HEADER TRANSPORT PROTEIN 29-SEP-19 6L1M TITLE STRUCTURE OF HUMAN STAR-RELATED LIPID TRANSFER PROTEIN 4 MUTANT - TITLE 2 LWNI107-110GG COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAR-RELATED LIPID TRANSFER PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: START DOMAIN-CONTAINING PROTEIN 4,STARD4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: STARD4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PHIS2-THR KEYWDS STARD4, LIPID TRANSPORT, STEROL, CHOLESTEROL, LIPID TRANSFER PROTEIN, KEYWDS 2 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.TONG,Y.J.IM REVDAT 3 22-NOV-23 6L1M 1 REMARK REVDAT 2 13-NOV-19 6L1M 1 JRNL REVDAT 1 30-OCT-19 6L1M 0 JRNL AUTH L.TAN,J.TONG,C.CHUN,Y.J.IM JRNL TITL STRUCTURAL ANALYSIS OF HUMAN STEROL TRANSFER PROTEIN STARD4. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 520 466 2019 JRNL REFN ESSN 1090-2104 JRNL PMID 31607485 JRNL DOI 10.1016/J.BBRC.2019.10.054 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19142 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) : 0.168 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 978 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 31.0200 - 3.2400 0.99 2759 142 0.1686 0.1567 REMARK 3 2 3.2400 - 2.5700 1.00 2637 131 0.1797 0.2168 REMARK 3 3 2.5700 - 2.2500 1.00 2603 137 0.1764 0.2278 REMARK 3 4 2.2500 - 2.0400 0.99 2570 130 0.1545 0.2020 REMARK 3 5 2.0400 - 1.9000 0.99 2574 133 0.1563 0.1792 REMARK 3 6 1.9000 - 1.7800 0.99 2513 153 0.1556 0.1954 REMARK 3 7 1.7800 - 1.7000 0.99 2508 152 0.1578 0.2048 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) : 0.129 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.557 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.95 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 : 0.005 1641 REMARK 3 ANGLE : 0.794 2226 REMARK 3 CHIRALITY : 0.056 241 REMARK 3 PLANARITY : 0.005 285 REMARK 3 DIHEDRAL : 17.262 974 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 6L1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-16 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 : 5C (4A) 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43200 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: 6L1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.0, 25% PEG 3350, 200 MM REMARK 280 NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K 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 21.45700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.89900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.67850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.89900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.45700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.67850 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 -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 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 37 15.02 -141.07 REMARK 500 LYS A 126 -129.31 53.54 REMARK 500 GLU A 140 97.06 -55.34 REMARK 500 GLN A 174 53.37 -149.46 REMARK 500 ARG A 178 161.41 68.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES 107-110 LWNI WERE MUTATED TO GG. DBREF 6L1M A 2 205 UNP Q96DR4 STAR4_HUMAN 2 205 SEQADV 6L1M GLY A -4 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M SER A -3 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M ALA A -2 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M MET A -1 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M GLY A 0 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M SER A 1 UNP Q96DR4 EXPRESSION TAG SEQADV 6L1M SER A 75 UNP Q96DR4 CYS 75 ENGINEERED MUTATION SEQADV 6L1M A UNP Q96DR4 LEU 107 SEE SEQUENCE DETAILS SEQADV 6L1M A UNP Q96DR4 TRP 108 SEE SEQUENCE DETAILS SEQADV 6L1M GLY A 107 UNP Q96DR4 ASN 109 SEE SEQUENCE DETAILS SEQADV 6L1M GLY A 108 UNP Q96DR4 ILE 110 SEE SEQUENCE DETAILS SEQRES 1 A 208 GLY SER ALA MET GLY SER GLU GLY LEU SER ASP VAL ALA SEQRES 2 A 208 SER PHE ALA THR LYS LEU LYS ASN THR LEU ILE GLN TYR SEQRES 3 A 208 HIS SER ILE GLU GLU ASP LYS TRP ARG VAL ALA LYS LYS SEQRES 4 A 208 THR LYS ASP VAL THR VAL TRP ARG LYS PRO SER GLU GLU SEQRES 5 A 208 PHE ASN GLY TYR LEU TYR LYS ALA GLN GLY VAL ILE ASP SEQRES 6 A 208 ASP LEU VAL TYR SER ILE ILE ASP HIS ILE ARG PRO GLY SEQRES 7 A 208 PRO SER ARG LEU ASP TRP ASP SER LEU MET THR SER LEU SEQRES 8 A 208 ASP ILE LEU GLU ASN PHE GLU GLU ASN CYS CYS VAL MET SEQRES 9 A 208 ARG TYR THR THR ALA GLY GLN GLY GLY ILE SER PRO ARG SEQRES 10 A 208 GLU PHE VAL ASP PHE SER TYR THR VAL GLY TYR LYS GLU SEQRES 11 A 208 GLY LEU LEU SER CYS GLY ILE SER LEU ASP TRP ASP GLU SEQRES 12 A 208 LYS ARG PRO GLU PHE VAL ARG GLY TYR ASN HIS PRO CYS SEQRES 13 A 208 GLY TRP PHE CYS VAL PRO LEU LYS ASP ASN PRO ASN GLN SEQRES 14 A 208 SER LEU LEU THR GLY TYR ILE GLN THR ASP LEU ARG GLY SEQRES 15 A 208 MET ILE PRO GLN SER ALA VAL ASP THR ALA MET ALA SER SEQRES 16 A 208 THR LEU THR ASN PHE TYR GLY ASP LEU ARG LYS ALA LEU FORMUL 2 HOH *146(H2 O) HELIX 1 AA1 ASP A 6 SER A 23 1 18 HELIX 2 AA2 ILE A 24 TRP A 29 5 6 HELIX 3 AA3 LEU A 62 ARG A 71 1 10 HELIX 4 AA4 GLY A 73 ASP A 80 1 8 HELIX 5 AA5 PRO A 182 LEU A 205 1 24 SHEET 1 AA1 9 ARG A 30 LYS A 34 0 SHEET 2 AA1 9 VAL A 38 PRO A 44 -1 O VAL A 40 N ALA A 32 SHEET 3 AA1 9 TYR A 51 ILE A 59 -1 O LYS A 54 N TRP A 41 SHEET 4 AA1 9 ASN A 163 ILE A 173 -1 O ILE A 173 N TYR A 53 SHEET 5 AA1 9 CYS A 153 LEU A 160 -1 N PHE A 156 O THR A 170 SHEET 6 AA1 9 GLY A 128 SER A 135 -1 N LEU A 129 O CYS A 157 SHEET 7 AA1 9 ARG A 114 TYR A 125 -1 N PHE A 119 O ILE A 134 SHEET 8 AA1 9 CYS A 96 THR A 103 -1 N CYS A 97 O SER A 120 SHEET 9 AA1 9 MET A 83 GLU A 93 -1 N ASP A 87 O ARG A 100 SHEET 1 AA2 8 ARG A 30 LYS A 34 0 SHEET 2 AA2 8 VAL A 38 PRO A 44 -1 O VAL A 40 N ALA A 32 SHEET 3 AA2 8 TYR A 51 ILE A 59 -1 O LYS A 54 N TRP A 41 SHEET 4 AA2 8 ASN A 163 ILE A 173 -1 O ILE A 173 N TYR A 53 SHEET 5 AA2 8 CYS A 153 LEU A 160 -1 N PHE A 156 O THR A 170 SHEET 6 AA2 8 GLY A 128 SER A 135 -1 N LEU A 129 O CYS A 157 SHEET 7 AA2 8 ARG A 114 TYR A 125 -1 N PHE A 119 O ILE A 134 SHEET 8 AA2 8 VAL A 146 ARG A 147 1 O VAL A 146 N GLU A 115 SHEET 1 AA3 2 TYR A 149 ASN A 150 0 SHEET 2 AA3 2 THR A 175 ASP A 176 -1 O ASP A 176 N TYR A 149 CRYST1 42.914 43.357 89.798 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 0.023302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011136 0.00000