HEADER ENDOCYTOSIS 03-JAN-18 5Z2N TITLE STRUCTURE OF ORP1L N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXYSTEROL-BINDING PROTEIN-RELATED PROTEIN 1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: OSBP-RELATED PROTEIN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: OSBPL1A, ORP1, ORP1A, ORP1L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS GTPASE, EFFECTOR, COMPLEX, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR X.L.MA,K.LIU,J.LI,H.H.LI,J.LI,C.L.YANG,H.H.LIANG REVDAT 3 22-NOV-23 5Z2N 1 REMARK REVDAT 2 19-SEP-18 5Z2N 1 JRNL REVDAT 1 08-AUG-18 5Z2N 0 JRNL AUTH X.MA,K.LIU,J.LI,H.LI,J.LI,Y.LIU,C.YANG,H.LIANG JRNL TITL A NON-CANONICAL GTPASE INTERACTION ENABLES ORP1L-RAB7-RILP JRNL TITL 2 COMPLEX FORMATION AND LATE ENDOSOME POSITIONING. JRNL REF J. BIOL. CHEM. V. 293 14155 2018 JRNL REFN ESSN 1083-351X JRNL PMID 30012887 JRNL DOI 10.1074/JBC.RA118.001854 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 28304 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1417 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 46.2869 - 4.6101 0.94 2716 147 0.1893 0.1646 REMARK 3 2 4.6101 - 3.6596 0.92 2644 137 0.2000 0.1872 REMARK 3 3 3.6596 - 3.1972 0.95 2696 141 0.2426 0.2594 REMARK 3 4 3.1972 - 2.9049 0.94 2716 143 0.2728 0.3275 REMARK 3 5 2.9049 - 2.6967 0.96 2707 141 0.2822 0.2915 REMARK 3 6 2.6967 - 2.5377 0.96 2736 143 0.2889 0.3222 REMARK 3 7 2.5377 - 2.4106 0.96 2779 149 0.2987 0.3178 REMARK 3 8 2.4106 - 2.3057 0.96 2713 140 0.3093 0.3487 REMARK 3 9 2.3057 - 2.2169 0.95 2780 150 0.3690 0.4314 REMARK 3 10 2.2169 - 2.1404 0.85 2400 126 0.3989 0.4405 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.940 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 2108 REMARK 3 ANGLE : 0.743 2837 REMARK 3 CHIRALITY : 0.046 325 REMARK 3 PLANARITY : 0.004 371 REMARK 3 DIHEDRAL : 17.098 791 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5Z2N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28304 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 46.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.230 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: 4K5B REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 0.1 M BIS-TRIS PH 6.5, 25% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.09650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.03050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.09650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.03050 REMARK 290 SMTRY3 4 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 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 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 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 LYS A 44 REMARK 465 SER A 45 REMARK 465 ASN A 46 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 O HOH B 214 O HOH B 224 1.94 REMARK 500 O HOH B 228 O HOH B 230 1.98 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 TYR A 103 30.07 -98.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z2N A 1 136 UNP Q91XL9 OSBL1_MOUSE 1 136 DBREF 5Z2N B 1 136 UNP Q91XL9 OSBL1_MOUSE 1 136 SEQRES 1 B 136 MET ASN THR GLU ALA GLU GLN GLN LEU LEU HIS HIS ALA SEQRES 2 B 136 ARG ASN GLY ASN ALA GLU GLU VAL ARG LYS LEU LEU ALA SEQRES 3 B 136 ALA MET ALA ARG MET GLU VAL VAL ALA ASP ILE ASP CYS SEQRES 4 B 136 LYS GLY ARG SER LYS SER ASN LEU GLY TRP THR PRO LEU SEQRES 5 B 136 HIS LEU ALA CYS TYR PHE GLY HIS LYS GLN VAL VAL GLU SEQRES 6 B 136 ASP LEU LEU LYS ALA GLY ALA LYS VAL ASN MET LEU ASN SEQRES 7 B 136 ASP MET GLY ASP THR PRO LEU HIS ARG ALA ALA PHE THR SEQRES 8 B 136 GLY ARG LYS GLU LEU VAL LEU LEU LEU LEU GLU TYR ASP SEQRES 9 B 136 ALA ASP SER THR VAL VAL ASN GLY SER GLY GLN THR ALA SEQRES 10 B 136 LYS GLU ALA THR HIS ASP LYS GLU ILE ARG ASN MET LEU SEQRES 11 B 136 GLU ALA VAL GLU ARG THR SEQRES 1 A 136 MET ASN THR GLU ALA GLU GLN GLN LEU LEU HIS HIS ALA SEQRES 2 A 136 ARG ASN GLY ASN ALA GLU GLU VAL ARG LYS LEU LEU ALA SEQRES 3 A 136 ALA MET ALA ARG MET GLU VAL VAL ALA ASP ILE ASP CYS SEQRES 4 A 136 LYS GLY ARG SER LYS SER ASN LEU GLY TRP THR PRO LEU SEQRES 5 A 136 HIS LEU ALA CYS TYR PHE GLY HIS LYS GLN VAL VAL GLU SEQRES 6 A 136 ASP LEU LEU LYS ALA GLY ALA LYS VAL ASN MET LEU ASN SEQRES 7 A 136 ASP MET GLY ASP THR PRO LEU HIS ARG ALA ALA PHE THR SEQRES 8 A 136 GLY ARG LYS GLU LEU VAL LEU LEU LEU LEU GLU TYR ASP SEQRES 9 A 136 ALA ASP SER THR VAL VAL ASN GLY SER GLY GLN THR ALA SEQRES 10 A 136 LYS GLU ALA THR HIS ASP LYS GLU ILE ARG ASN MET LEU SEQRES 11 A 136 GLU ALA VAL GLU ARG THR FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 THR B 3 GLY B 16 1 14 HELIX 2 AA2 ASN B 17 ARG B 30 1 14 HELIX 3 AA3 THR B 50 GLY B 59 1 10 HELIX 4 AA4 HIS B 60 ALA B 70 1 11 HELIX 5 AA5 THR B 83 THR B 91 1 9 HELIX 6 AA6 ARG B 93 TYR B 103 1 11 HELIX 7 AA7 THR B 116 THR B 121 1 6 HELIX 8 AA8 ASP B 123 THR B 136 1 14 HELIX 9 AA9 THR A 3 GLY A 16 1 14 HELIX 10 AB1 ASN A 17 ARG A 30 1 14 HELIX 11 AB2 THR A 50 PHE A 58 1 9 HELIX 12 AB3 HIS A 60 ALA A 70 1 11 HELIX 13 AB4 THR A 83 THR A 91 1 9 HELIX 14 AB5 ARG A 93 TYR A 103 1 11 HELIX 15 AB6 THR A 116 THR A 121 1 6 HELIX 16 AB7 ASP A 123 THR A 136 1 14 CRYST1 122.193 30.061 95.055 90.00 126.06 90.00 C 1 2 1 8 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 0.008184 0.000000 0.005959 0.00000 SCALE2 0.000000 0.033266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013014 0.00000