PDB Short entry for 6BYM HEADER LIPID TRANSPORT 20-DEC-17 6BYM TITLE CRYSTAL STRUCTURE OF THE STEROL-BOUND SECOND START DOMAIN OF YEAST TITLE 2 LAM4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROL-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LAM4 (YHR080C)-STARKIN DOMAIN; COMPND 5 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 GENE: LAM4, SCKG_4597; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STEROL TRANSPORT, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JENTSCH,I.N.KIBURU,J.WU,K.PANDEY,O.BOUDKER,A.K.MENON REVDAT 8 13-MAR-24 6BYM 1 REMARK REVDAT 7 08-JAN-20 6BYM 1 REMARK REVDAT 6 25-APR-18 6BYM 1 JRNL REVDAT 5 07-MAR-18 6BYM 1 JRNL REVDAT 4 14-FEB-18 6BYM 1 REMARK REVDAT 3 31-JAN-18 6BYM 1 TITLE REVDAT 2 24-JAN-18 6BYM 1 SOURCE JRNL REVDAT 1 17-JAN-18 6BYM 0 JRNL AUTH J.A.JENTSCH,I.KIBURU,K.PANDEY,M.TIMME,T.RAMLALL,B.LEVKAU, JRNL AUTH 2 J.WU,D.ELIEZER,O.BOUDKER,A.K.MENON JRNL TITL STRUCTURAL BASIS OF STEROL BINDING AND TRANSPORT BY A YEAST JRNL TITL 2 STARKIN DOMAIN. JRNL REF J. BIOL. CHEM. V. 293 5522 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29463678 JRNL DOI 10.1074/JBC.RA118.001881 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 17131 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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 42.3892 - 3.9969 0.99 2759 142 0.1411 0.1933 REMARK 3 2 3.9969 - 3.1728 0.99 2696 154 0.1577 0.2017 REMARK 3 3 3.1728 - 2.7718 0.98 2707 154 0.1847 0.2515 REMARK 3 4 2.7718 - 2.5184 0.98 2734 136 0.1875 0.2675 REMARK 3 5 2.5184 - 2.3379 0.98 2704 148 0.1904 0.2789 REMARK 3 6 2.3379 - 2.2001 0.96 2661 136 0.1904 0.3185 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.55 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 : 0.008 3231 REMARK 3 ANGLE : 0.999 4393 REMARK 3 CHIRALITY : 0.058 514 REMARK 3 PLANARITY : 0.006 548 REMARK 3 DIHEDRAL : 14.227 1976 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND RESID 4 THROUGH 196) REMARK 3 SELECTION : (CHAIN B AND RESID 4 THROUGH 196) REMARK 3 ATOM PAIRS NUMBER : 1830 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00001 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17147 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM CHLORIDE 0.7M 0.1M HEPES PH REMARK 280 7.5 24% PEG6000, VAPOR DIFFUSION, TEMPERATURE 293.15K 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 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 1 REMARK 465 PRO A 2 REMARK 465 MET A 3 REMARK 465 GLY B 1 REMARK 465 LYS B 197 REMARK 465 SER B 198 REMARK 465 LYS B 199 REMARK 465 LYS B 200 REMARK 465 PRO B 201 REMARK 465 VAL B 202 REMARK 465 LYS B 203 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 LYS A 199 CG CD CE NZ 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 21 72.42 -113.04 REMARK 500 ASN A 115 -79.18 -138.38 REMARK 500 ASN B 92 -101.60 -101.90 REMARK 500 ASN B 115 -82.37 -137.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HC3 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HC3 B 301 DBREF1 6BYM A 4 203 UNP A0A250WL92_YEASX DBREF2 6BYM A A0A250WL92 946 1145 DBREF1 6BYM B 4 203 UNP A0A250WL92_YEASX DBREF2 6BYM B A0A250WL92 946 1145 SEQADV 6BYM GLY A 1 UNP A0A250WL9 EXPRESSION TAG SEQADV 6BYM PRO A 2 UNP A0A250WL9 EXPRESSION TAG SEQADV 6BYM MET A 3 UNP A0A250WL9 EXPRESSION TAG SEQADV 6BYM GLY B 1 UNP A0A250WL9 EXPRESSION TAG SEQADV 6BYM PRO B 2 UNP A0A250WL9 EXPRESSION TAG SEQADV 6BYM MET B 3 UNP A0A250WL9 EXPRESSION TAG SEQRES 1 A 203 GLY PRO MET THR LEU PRO LYS MET GLU PRO SER SER HIS SEQRES 2 A 203 ALA PRO THR GLU PRO ASP ILE GLN LYS ASP LYS ASP ASP SEQRES 3 A 203 SER ILE ILE ARG GLU ASN GLU ASN ILE PRO ALA PRO LEU SEQRES 4 A 203 GLY THR VAL VAL GLN LEU LEU PHE GLY SER ASN THR GLU SEQRES 5 A 203 TYR MET GLN LYS VAL ILE THR ARG ASP LYS ASN ASN VAL SEQRES 6 A 203 ASN VAL GLU THR ILE PRO LYS PHE THR PRO SER LEU VAL SEQRES 7 A 203 GLU GLY GLY SER ARG HIS TYR GLU TYR THR LYS LYS LEU SEQRES 8 A 203 ASN ASN SER ILE GLY PRO LYS GLN THR LYS CYS LEU LEU SEQRES 9 A 203 THR GLU SER ILE GLU HIS MET ASP ILE ASN ASN TYR VAL SEQRES 10 A 203 LEU VAL THR GLN THR THR LYS THR PRO ASP VAL PRO SER SEQRES 11 A 203 GLY SER ASN PHE ALA VAL GLU SER LYS ILE PHE LEU PHE SEQRES 12 A 203 TRP GLY GLN HIS ASP THR THR ASN MET THR VAL ILE THR SEQRES 13 A 203 LYS ILE ASN TRP THR SER LYS SER PHE LEU LYS GLY ALA SEQRES 14 A 203 ILE GLU LYS GLY SER VAL GLU GLY GLN LYS VAL SER VAL SEQRES 15 A 203 ASP TYR MET LEU SER GLU LEU ARG ASP ILE ILE SER ARG SEQRES 16 A 203 ALA LYS SER LYS LYS PRO VAL LYS SEQRES 1 B 203 GLY PRO MET THR LEU PRO LYS MET GLU PRO SER SER HIS SEQRES 2 B 203 ALA PRO THR GLU PRO ASP ILE GLN LYS ASP LYS ASP ASP SEQRES 3 B 203 SER ILE ILE ARG GLU ASN GLU ASN ILE PRO ALA PRO LEU SEQRES 4 B 203 GLY THR VAL VAL GLN LEU LEU PHE GLY SER ASN THR GLU SEQRES 5 B 203 TYR MET GLN LYS VAL ILE THR ARG ASP LYS ASN ASN VAL SEQRES 6 B 203 ASN VAL GLU THR ILE PRO LYS PHE THR PRO SER LEU VAL SEQRES 7 B 203 GLU GLY GLY SER ARG HIS TYR GLU TYR THR LYS LYS LEU SEQRES 8 B 203 ASN ASN SER ILE GLY PRO LYS GLN THR LYS CYS LEU LEU SEQRES 9 B 203 THR GLU SER ILE GLU HIS MET ASP ILE ASN ASN TYR VAL SEQRES 10 B 203 LEU VAL THR GLN THR THR LYS THR PRO ASP VAL PRO SER SEQRES 11 B 203 GLY SER ASN PHE ALA VAL GLU SER LYS ILE PHE LEU PHE SEQRES 12 B 203 TRP GLY GLN HIS ASP THR THR ASN MET THR VAL ILE THR SEQRES 13 B 203 LYS ILE ASN TRP THR SER LYS SER PHE LEU LYS GLY ALA SEQRES 14 B 203 ILE GLU LYS GLY SER VAL GLU GLY GLN LYS VAL SER VAL SEQRES 15 B 203 ASP TYR MET LEU SER GLU LEU ARG ASP ILE ILE SER ARG SEQRES 16 B 203 ALA LYS SER LYS LYS PRO VAL LYS HET HC3 A 301 75 HET HC3 B 301 75 HETNAM HC3 25-HYDROXYCHOLESTEROL HETSYN HC3 (3BETA)-CHOLEST-5-ENE-3,25-DIOL FORMUL 3 HC3 2(C27 H46 O2) FORMUL 5 HOH *143(H2 O) HELIX 1 AA1 PRO A 38 GLY A 48 1 11 HELIX 2 AA2 THR A 51 ARG A 60 1 10 HELIX 3 AA3 LEU A 166 SER A 198 1 33 HELIX 4 AA4 PRO B 38 GLY B 48 1 11 HELIX 5 AA5 THR B 51 ASP B 61 1 11 HELIX 6 AA6 SER B 130 SER B 132 5 3 HELIX 7 AA7 GLN B 146 ASP B 148 5 3 HELIX 8 AA8 LEU B 166 ALA B 196 1 31 SHEET 1 AA1 7 SER A 27 ILE A 35 0 SHEET 2 AA1 7 THR A 150 TRP A 160 -1 O VAL A 154 N ILE A 29 SHEET 3 AA1 7 PHE A 134 TRP A 144 -1 N LYS A 139 O ILE A 155 SHEET 4 AA1 7 TYR A 116 LYS A 124 -1 N GLN A 121 O SER A 138 SHEET 5 AA1 7 GLN A 99 ASP A 112 -1 N SER A 107 O THR A 120 SHEET 6 AA1 7 SER A 82 LYS A 90 -1 N TYR A 87 O CYS A 102 SHEET 7 AA1 7 ASN A 64 VAL A 65 -1 N VAL A 65 O THR A 88 SHEET 1 AA2 7 SER B 27 ILE B 35 0 SHEET 2 AA2 7 THR B 150 TRP B 160 -1 O VAL B 154 N ILE B 29 SHEET 3 AA2 7 PHE B 134 TRP B 144 -1 N LYS B 139 O ILE B 155 SHEET 4 AA2 7 TYR B 116 LYS B 124 -1 N GLN B 121 O SER B 138 SHEET 5 AA2 7 GLN B 99 MET B 111 -1 N THR B 105 O THR B 122 SHEET 6 AA2 7 SER B 82 LYS B 90 -1 N TYR B 85 O LEU B 104 SHEET 7 AA2 7 ASN B 64 VAL B 65 -1 N VAL B 65 O THR B 88 CISPEP 1 GLU A 9 PRO A 10 0 -7.52 CISPEP 2 THR A 74 PRO A 75 0 2.56 CISPEP 3 GLU B 9 PRO B 10 0 -5.03 CISPEP 4 THR B 74 PRO B 75 0 4.29 SITE 1 AC1 8 ILE A 95 GLY A 96 GLN A 121 THR A 123 SITE 2 AC1 8 PRO A 129 GLY A 173 SER A 181 HOH A 426 SITE 1 AC2 10 LYS B 89 ILE B 95 GLN B 121 THR B 123 SITE 2 AC2 10 VAL B 128 GLY B 173 GLY B 177 SER B 181 SITE 3 AC2 10 HOH B 425 HOH B 427 CRYST1 38.179 47.301 55.996 111.21 101.63 100.33 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 0.026192 0.004772 0.008083 0.00000 SCALE2 0.000000 0.021489 0.009744 0.00000 SCALE3 0.000000 0.000000 0.020020 0.00000