HEADER TRANSPORT PROTEIN 07-NOV-17 5YQQ TITLE CRYSTAL STRUCTURE OF A DOMAIN-SWAPPED DIMER OF THE SECOND STARKIN TITLE 2 DOMAIN OF LAM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE-ANCHORED LIPID-BINDING PROTEIN YSP2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LIPID TRANSFER AT CONTACT SITE PROTEIN 4,LIPID TRANSFER COMPND 5 PROTEIN ANCHORED AT MEMBRANE CONTACT SITES 3,YEAST SUICIDE PROTEIN 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: YSP2, LAM2, LTC4, YDR326C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PHIS2-THR KEYWDS LIGAND BINDING DOMAIN, STEROL, LIPID TRANSPORT, YSP2, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.TONG,Y.J.IM REVDAT 4 22-NOV-23 5YQQ 1 REMARK REVDAT 3 14-FEB-18 5YQQ 1 JRNL REVDAT 2 07-FEB-18 5YQQ 1 REMARK REVDAT 1 31-JAN-18 5YQQ 0 JRNL AUTH J.TONG,M.K.MANIK,Y.J.IM JRNL TITL STRUCTURAL BASIS OF STEROL RECOGNITION AND NONVESICULAR JRNL TITL 2 TRANSPORT BY LIPID TRANSFER PROTEINS ANCHORED AT MEMBRANE JRNL TITL 3 CONTACT SITES JRNL REF PROC. NATL. ACAD. SCI. V. 115 E856 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29339490 JRNL DOI 10.1073/PNAS.1719709115 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 25975 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1284 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 24.0185 - 3.9137 0.96 2750 119 0.1616 0.2043 REMARK 3 2 3.9137 - 3.1085 0.99 2815 126 0.1756 0.2107 REMARK 3 3 3.1085 - 2.7162 0.98 2806 144 0.2146 0.2743 REMARK 3 4 2.7162 - 2.4681 0.98 2765 130 0.2217 0.2596 REMARK 3 5 2.4681 - 2.2914 0.98 2791 146 0.2231 0.2584 REMARK 3 6 2.2914 - 2.1564 0.97 2712 179 0.2234 0.2755 REMARK 3 7 2.1564 - 2.0484 0.97 2766 140 0.2211 0.2993 REMARK 3 8 2.0484 - 1.9593 0.97 2719 162 0.2309 0.2700 REMARK 3 9 1.9593 - 1.8839 0.92 2567 138 0.2198 0.2869 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.00 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 : 0.006 2583 REMARK 3 ANGLE : 0.862 3489 REMARK 3 CHIRALITY : 0.055 406 REMARK 3 PLANARITY : 0.006 436 REMARK 3 DIHEDRAL : 12.905 1559 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 5YQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-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) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.27900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 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: 5YQJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.0, 30% PEG 8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: 5630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLY A 1054 REMARK 465 SER A 1055 REMARK 465 ALA A 1056 REMARK 465 LEU A 1119 REMARK 465 ASN A 1120 REMARK 465 ASN A 1121 REMARK 465 SER A 1122 REMARK 465 PHE A 1123 REMARK 465 GLY A 1124 REMARK 465 PRO A 1125 REMARK 465 LYS A 1126 REMARK 465 GLY B 1054 REMARK 465 SER B 1055 REMARK 465 ALA B 1056 REMARK 465 MET B 1057 REMARK 465 GLY B 1058 REMARK 465 ASN B 1120 REMARK 465 ASN B 1121 REMARK 465 SER B 1122 REMARK 465 PHE B 1123 REMARK 465 GLY B 1124 REMARK 465 PRO B 1125 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 1199 O HOH A 1301 2.12 REMARK 500 OE2 GLU B 1065 O HOH B 1301 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A1064 128.68 -174.94 REMARK 500 PRO A1070 31.05 -79.11 REMARK 500 GLN A1095 34.49 -95.32 REMARK 500 SER A1143 -44.24 -145.20 REMARK 500 THR A1177 -169.02 -112.68 REMARK 500 PRO B1070 43.03 -80.63 REMARK 500 SER B1143 -47.77 -154.38 REMARK 500 LYS B1191 18.98 58.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YQQ A 1060 1223 UNP Q06681 YSP2_YEAST 1060 1223 DBREF 5YQQ B 1060 1223 UNP Q06681 YSP2_YEAST 1060 1223 SEQADV 5YQQ GLY A 1054 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ SER A 1055 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ ALA A 1056 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ MET A 1057 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ GLY A 1058 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ SER A 1059 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ GLY B 1054 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ SER B 1055 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ ALA B 1056 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ MET B 1057 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ GLY B 1058 UNP Q06681 EXPRESSION TAG SEQADV 5YQQ SER B 1059 UNP Q06681 EXPRESSION TAG SEQRES 1 A 170 GLY SER ALA MET GLY SER ASP THR VAL ILE ASP GLU LYS SEQRES 2 A 170 ILE ASN ILE PRO VAL PRO LEU GLY THR VAL PHE SER LEU SEQRES 3 A 170 LEU TYR GLY ASP ASP THR SER TYR ILE LYS LYS ILE ILE SEQRES 4 A 170 GLU ASN GLN ASN ASN PHE ASN VAL CYS ASP ILE PRO LYS SEQRES 5 A 170 PHE VAL ASN ASN ALA ARG GLU ILE THR TYR THR LYS LYS SEQRES 6 A 170 LEU ASN ASN SER PHE GLY PRO LYS GLN THR LYS CYS ILE SEQRES 7 A 170 VAL THR GLU THR ILE GLU HIS MET ASP LEU ASN SER PHE SEQRES 8 A 170 PHE MET VAL LYS GLN ILE VAL ARG SER PRO ASP VAL PRO SEQRES 9 A 170 TYR GLY SER SER PHE SER VAL HIS THR ARG PHE PHE TYR SEQRES 10 A 170 SER TRP GLY ASP HIS ASN THR THR ASN MET LYS VAL VAL SEQRES 11 A 170 THR ASN VAL VAL TRP THR GLY LYS SER MET LEU LYS GLY SEQRES 12 A 170 THR ILE GLU LYS GLY SER ILE ASP GLY GLN ARG SER SER SEQRES 13 A 170 THR LYS GLN LEU VAL ASP ASP LEU LYS LYS ILE ILE SER SEQRES 14 A 170 ASN SEQRES 1 B 170 GLY SER ALA MET GLY SER ASP THR VAL ILE ASP GLU LYS SEQRES 2 B 170 ILE ASN ILE PRO VAL PRO LEU GLY THR VAL PHE SER LEU SEQRES 3 B 170 LEU TYR GLY ASP ASP THR SER TYR ILE LYS LYS ILE ILE SEQRES 4 B 170 GLU ASN GLN ASN ASN PHE ASN VAL CYS ASP ILE PRO LYS SEQRES 5 B 170 PHE VAL ASN ASN ALA ARG GLU ILE THR TYR THR LYS LYS SEQRES 6 B 170 LEU ASN ASN SER PHE GLY PRO LYS GLN THR LYS CYS ILE SEQRES 7 B 170 VAL THR GLU THR ILE GLU HIS MET ASP LEU ASN SER PHE SEQRES 8 B 170 PHE MET VAL LYS GLN ILE VAL ARG SER PRO ASP VAL PRO SEQRES 9 B 170 TYR GLY SER SER PHE SER VAL HIS THR ARG PHE PHE TYR SEQRES 10 B 170 SER TRP GLY ASP HIS ASN THR THR ASN MET LYS VAL VAL SEQRES 11 B 170 THR ASN VAL VAL TRP THR GLY LYS SER MET LEU LYS GLY SEQRES 12 B 170 THR ILE GLU LYS GLY SER ILE ASP GLY GLN ARG SER SER SEQRES 13 B 170 THR LYS GLN LEU VAL ASP ASP LEU LYS LYS ILE ILE SER SEQRES 14 B 170 ASN FORMUL 3 HOH *223(H2 O) HELIX 1 AA1 PRO A 1072 GLY A 1082 1 11 HELIX 2 AA2 THR A 1085 GLN A 1095 1 11 HELIX 3 AA3 TYR A 1158 SER A 1160 5 3 HELIX 4 AA4 SER A 1192 SER A 1222 1 31 HELIX 5 AA5 PRO B 1072 GLY B 1082 1 11 HELIX 6 AA6 THR B 1085 ASN B 1094 1 10 HELIX 7 AA7 SER B 1192 ASN B 1223 1 32 SHEET 1 AA1 7 THR A1061 ILE A1069 0 SHEET 2 AA1 7 THR A1177 TRP A1188 -1 O THR A1184 N THR A1061 SHEET 3 AA1 7 PHE A1162 GLY A1173 -1 N SER A1171 O ASN A1179 SHEET 4 AA1 7 PHE A1144 ARG A1152 -1 N GLN A1149 O THR A1166 SHEET 5 AA1 7 THR A1128 ASP A1140 -1 N GLU A1137 O MET A1146 SHEET 6 AA1 7 ALA A1110 LYS A1117 -1 N ILE A1113 O VAL A1132 SHEET 7 AA1 7 ASN A1097 PHE A1098 -1 N PHE A1098 O THR A1116 SHEET 1 AA2 7 THR B1061 ILE B1069 0 SHEET 2 AA2 7 THR B1177 TRP B1188 -1 O THR B1178 N ILE B1069 SHEET 3 AA2 7 PHE B1162 GLY B1173 -1 N GLY B1173 O THR B1177 SHEET 4 AA2 7 PHE B1144 ARG B1152 -1 N GLN B1149 O THR B1166 SHEET 5 AA2 7 THR B1128 ASP B1140 -1 N THR B1135 O LYS B1148 SHEET 6 AA2 7 ALA B1110 LYS B1117 -1 N ILE B1113 O VAL B1132 SHEET 7 AA2 7 ASN B1097 PHE B1098 -1 N PHE B1098 O THR B1116 CRYST1 33.862 52.124 53.021 107.81 90.17 105.05 P 1 2 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 0.029532 0.007941 0.002749 0.00000 SCALE2 0.000000 0.019866 0.006652 0.00000 SCALE3 0.000000 0.000000 0.019890 0.00000