-500.9990.01946.515181891640.02386.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→48.725 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 6030 4.93 %RANDOM
Rwork0.1537 ---
obs0.1556 122324 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.97 Å2 / Biso mean: 20.5473 Å2 / Biso min: 3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9213 0 200 1389 10802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129764
X-RAY DIFFRACTIONf_angle_d1.37613227
X-RAY DIFFRACTIONf_chiral_restr0.0921379
X-RAY DIFFRACTIONf_plane_restr0.0061693
X-RAY DIFFRACTIONf_dihedral_angle_d14.6173639
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 (%)
1.8-1.82050.2691150.25582190230556
1.8205-1.84190.29741500.24282848299873
1.8419-1.86430.24641640.227439994163100
1.8643-1.88790.25411900.213838944084100
1.8879-1.91280.25282070.208939334140100
1.9128-1.9390.22282060.194939614167100
1.939-1.96670.20362060.192539194125100
1.9667-1.99610.24122040.192339284132100
1.9961-2.02720.22092110.176739104121100
2.0272-2.06050.21042090.169739674176100
2.0605-2.0960.2112020.16439224124100
2.096-2.13410.21332080.16139394147100
2.1341-2.17520.19712060.160239534159100
2.1752-2.21960.20822100.15739384148100
2.2196-2.26780.22642050.160939164121100
2.2678-2.32060.21532080.154339434151100
2.3206-2.37860.22582070.153539764183100
2.3786-2.44290.21222080.15639514159100
2.4429-2.51480.20412080.150739644172100
2.5148-2.5960.19222040.141839534157100
2.596-2.68880.17112150.145439764191100
2.6888-2.79640.19422090.145939534162100
2.7964-2.92360.18052050.140739794184100
2.9236-3.07780.17182100.142439824192100
3.0778-3.27060.19262090.135640074216100
3.2706-3.5230.15692120.128240124224100
3.523-3.87740.16052080.122240084216100
3.8774-4.43820.14342080.116440484256100
4.4382-5.59030.18152120.141940914303100
5.5903-48.74270.17112140.18294234444899
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)
10.92520.1480.31050.60810.03060.5282-0.04240.1983-0.0003-0.09280.0344-0.0717-0.03190.0856-0.00110.0973-0.03380.01120.1351-0.00130.0646-28.91131.0875-29.639
21.4272-0.28390.29011.3974-0.15611.5316-0.10770.39750.4125-0.26780.063-0.26-0.40010.185-0.2630.2775-0.1133-0.02630.24640.07940.2583-21.353952.9272-33.8478
30.78780.37470.04850.83120.11170.5930.0315-0.214-0.02930.1997-0.0238-0.00370.00490.030.06610.1151-0.0093-0.0080.12780.00570.0727-29.255226.2676-2.7191
40.83410.00350.07540.734-0.04650.4092-0.00190.002-0.1270.04260.0261-0.21560.04860.10070.0480.09940.0108-0.02340.1418-0.01960.1641-7.070419.8401-11.6554
51.32-0.2950.15431.0244-0.69391.3115-0.1270.13390.36710.008-0.0252-0.1868-0.25850.2405-0.01340.1489-0.0488-0.02890.13460.01060.164-20.986349.227-19.1918
60.551-0.0614-0.10910.7905-0.74180.74730.009-0.2809-0.06830.2004-0.0247-0.0363-0.0564-0.00830.06950.1776-0.0305-0.01470.17460.02820.1071-45.740215.91070.5813
70.6984-0.0120.16980.6673-0.06240.37770.04430.098-0.1291-0.06430.00310.00930.08860.04370.01260.113-0.0121-0.0120.0934-0.02880.0908-51.5889.3747-35.3109
81.12750.2792-0.08771.30920.33520.5147-0.00910.1068-0.3004-0.10830.0770.11890.370.0297-0.16650.33020.0023-0.09770.1307-0.05130.2756-55.9229-13.2063-39.3221
90.8107-0.040.17540.8206-0.2040.8694-0.0153-0.1525-0.04610.11390.02330.12080.0099-0.1001-0.00290.1106-0.01560.01120.12660.01370.0927-68.547519.4747-16.8068
100.9372-0.43330.11410.68430.10.36760.02470.0397-0.1329-0.065-0.01330.17130.0779-0.0306-0.00720.1036-0.034-0.01530.0890.00250.1084-79.289221.9356-38.5613
110.4381-0.5293-0.06250.8428-0.21470.41990.0943-0.0047-0.29060.11190.02260.10680.4072-0.12720.06790.2574-0.0599-0.03840.11090.00510.2202-65.381-6.9502-29.2531
122.12290.97671.45371.08850.97271.8815-0.2833-0.49070.99670.21140.02680.5002-0.469-0.24080.08190.30360.009-0.01830.2321-0.08550.4387-53.974833.4677-8.9498
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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