HEADER LIPID TRANSPORT 09-DEC-21 7W9A TITLE DYNAMICS OF LIPID DISPLACEMENT INSIDE THE HYDROPHOBIC CAVITY OF A NON- TITLE 2 SPECIFIC LIPID TRANSFER PROTEIN FROM SOLANUM MELONGENA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC LIPID-TRANSFER PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM MELONGENA; SOURCE 3 ORGANISM_COMMON: EGGPLANT; SOURCE 4 ORGANISM_TAXID: 4111 KEYWDS NSLTP, LAURIC ACID, LIPID TRANSFER PROTEIN, LIPID BINDING DYNAMICS, KEYWDS 2 LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Z.K.MADNI,A.KUMAR,D.M.SALUNKE REVDAT 5 06-NOV-24 7W9A 1 REMARK REVDAT 4 29-NOV-23 7W9A 1 REMARK REVDAT 3 19-JUL-23 7W9A 1 JRNL REVDAT 2 27-JUL-22 7W9A 1 JRNL REVDAT 1 13-JUL-22 7W9A 0 JRNL AUTH Z.K.MADNI,A.KUMAR,U.KUMAR,D.JAISWAL,D.M.SALUNKE JRNL TITL DYNAMICS OF LIPID DISPLACEMENT INSIDE THE HYDROPHOBIC CAVITY JRNL TITL 2 OF A NONSPECIFIC LIPID TRANSFER PROTEIN FROM SOLANUM JRNL TITL 3 MELONGENA . JRNL REF J.BIOMOL.STRUCT.DYN. V. 41 5839 2023 JRNL REFN ESSN 1538-0254 JRNL PMID 35838149 JRNL DOI 10.1080/07391102.2022.2097956 REMARK 2 REMARK 2 RESOLUTION. 2.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 4080 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.1960 - 2.1200 1.00 3899 209 0.1962 0.2388 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 669 REMARK 3 ANGLE : 0.599 902 REMARK 3 CHIRALITY : 0.043 105 REMARK 3 PLANARITY : 0.006 121 REMARK 3 DIHEDRAL : 14.881 115 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7W9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300025033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4080 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9250 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.68200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6IWM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES AT PH 7.5 AND 1.5M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.62250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 19.62250 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.35800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.62250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.67900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.62250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.03700 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.62250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.62250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.35800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 19.62250 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 71.03700 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 19.62250 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.67900 REMARK 290 REMARK 290 REMARK: NULL 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 0 REMARK 465 SER A 91 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 64 CG OD1 OD2 REMARK 470 ILE A 75 CD1 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 GLN A 39 -60.20 -99.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6IWP RELATED DB: PDB REMARK 900 6IWP CONTAINS THE SAME PROTEIN COMPLEXED WITH LAURIC ACID DBREF1 7W9A A 0 91 UNP A0A247D6Y2_SOLME DBREF2 7W9A A A0A247D6Y2 1 92 SEQRES 1 A 92 ALA VAL THR CYS GLY GLN VAL ASP ALA ASN LEU ALA PRO SEQRES 2 A 92 CYS VAL PRO PHE LEU THR GLN GLY GLY GLU PRO GLY ALA SEQRES 3 A 92 ALA CYS CYS SER GLY VAL LYS THR LEU ASN GLY ASN ALA SEQRES 4 A 92 GLN SER PRO ASP ASP ARG LYS THR ALA CYS ASN CYS ILE SEQRES 5 A 92 LYS ALA ALA ALA ASN ARG TYR PRO ASN LEU LYS ASP ASP SEQRES 6 A 92 ALA ALA GLN SER LEU PRO SER LYS CYS GLY ILE SER LEU SEQRES 7 A 92 ASN VAL PRO ILE SER ARG THR ILE ASN CYS ASP THR ILE SEQRES 8 A 92 SER HET DAO A 101 14 HET DAO A 102 14 HETNAM DAO LAURIC ACID FORMUL 2 DAO 2(C12 H24 O2) FORMUL 4 HOH *13(H2 O) HELIX 1 AA1 THR A 2 ALA A 11 1 10 HELIX 2 AA2 CYS A 13 GLY A 20 1 8 HELIX 3 AA3 GLY A 24 ALA A 38 1 15 HELIX 4 AA4 SER A 40 TYR A 58 1 19 HELIX 5 AA5 ASP A 63 CYS A 73 1 11 SSBOND 1 CYS A 3 CYS A 50 1555 1555 2.03 SSBOND 2 CYS A 13 CYS A 27 1555 1555 2.03 SSBOND 3 CYS A 28 CYS A 73 1555 1555 2.03 SSBOND 4 CYS A 48 CYS A 87 1555 1555 2.03 CRYST1 39.245 39.245 94.716 90.00 90.00 90.00 I 41 8 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 0.025481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010558 0.00000 CONECT 20 342 CONECT 87 180 CONECT 180 87 CONECT 186 511 CONECT 328 612 CONECT 342 20 CONECT 511 186 CONECT 612 328 CONECT 637 639 CONECT 638 639 CONECT 639 637 638 640 CONECT 640 639 641 CONECT 641 640 642 CONECT 642 641 643 CONECT 643 642 644 CONECT 644 643 645 CONECT 645 644 646 CONECT 646 645 647 CONECT 647 646 648 CONECT 648 647 649 CONECT 649 648 650 CONECT 650 649 CONECT 651 653 CONECT 652 653 CONECT 653 651 652 654 CONECT 654 653 655 CONECT 655 654 656 CONECT 656 655 657 CONECT 657 656 658 CONECT 658 657 659 CONECT 659 658 660 CONECT 660 659 661 CONECT 661 660 662 CONECT 662 661 663 CONECT 663 662 664 CONECT 664 663 MASTER 242 0 2 5 0 0 0 6 676 1 36 8 END