HEADER LIPID BINDING PROTEIN 24-NOV-20 7DKL TITLE CRYSTAL STRUCTURE OF THE TANDEM DEP DOMAINS OF DEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEP DOMAIN-CONTAINING MTOR-INTERACTING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEP DOMAIN-CONTAINING PROTEIN 6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DEPTOR, DEPDC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MTOR INHIBITOR, PA BINDING PROTEIN, DEP DOMAIN, ANIONIC LIPID BINDING KEYWDS 2 PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.F.WENG,X.X.SHEN,Y.F.LIU REVDAT 3 29-NOV-23 7DKL 1 REMARK REVDAT 2 22-JUN-22 7DKL 1 JRNL REVDAT 1 08-DEC-21 7DKL 0 JRNL AUTH Z.WENG,X.SHEN,J.ZHENG,H.LIANG,Y.LIU JRNL TITL STRUCTURAL BASIS OF DEPTOR TO RECOGNIZE PHOSPHATIDIC ACID JRNL TITL 2 USING ITS TANDEM DEP DOMAINS. JRNL REF J.MOL.BIOL. V. 433 66989 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 33865870 JRNL DOI 10.1016/J.JMB.2021.166989 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 36115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1844 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 25.8760 - 3.5233 0.99 2863 147 0.1773 0.2216 REMARK 3 2 3.5233 - 2.7976 1.00 2743 137 0.1977 0.2155 REMARK 3 3 2.7976 - 2.4443 0.99 2693 140 0.1922 0.2097 REMARK 3 4 2.4443 - 2.2209 0.99 2683 132 0.1776 0.2140 REMARK 3 5 2.2209 - 2.0618 0.98 2650 142 0.1737 0.1978 REMARK 3 6 2.0618 - 1.9403 0.98 2604 167 0.1722 0.2455 REMARK 3 7 1.9403 - 1.8431 0.98 2613 137 0.1725 0.2312 REMARK 3 8 1.8431 - 1.7629 0.98 2594 145 0.1654 0.2143 REMARK 3 9 1.7629 - 1.6951 0.98 2627 128 0.1485 0.1992 REMARK 3 10 1.6951 - 1.6366 0.98 2569 138 0.1514 0.2103 REMARK 3 11 1.6366 - 1.5854 0.97 2548 144 0.1471 0.2083 REMARK 3 12 1.5854 - 1.5401 0.96 2563 130 0.1575 0.2311 REMARK 3 13 1.5401 - 1.5000 0.96 2521 157 0.1599 0.2341 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.09 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 1802 REMARK 3 ANGLE : 0.777 2423 REMARK 3 CHIRALITY : 0.073 260 REMARK 3 PLANARITY : 0.004 317 REMARK 3 DIHEDRAL : 10.211 684 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 7DKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-19 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36176 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.65800 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: PHASER REMARK 200 STARTING MODEL: 1O7F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M AMMONIUM ACETATE, 24% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 19.79100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.54050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.79100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.54050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.79100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.79100 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 SER A 20 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 GLN A 23 CG CD OE1 NE2 REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 VAL A 159 CG1 CG2 REMARK 470 LYS A 160 CG CD CE NZ REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 224 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 LYS A 234 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 SER A 203 -52.06 76.76 REMARK 500 SER A 211 -176.40 -172.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DKL A 21 235 UNP Q8TB45 DPTOR_HUMAN 21 235 SEQADV 7DKL SER A 20 UNP Q8TB45 EXPRESSION TAG SEQADV 7DKL SER A 204 UNP Q8TB45 ASN 204 VARIANT SEQRES 1 A 216 SER GLY ALA GLN GLN ARG GLU LEU GLU ARG MET ALA GLU SEQRES 2 A 216 VAL LEU VAL THR GLY GLU GLN LEU ARG LEU ARG LEU HIS SEQRES 3 A 216 GLU GLU LYS VAL ILE LYS ASP ARG ARG HIS HIS LEU LYS SEQRES 4 A 216 THR TYR PRO ASN CYS PHE VAL ALA LYS GLU LEU ILE ASP SEQRES 5 A 216 TRP LEU ILE GLU HIS LYS GLU ALA SER ASP ARG GLU THR SEQRES 6 A 216 ALA ILE LYS LEU MET GLN LYS LEU ALA ASP ARG GLY ILE SEQRES 7 A 216 ILE HIS HIS VAL CYS ASP GLU HIS LYS GLU PHE LYS ASP SEQRES 8 A 216 VAL LYS LEU PHE TYR ARG PHE ARG LYS ASP ASP GLY THR SEQRES 9 A 216 PHE PRO LEU ASP ASN GLU VAL LYS ALA PHE MET ARG GLY SEQRES 10 A 216 GLN ARG LEU TYR GLU LYS LEU MET SER PRO GLU ASN THR SEQRES 11 A 216 LEU LEU GLN PRO ARG GLU GLU GLU GLY VAL LYS TYR GLU SEQRES 12 A 216 ARG THR PHE MET ALA SER GLU PHE LEU ASP TRP LEU VAL SEQRES 13 A 216 GLN GLU GLY GLU ALA THR THR ARG LYS GLU ALA GLU GLN SEQRES 14 A 216 LEU CYS HIS ARG LEU MET GLU HIS GLY ILE ILE GLN HIS SEQRES 15 A 216 VAL SER SER LYS HIS PRO PHE VAL ASP SER ASN LEU LEU SEQRES 16 A 216 TYR GLN PHE ARG MET ASN PHE ARG ARG ARG ARG ARG LEU SEQRES 17 A 216 MET GLU LEU LEU ASN GLU LYS SER FORMUL 2 HOH *99(H2 O) HELIX 1 AA1 GLY A 21 GLU A 47 1 27 HELIX 2 AA2 ALA A 66 HIS A 76 1 11 HELIX 3 AA3 ASP A 81 ARG A 95 1 15 HELIX 4 AA4 LYS A 119 GLY A 122 5 4 HELIX 5 AA5 ASP A 127 MET A 144 1 18 HELIX 6 AA6 ALA A 167 GLU A 177 1 11 HELIX 7 AA7 THR A 182 HIS A 196 1 15 HELIX 8 AA8 ARG A 226 ASN A 232 5 7 SHEET 1 AA1 4 LYS A 51 HIS A 55 0 SHEET 2 AA1 4 LYS A 58 VAL A 65 -1 O TYR A 60 N ARG A 53 SHEET 3 AA1 4 PHE A 114 PHE A 117 -1 O TYR A 115 N PHE A 64 SHEET 4 AA1 4 ILE A 98 HIS A 100 -1 N HIS A 99 O ARG A 116 SHEET 1 AA2 4 GLN A 152 GLU A 156 0 SHEET 2 AA2 4 VAL A 159 MET A 166 -1 O TYR A 161 N ARG A 154 SHEET 3 AA2 4 LEU A 214 PHE A 217 -1 O TYR A 215 N PHE A 165 SHEET 4 AA2 4 ILE A 199 HIS A 201 -1 N GLN A 200 O GLN A 216 CRYST1 39.582 63.582 89.081 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 0.025264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011226 0.00000