HEADER LIPID BINDING PROTEIN 31-MAY-15 5BRL TITLE CRYSTAL STRUCTURE OF L124D STARD4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAR-RELATED LIPID TRANSFER PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 13-222; COMPND 5 SYNONYM: START DOMAIN-CONTAINING PROTEIN 4,STARD4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: STARD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS LIPID BINDING PROTEIN, ALPHA HELIX GRIP EXPDTA X-RAY DIFFRACTION AUTHOR D.B.IAEA,I.DIKIY,I.KIBURU,D.E.ELIEZER,F.R.MAXFIELD REVDAT 6 27-SEP-23 5BRL 1 REMARK REVDAT 5 25-DEC-19 5BRL 1 REMARK REVDAT 4 27-SEP-17 5BRL 1 JRNL REMARK REVDAT 3 12-AUG-15 5BRL 1 JRNL REVDAT 2 29-JUL-15 5BRL 1 JRNL REVDAT 1 22-JUL-15 5BRL 0 JRNL AUTH D.B.IAEA,I.DIKIY,I.KIBURU,D.ELIEZER,F.R.MAXFIELD JRNL TITL STARD4 MEMBRANE INTERACTIONS AND STEROL BINDING. JRNL REF BIOCHEMISTRY V. 54 4623 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26168008 JRNL DOI 10.1021/ACS.BIOCHEM.5B00618 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 26066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1332 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 39.4337 - 4.3127 0.72 2289 143 0.1862 0.1873 REMARK 3 2 4.3127 - 3.4238 0.76 2368 128 0.1708 0.2181 REMARK 3 3 3.4238 - 2.9911 0.79 2440 114 0.1862 0.2179 REMARK 3 4 2.9911 - 2.7177 0.79 2476 116 0.2058 0.2810 REMARK 3 5 2.7177 - 2.5230 0.82 2486 137 0.2009 0.2318 REMARK 3 6 2.5230 - 2.3742 0.82 2498 148 0.2067 0.2542 REMARK 3 7 2.3742 - 2.2554 0.84 2526 141 0.1911 0.2521 REMARK 3 8 2.2554 - 2.1572 0.83 2551 138 0.1812 0.2531 REMARK 3 9 2.1572 - 2.0741 0.84 2562 128 0.1822 0.2047 REMARK 3 10 2.0741 - 2.0026 0.83 2538 139 0.1874 0.2483 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.54 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 : 0.007 3466 REMARK 3 ANGLE : 1.050 4702 REMARK 3 CHIRALITY : 0.044 512 REMARK 3 PLANARITY : 0.005 602 REMARK 3 DIHEDRAL : 14.225 1280 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 5BRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 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 : 26090 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 80.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 1JSS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.2, 2.2 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.84150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A 124 58.87 29.99 REMARK 500 GLU A 142 -119.25 47.04 REMARK 500 TRP A 154 71.27 -161.89 REMARK 500 ASP A 178 -1.73 70.48 REMARK 500 GLN A 190 44.85 -143.03 REMARK 500 ARG A 194 -173.73 59.56 REMARK 500 LEU B 123 70.74 52.02 REMARK 500 ASP B 124 43.18 38.17 REMARK 500 GLU B 142 -123.21 45.24 REMARK 500 GLN B 190 45.66 -147.90 REMARK 500 ARG B 194 -172.14 60.20 REMARK 500 REMARK 500 REMARK: NULL DBREF 5BRL A 13 222 UNP Q99JV5 STAR4_MOUSE 13 222 DBREF 5BRL B 13 222 UNP Q99JV5 STAR4_MOUSE 13 222 SEQADV 5BRL ASP A 124 UNP Q99JV5 LEU 124 ENGINEERED MUTATION SEQADV 5BRL ASP B 124 UNP Q99JV5 LEU 124 ENGINEERED MUTATION SEQRES 1 A 210 ARG LYS ILE LYS LEU GLU GLY LEU SER ASP VAL ALA SER SEQRES 2 A 210 ILE SER THR LYS LEU GLN ASN THR LEU ILE GLN TYR HIS SEQRES 3 A 210 SER ILE LYS GLU ASP GLU TRP ARG VAL ALA LYS LYS VAL SEQRES 4 A 210 LYS ASP VAL THR VAL TRP ARG LYS PRO SER GLU GLU PHE SEQRES 5 A 210 ASN GLY TYR LEU TYR LYS ALA GLN GLY VAL MET ASP ASP SEQRES 6 A 210 VAL VAL ASN ASN VAL ILE ASP HIS ILE ARG PRO GLY PRO SEQRES 7 A 210 TRP ARG LEU ASP TRP ASP ARG LEU MET THR SER LEU ASP SEQRES 8 A 210 VAL LEU GLU HIS PHE GLU GLU ASN CYS CYS VAL MET ARG SEQRES 9 A 210 TYR THR THR ALA GLY GLN LEU ASP ASN ILE ILE SER PRO SEQRES 10 A 210 ARG GLU PHE VAL ASP PHE SER TYR THR VAL GLY TYR GLU SEQRES 11 A 210 GLU GLY LEU LEU SER CYS GLY VAL SER VAL GLU TRP SER SEQRES 12 A 210 GLU THR ARG PRO GLU PHE VAL ARG GLY TYR ASN HIS PRO SEQRES 13 A 210 CYS GLY TRP PHE CYS VAL PRO LEU LYS ASP SER PRO SER SEQRES 14 A 210 GLN SER LEU LEU THR GLY TYR ILE GLN THR ASP LEU ARG SEQRES 15 A 210 GLY MET ILE PRO GLN SER ALA VAL ASP THR ALA MET ALA SEQRES 16 A 210 SER THR LEU ALA ASN PHE TYR SER ASP LEU ARG LYS GLY SEQRES 17 A 210 LEU ARG SEQRES 1 B 210 ARG LYS ILE LYS LEU GLU GLY LEU SER ASP VAL ALA SER SEQRES 2 B 210 ILE SER THR LYS LEU GLN ASN THR LEU ILE GLN TYR HIS SEQRES 3 B 210 SER ILE LYS GLU ASP GLU TRP ARG VAL ALA LYS LYS VAL SEQRES 4 B 210 LYS ASP VAL THR VAL TRP ARG LYS PRO SER GLU GLU PHE SEQRES 5 B 210 ASN GLY TYR LEU TYR LYS ALA GLN GLY VAL MET ASP ASP SEQRES 6 B 210 VAL VAL ASN ASN VAL ILE ASP HIS ILE ARG PRO GLY PRO SEQRES 7 B 210 TRP ARG LEU ASP TRP ASP ARG LEU MET THR SER LEU ASP SEQRES 8 B 210 VAL LEU GLU HIS PHE GLU GLU ASN CYS CYS VAL MET ARG SEQRES 9 B 210 TYR THR THR ALA GLY GLN LEU ASP ASN ILE ILE SER PRO SEQRES 10 B 210 ARG GLU PHE VAL ASP PHE SER TYR THR VAL GLY TYR GLU SEQRES 11 B 210 GLU GLY LEU LEU SER CYS GLY VAL SER VAL GLU TRP SER SEQRES 12 B 210 GLU THR ARG PRO GLU PHE VAL ARG GLY TYR ASN HIS PRO SEQRES 13 B 210 CYS GLY TRP PHE CYS VAL PRO LEU LYS ASP SER PRO SER SEQRES 14 B 210 GLN SER LEU LEU THR GLY TYR ILE GLN THR ASP LEU ARG SEQRES 15 B 210 GLY MET ILE PRO GLN SER ALA VAL ASP THR ALA MET ALA SEQRES 16 B 210 SER THR LEU ALA ASN PHE TYR SER ASP LEU ARG LYS GLY SEQRES 17 B 210 LEU ARG FORMUL 3 HOH *193(H2 O) HELIX 1 AA1 GLY A 19 SER A 39 1 21 HELIX 2 AA2 ILE A 40 TRP A 45 5 6 HELIX 3 AA3 VAL A 78 ARG A 87 1 10 HELIX 4 AA4 GLY A 89 ASP A 96 1 8 HELIX 5 AA5 PRO A 198 ARG A 222 1 25 HELIX 6 AA6 GLY B 19 ILE B 40 1 22 HELIX 7 AA7 LYS B 41 TRP B 45 5 5 HELIX 8 AA8 VAL B 78 ARG B 87 1 10 HELIX 9 AA9 GLY B 89 ASP B 96 1 8 HELIX 10 AB1 PRO B 198 LEU B 221 1 24 SHEET 1 AA1 9 ARG A 46 LYS A 50 0 SHEET 2 AA1 9 THR A 55 PRO A 60 -1 O VAL A 56 N LYS A 49 SHEET 3 AA1 9 TYR A 67 MET A 75 -1 O LYS A 70 N TRP A 57 SHEET 4 AA1 9 SER A 179 ILE A 189 -1 O ILE A 189 N TYR A 69 SHEET 5 AA1 9 CYS A 169 LEU A 176 -1 N PHE A 172 O THR A 186 SHEET 6 AA1 9 GLY A 144 SER A 151 -1 N LEU A 145 O CYS A 173 SHEET 7 AA1 9 GLU A 131 TYR A 141 -1 N PHE A 135 O VAL A 150 SHEET 8 AA1 9 CYS A 112 THR A 119 -1 N CYS A 113 O SER A 136 SHEET 9 AA1 9 MET A 99 GLU A 109 -1 N LEU A 105 O VAL A 114 SHEET 1 AA2 2 TYR A 165 ASN A 166 0 SHEET 2 AA2 2 THR A 191 ASP A 192 -1 O ASP A 192 N TYR A 165 SHEET 1 AA3 9 ARG B 46 LYS B 50 0 SHEET 2 AA3 9 THR B 55 PRO B 60 -1 O VAL B 56 N ALA B 48 SHEET 3 AA3 9 TYR B 67 MET B 75 -1 O LYS B 70 N TRP B 57 SHEET 4 AA3 9 SER B 179 ILE B 189 -1 O ILE B 189 N TYR B 69 SHEET 5 AA3 9 CYS B 169 LEU B 176 -1 N PHE B 172 O THR B 186 SHEET 6 AA3 9 GLY B 144 SER B 151 -1 N GLY B 149 O CYS B 169 SHEET 7 AA3 9 ARG B 130 TYR B 141 -1 N TYR B 141 O GLY B 144 SHEET 8 AA3 9 CYS B 112 THR B 119 -1 N CYS B 113 O SER B 136 SHEET 9 AA3 9 MET B 99 GLU B 109 -1 N ASP B 103 O ARG B 116 SHEET 1 AA4 2 TYR B 165 ASN B 166 0 SHEET 2 AA4 2 THR B 191 ASP B 192 -1 O ASP B 192 N TYR B 165 CRYST1 47.379 41.683 121.464 90.00 90.02 90.00 P 1 21 1 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 0.021106 0.000000 0.000007 0.00000 SCALE2 0.000000 0.023991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008233 0.00000