HEADER LIPID TRANSPORT 05-DEC-18 6IWO TITLE STRUCTURAL INSIGHT INTO PROBABLE LIPID TRANSFER MECHANISM OF NON- TITLE 2 SPECIFIC LIPID TRANSFER PROTEIN VIA INTERMEDIATE STRUCTURES IN TITLE 3 SOLANUM MELONGENA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC LIPID-TRANSFER PROTEIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM MELONGENA; SOURCE 3 ORGANISM_COMMON: EGGPLANT; SOURCE 4 ORGANISM_TAXID: 4111 KEYWDS NSLTP, MYRISTIC ACID, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Z.K.MADNI,D.M.SALUNKE REVDAT 4 22-NOV-23 6IWO 1 REMARK REVDAT 3 13-MAY-20 6IWO 1 JRNL REVDAT 2 25-DEC-19 6IWO 1 JRNL REVDAT 1 11-DEC-19 6IWO 0 JRNL AUTH Z.K.MADNI,S.K.TRIPATHI,D.M.SALUNKE JRNL TITL STRUCTURAL INSIGHTS INTO THE LIPID TRANSFER MECHANISM OF A JRNL TITL 2 NON-SPECIFIC LIPID TRANSFER PROTEIN. JRNL REF PLANT J. V. 102 340 2020 JRNL REFN ESSN 1365-313X JRNL PMID 31793077 JRNL DOI 10.1111/TPJ.14627 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2747: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9383 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 460 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 3.3879 - 2.6893 1.00 2976 160 0.2159 0.2410 REMARK 3 2 2.4300 - 2.3500 1.00 2922 157 0.2514 0.3037 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 1346 REMARK 3 ANGLE : 0.736 1830 REMARK 3 CHIRALITY : 0.047 212 REMARK 3 PLANARITY : 0.005 243 REMARK 3 DIHEDRAL : 8.083 836 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 6IWO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6IWM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 8.0, 2M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.89633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.79267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.34450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.24083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.44817 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 87.69100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -25.34450 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 B 1 REMARK 465 SER B 92 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 B 40 -62.52 -90.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 228 DISTANCE = 5.99 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MYR A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6IWM RELATED DB: PDB REMARK 900 6IWM CONTAINS THE SAME PROTEIN DBREF1 6IWO A 1 92 UNP A0A247D6Y2_SOLME DBREF2 6IWO A A0A247D6Y2 1 92 DBREF1 6IWO B 1 92 UNP A0A247D6Y2_SOLME DBREF2 6IWO B 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 SEQRES 1 B 92 ALA VAL THR CYS GLY GLN VAL ASP ALA ASN LEU ALA PRO SEQRES 2 B 92 CYS VAL PRO PHE LEU THR GLN GLY GLY GLU PRO GLY ALA SEQRES 3 B 92 ALA CYS CYS SER GLY VAL LYS THR LEU ASN GLY ASN ALA SEQRES 4 B 92 GLN SER PRO ASP ASP ARG LYS THR ALA CYS ASN CYS ILE SEQRES 5 B 92 LYS ALA ALA ALA ASN ARG TYR PRO ASN LEU LYS ASP ASP SEQRES 6 B 92 ALA ALA GLN SER LEU PRO SER LYS CYS GLY ILE SER LEU SEQRES 7 B 92 ASN VAL PRO ILE SER ARG THR ILE ASN CYS ASP THR ILE SEQRES 8 B 92 SER HET GOL A 101 6 HET MYR A 102 16 HET SO4 B 101 5 HET SO4 B 102 5 HET GOL B 103 6 HETNAM GOL GLYCEROL HETNAM MYR MYRISTIC ACID HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 4 MYR C14 H28 O2 FORMUL 5 SO4 2(O4 S 2-) FORMUL 8 HOH *58(H2 O) HELIX 1 AA1 THR A 3 ALA A 12 1 10 HELIX 2 AA2 CYS A 14 GLY A 21 1 8 HELIX 3 AA3 GLY A 25 ALA A 39 1 15 HELIX 4 AA4 SER A 41 TYR A 59 1 19 HELIX 5 AA5 LYS A 63 GLY A 75 1 13 HELIX 6 AA6 ASN A 87 ILE A 91 5 5 HELIX 7 AA7 THR B 3 ALA B 12 1 10 HELIX 8 AA8 CYS B 14 GLY B 21 1 8 HELIX 9 AA9 GLY B 25 ALA B 39 1 15 HELIX 10 AB1 SER B 41 TYR B 59 1 19 HELIX 11 AB2 LYS B 63 GLY B 75 1 13 HELIX 12 AB3 ASN B 87 ILE B 91 5 5 SSBOND 1 CYS A 4 CYS A 51 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 28 1555 1555 2.04 SSBOND 3 CYS A 29 CYS A 74 1555 1555 2.04 SSBOND 4 CYS A 49 CYS A 88 1555 1555 2.05 SSBOND 5 CYS B 4 CYS B 51 1555 1555 2.04 SSBOND 6 CYS B 14 CYS B 28 1555 1555 2.04 SSBOND 7 CYS B 29 CYS B 74 1555 1555 2.04 SSBOND 8 CYS B 49 CYS B 88 1555 1555 2.04 SITE 1 AC1 4 LEU A 62 LYS A 63 ASP A 64 ASP A 65 SITE 1 AC2 17 GLU A 23 GLY A 25 ALA A 26 ALA A 27 SITE 2 AC2 17 ALA A 39 GLN A 40 ARG A 45 SER A 77 SITE 3 AC2 17 LEU A 78 ASN A 79 HOH A 207 HOH A 216 SITE 4 AC2 17 HOH A 220 PRO B 71 SER B 72 GLY B 75 SITE 5 AC2 17 ILE B 76 SITE 1 AC3 8 GLN A 6 ASN A 10 THR A 34 GLY B 25 SITE 2 AC3 8 ALA B 26 ALA B 27 HOH B 202 HOH B 205 SITE 1 AC4 3 PRO B 60 ASN B 61 ARG B 84 SITE 1 AC5 3 LYS B 63 ASP B 64 ASP B 65 CRYST1 87.691 87.691 50.689 90.00 90.00 120.00 P 61 12 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 0.011404 0.006584 0.000000 0.00000 SCALE2 0.000000 0.013168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019728 0.00000