HEADER LIPID TRANSPORT 17-AUG-16 5LQV TITLE SPATIAL STRUCTURE OF THE LENTIL LIPID TRANSFER PROTEIN IN COMPLEX WITH TITLE 2 ANIONIC LYSOLIPID LPPG CAVEAT 5LQV PGM A 101 HAS WRONG CHIRALITY AT ATOM C2 PGM A 101 HAS WRONG CAVEAT 2 5LQV CHIRALITY AT ATOM C8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC LIPID-TRANSFER PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LTP2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LENS CULINARIS; SOURCE 3 ORGANISM_COMMON: LENTIL; SOURCE 4 ORGANISM_TAXID: 3864; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLANT DEFENSE PEPTIDE LIPID TRANSFER PROTEIN LENS CULINARIS COMPLEX KEYWDS 2 WITH LIPID, STRUCTURE FROM CYANA 3.0, LIPID TRANSFER, LIPID KEYWDS 3 TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.S.MINEEV,Z.O.SHENKAREV,A.S.ARSENIEV,D.N.MELNIKOVA,E.I.FINKINA, AUTHOR 2 T.V.OVCHINNIKOVA REVDAT 2 08-MAY-19 5LQV 1 REMARK REVDAT 1 28-JUN-17 5LQV 0 JRNL AUTH Z.O.SHENKAREV,D.N.MELNIKOVA,E.I.FINKINA,S.V.SUKHANOV, JRNL AUTH 2 I.A.BOLDYREV,A.K.GIZATULLINA,K.S.MINEEV,A.S.ARSENIEV, JRNL AUTH 3 T.V.OVCHINNIKOVA JRNL TITL LIGAND BINDING PROPERTIES OF THE LENTIL LIPID TRANSFER JRNL TITL 2 PROTEIN: MOLECULAR INSIGHT INTO THE POSSIBLE MECHANISM OF JRNL TITL 3 LIPID UPTAKE. JRNL REF BIOCHEMISTRY V. 56 1785 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28266846 JRNL DOI 10.1021/ACS.BIOCHEM.6B01079 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001218. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-99% 13C; U-99% 15N] REMARK 210 LTP2, 2 MM LPPG, 20 MM SODIUM REMARK 210 ACETATE, 0.01 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY ALIPHATIC; 3D REMARK 210 HCCH-TOCSY; 3D HNCACB; 3D 1H-15N REMARK 210 NOESY; 13C-FILTERED NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCEIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.9.1, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ILE A 78 87.62 -154.63 REMARK 500 1 ILE A 82 100.97 59.82 REMARK 500 2 SER A 83 118.81 -167.61 REMARK 500 3 ILE A 82 98.91 59.66 REMARK 500 4 THR A 19 31.60 -94.84 REMARK 500 5 THR A 41 -75.64 -106.81 REMARK 500 5 THR A 42 -56.59 178.67 REMARK 500 5 ILE A 82 97.45 58.13 REMARK 500 6 LYS A 81 98.55 -64.81 REMARK 500 6 ILE A 82 103.41 -51.31 REMARK 500 7 ILE A 78 85.41 -150.66 REMARK 500 7 ILE A 82 100.22 59.83 REMARK 500 8 ILE A 2 -175.82 -66.48 REMARK 500 8 ILE A 82 103.32 -50.87 REMARK 500 10 ILE A 82 91.55 54.28 REMARK 500 10 THR A 90 40.29 -95.72 REMARK 500 11 ILE A 78 84.23 -150.10 REMARK 500 11 ILE A 82 99.64 59.75 REMARK 500 13 THR A 90 42.06 -101.27 REMARK 500 15 THR A 41 -76.76 -101.67 REMARK 500 15 THR A 42 -57.58 179.04 REMARK 500 16 THR A 41 -76.22 -107.44 REMARK 500 16 THR A 42 -56.73 179.23 REMARK 500 16 SER A 83 106.34 -44.36 REMARK 500 17 SER A 83 117.09 -162.25 REMARK 500 18 PRO A 79 74.10 -69.78 REMARK 500 18 LYS A 92 102.70 -160.64 REMARK 500 19 ILE A 82 97.33 56.76 REMARK 500 20 THR A 90 40.34 -105.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGM A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34036 RELATED DB: BMRB REMARK 900 SPATIAL STRUCTURE OF THE LENTIL LIPID TRANSFER PROTEIN IN COMPLEX REMARK 900 WITH ANIONIC LYSOLIPID LPPG DBREF 5LQV A 1 93 UNP A0AT29 NLTP2_LENCU 26 118 SEQRES 1 A 93 ALA ILE SER CYS GLY ALA VAL THR SER ASP LEU SER PRO SEQRES 2 A 93 CYS LEU THR TYR LEU THR GLY GLY PRO GLY PRO SER PRO SEQRES 3 A 93 GLN CYS CYS GLY GLY VAL LYS LYS LEU LEU ALA ALA ALA SEQRES 4 A 93 ASN THR THR PRO ASP ARG GLN ALA ALA CYS ASN CYS LEU SEQRES 5 A 93 LYS SER ALA ALA GLY SER ILE THR LYS LEU ASN THR ASN SEQRES 6 A 93 ASN ALA ALA ALA LEU PRO GLY LYS CYS GLY VAL ASN ILE SEQRES 7 A 93 PRO TYR LYS ILE SER THR THR THR ASN CYS ASN THR VAL SEQRES 8 A 93 LYS PHE HET PGM A 101 76 HETNAM PGM 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1- HETNAM 2 PGM GLYCEROL)] HETSYN PGM LYSOPHOSPHATIDYLGLYCEROL FORMUL 2 PGM C22 H44 O9 P 1- HELIX 1 AA1 SER A 3 ASP A 10 1 8 HELIX 2 AA2 PRO A 13 THR A 19 1 7 HELIX 3 AA3 SER A 25 ALA A 39 1 15 HELIX 4 AA4 THR A 41 SER A 58 1 18 HELIX 5 AA5 ASN A 63 CYS A 74 1 12 HELIX 6 AA6 ASN A 87 VAL A 91 5 5 SSBOND 1 CYS A 4 CYS A 51 1555 1555 2.01 SSBOND 2 CYS A 14 CYS A 28 1555 1555 2.10 SSBOND 3 CYS A 29 CYS A 74 1555 1555 1.99 SSBOND 4 CYS A 49 CYS A 88 1555 1555 1.98 CISPEP 1 GLY A 23 PRO A 24 1 0.06 CISPEP 2 GLY A 23 PRO A 24 2 0.03 CISPEP 3 GLY A 23 PRO A 24 3 0.02 CISPEP 4 GLY A 23 PRO A 24 4 0.07 CISPEP 5 GLY A 23 PRO A 24 5 0.05 CISPEP 6 GLY A 23 PRO A 24 6 0.09 CISPEP 7 GLY A 23 PRO A 24 7 0.08 CISPEP 8 GLY A 23 PRO A 24 8 0.11 CISPEP 9 GLY A 23 PRO A 24 9 0.10 CISPEP 10 GLY A 23 PRO A 24 10 0.07 CISPEP 11 GLY A 23 PRO A 24 11 0.07 CISPEP 12 GLY A 23 PRO A 24 12 0.04 CISPEP 13 GLY A 23 PRO A 24 13 0.03 CISPEP 14 GLY A 23 PRO A 24 14 0.02 CISPEP 15 GLY A 23 PRO A 24 15 0.02 CISPEP 16 GLY A 23 PRO A 24 16 0.10 CISPEP 17 GLY A 23 PRO A 24 17 0.10 CISPEP 18 GLY A 23 PRO A 24 18 0.03 CISPEP 19 GLY A 23 PRO A 24 19 0.01 CISPEP 20 GLY A 23 PRO A 24 20 0.03 SITE 1 AC1 10 THR A 8 LEU A 15 LEU A 35 LEU A 36 SITE 2 AC1 10 LEU A 52 LYS A 53 ALA A 55 ALA A 56 SITE 3 AC1 10 ALA A 67 ILE A 82 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1