PDB Short entry for 5YQI HEADER TRANSPORT PROTEIN 06-NOV-17 5YQI TITLE CRYSTAL STRUCTURE OF THE FIRST STARKIN DOMAIN OF LAM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE-ANCHORED LIPID-BINDING PROTEIN YSP2; COMPND 3 CHAIN: A; 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; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS2-THR KEYWDS LIGAND BINDING DOMAIN, STEROL, LIPID TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.TONG,Y.J.IM REVDAT 2 14-FEB-18 5YQI 1 SOURCE JRNL REVDAT 1 31-JAN-18 5YQI 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 22588 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1122 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 23.9754 - 3.1959 0.91 2651 113 0.1997 0.2426 REMARK 3 2 3.1959 - 2.5376 1.00 2763 128 0.2087 0.2363 REMARK 3 3 2.5376 - 2.2171 1.00 2718 137 0.2121 0.2813 REMARK 3 4 2.2171 - 2.0145 1.00 2706 150 0.2000 0.2294 REMARK 3 5 2.0145 - 1.8701 1.00 2667 157 0.2047 0.2467 REMARK 3 6 1.8701 - 1.7599 1.00 2681 139 0.2192 0.2395 REMARK 3 7 1.7599 - 1.6718 1.00 2657 168 0.2142 0.2508 REMARK 3 8 1.6718 - 1.5990 0.98 2623 130 0.2228 0.2455 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.230 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 : 0.006 1355 REMARK 3 ANGLE : 0.746 1836 REMARK 3 CHIRALITY : 0.053 214 REMARK 3 PLANARITY : 0.005 226 REMARK 3 DIHEDRAL : 14.208 820 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 5YQI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : 22632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300 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 (%): 43.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES-NAOH PH 6.0, 30% PEG3350, REMARK 280 0.1M KNO3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 16.71650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.14500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.75250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.14500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.71650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.75250 REMARK 290 SMTRY3 4 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: 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 GLY A 846 REMARK 465 SER A 847 REMARK 465 SER A 913 REMARK 465 GLY A 914 REMARK 465 SER A 915 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 MET A 849 63.84 -100.20 REMARK 500 ASP A 936 -81.75 -143.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YQI A 851 1016 UNP Q06681 YSP2_YEAST 851 1016 SEQADV 5YQI GLY A 846 UNP Q06681 EXPRESSION TAG SEQADV 5YQI SER A 847 UNP Q06681 EXPRESSION TAG SEQADV 5YQI ALA A 848 UNP Q06681 EXPRESSION TAG SEQADV 5YQI MET A 849 UNP Q06681 EXPRESSION TAG SEQADV 5YQI ASP A 850 UNP Q06681 EXPRESSION TAG SEQRES 1 A 171 GLY SER ALA MET ASP ASN ASP HIS LEU VAL ILE GLU ALA SEQRES 2 A 171 ASN ILE ASN ALA PRO LEU GLY LYS VAL VAL ASN LEU LEU SEQRES 3 A 171 TYR GLY GLU ASP VAL SER TYR TYR GLU ARG ILE LEU LYS SEQRES 4 A 171 ALA GLN LYS ASN PHE GLU ILE SER PRO ILE PRO ASN ASN SEQRES 5 A 171 PHE LEU THR LYS LYS ILE ARG ASP TYR ALA TYR THR LYS SEQRES 6 A 171 PRO LEU SER GLY SER ILE GLY PRO SER LYS THR LYS CYS SEQRES 7 A 171 LEU ILE THR ASP THR LEU GLU HIS TYR ASP LEU GLU ASP SEQRES 8 A 171 TYR VAL LYS VAL LEU SER ILE THR LYS ASN PRO ASP VAL SEQRES 9 A 171 PRO SER GLY ASN ILE PHE SER VAL LYS THR VAL PHE LEU SEQRES 10 A 171 PHE SER TRP ASP LYS ASN ASN SER THR LYS LEU THR VAL SEQRES 11 A 171 TYR ASN SER VAL ASP TRP THR GLY LYS SER TRP ILE LYS SEQRES 12 A 171 SER MET ILE GLU LYS GLY THR PHE ASP GLY VAL ALA ASP SEQRES 13 A 171 THR THR LYS ILE MET ILE SER GLU ILE LYS LYS ILE LEU SEQRES 14 A 171 SER ASP FORMUL 2 HOH *119(H2 O) HELIX 1 AA1 ASP A 850 ASP A 852 5 3 HELIX 2 AA2 PRO A 863 GLY A 873 1 11 HELIX 3 AA3 VAL A 876 GLN A 886 1 11 HELIX 4 AA4 ASN A 897 LYS A 902 1 6 HELIX 5 AA5 ILE A 987 LEU A 1014 1 28 SHEET 1 AA1 6 LEU A 854 ILE A 860 0 SHEET 2 AA1 6 SER A 970 TRP A 981 -1 O LEU A 973 N ALA A 858 SHEET 3 AA1 6 PHE A 955 ASP A 966 -1 N LEU A 962 O THR A 974 SHEET 4 AA1 6 TYR A 937 LYS A 945 -1 N SER A 942 O THR A 959 SHEET 5 AA1 6 LYS A 920 ASP A 933 -1 N THR A 926 O ILE A 943 SHEET 6 AA1 6 ILE A 903 PRO A 911 -1 N TYR A 908 O CYS A 923 CRYST1 33.433 59.505 84.290 90.00 90.00 90.00 P 21 21 21 4 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 0.029911 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011864 0.00000