HEADER LIPID TRANSPORT 05-DEC-18 6IWM 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, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Z.K.MADNI,D.M.SALUNKE REVDAT 4 22-NOV-23 6IWM 1 REMARK REVDAT 3 13-MAY-20 6IWM 1 JRNL REVDAT 2 25-DEC-19 6IWM 1 JRNL REVDAT 1 11-DEC-19 6IWM 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. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15253 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 754 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 2.0500 - 1.9800 0.99 2859 158 0.2159 0.2771 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.440 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 : NULL NULL REMARK 3 ANGLE : 0.930 1829 REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6IWM 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_1300009981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 15253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 : 8.400 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.63900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.420 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: 5TVI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 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 16.78067 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 33.56133 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 25.17100 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 41.95167 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 8.39033 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 8.39033 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 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 SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 104 DBREF1 6IWM A 1 92 UNP A0A247D6Y2_SOLME DBREF2 6IWM A A0A247D6Y2 1 92 DBREF1 6IWM B 1 92 UNP A0A247D6Y2_SOLME DBREF2 6IWM 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 SO4 A 102 5 HET GOL B 101 6 HET GOL B 102 6 HET TRS B 103 8 HET SO4 B 104 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 3 GOL 3(C3 H8 O3) FORMUL 4 SO4 2(O4 S 2-) FORMUL 7 TRS C4 H12 N O3 1+ FORMUL 9 HOH *84(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 2.05 SSBOND 2 CYS A 14 CYS A 28 1555 1555 2.05 SSBOND 3 CYS A 29 CYS A 74 1555 1555 2.06 SSBOND 4 CYS A 49 CYS A 88 1555 1555 2.10 SSBOND 5 CYS B 4 CYS B 51 1555 1555 2.05 SSBOND 6 CYS B 14 CYS B 28 1555 1555 2.07 SSBOND 7 CYS B 29 CYS B 74 1555 1555 2.05 SSBOND 8 CYS B 49 CYS B 88 1555 1555 2.07 SITE 1 AC1 4 LEU A 62 LYS A 63 ASP A 64 ASP A 65 SITE 1 AC2 4 TYR A 59 PRO A 60 ASN A 61 HOH A 202 SITE 1 AC3 3 LYS B 63 ASP B 64 ASP B 65 SITE 1 AC4 1 ASN B 87 SITE 1 AC5 6 GLN A 6 ASN A 10 THR A 34 ASN A 38 SITE 2 AC5 6 ALA B 26 ALA B 27 SITE 1 AC6 5 TYR B 59 PRO B 60 ASN B 61 LEU B 62 SITE 2 AC6 5 ARG B 84 CRYST1 87.036 87.036 50.342 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 0.011489 0.006633 0.000000 0.00000 SCALE2 0.000000 0.013267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019864 0.00000