HEADER PROTEIN BINDING 11-DEC-24 9KZN TITLE CRYSTAL STRUCTURE OF TOM1 IN COMPLEX WITH TOLLIP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-INTERACTING PROTEIN, TARGET OF MYB1 MEMBRANE COMPND 3 TRAFFICKING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOM1, TOLLIP, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.WANG,X.Y.GONG REVDAT 1 17-DEC-25 9KZN 0 JRNL AUTH Y.L.WANG,X.Y.GONG JRNL TITL TOLLIP TBD COORDINATES UNCANONICAL PARKIN-DEPENDENT JRNL TITL 2 MITOCHONDRIAL CLEARANCE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1186 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 24.5100 - 2.6900 1.00 2922 154 0.1650 0.1643 REMARK 3 2 2.6900 - 2.1400 1.00 2901 150 0.1747 0.1958 REMARK 3 3 2.1400 - 1.8700 1.00 2860 169 0.1891 0.1845 REMARK 3 4 1.8700 - 1.7000 1.00 2914 127 0.1774 0.2418 REMARK 3 5 1.7000 - 1.5700 1.00 2886 137 0.1833 0.2173 REMARK 3 6 1.5700 - 1.4800 1.00 2888 145 0.1713 0.2169 REMARK 3 7 1.4800 - 1.4100 1.00 2857 165 0.1902 0.2371 REMARK 3 8 1.4100 - 1.3500 1.00 2861 139 0.2314 0.2896 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.162 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.586 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.92 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 : 0.015 984 REMARK 3 ANGLE : 1.369 1330 REMARK 3 CHIRALITY : 0.085 155 REMARK 3 PLANARITY : 0.013 177 REMARK 3 DIHEDRAL : 15.917 394 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 9KZN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300052133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-23 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24279 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 43.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5; 28% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 29.73850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.60775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.86925 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 THR A 206 REMARK 465 PRO A 207 REMARK 465 THR A 208 REMARK 465 SER A 209 REMARK 465 GLY A 210 REMARK 465 SER A 211 REMARK 465 GLY A 212 REMARK 465 SER A 213 REMARK 465 GLY A 214 REMARK 465 GLU A 215 REMARK 465 GLN A 308 DBREF 9KZN A -1 308 PDB 9KZN 9KZN -1 308 SEQRES 1 A 129 GLY PRO MET ALA THR THR VAL SER THR GLN ARG GLY PRO SEQRES 2 A 129 VAL TYR ILE GLY GLU LEU PRO GLN ASP PHE LEU ARG ILE SEQRES 3 A 129 THR PRO THR SER GLY SER GLY SER GLY GLU GLN ILE GLY SEQRES 4 A 129 LYS LEU ARG SER GLU LEU GLU MET VAL SER GLY ASN VAL SEQRES 5 A 129 ARG VAL MET SER GLU MET LEU THR GLU LEU VAL PRO THR SEQRES 6 A 129 GLN ALA GLU PRO ALA ASP LEU GLU LEU LEU GLN GLU LEU SEQRES 7 A 129 ASN ARG THR CYS ARG ALA MET GLN GLN ARG VAL LEU GLU SEQRES 8 A 129 LEU ILE PRO GLN ILE ALA ASN GLU GLN LEU THR GLU GLU SEQRES 9 A 129 LEU LEU ILE VAL ASN ASP ASN LEU ASN ASN VAL PHE LEU SEQRES 10 A 129 ARG HIS GLU ARG PHE GLU ARG PHE ARG THR GLY GLN HET GOL A 401 14 HET GOL A 402 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *67(H2 O) HELIX 1 AA1 ILE A 217 LEU A 241 1 25 HELIX 2 AA2 GLU A 247 ILE A 272 1 26 HELIX 3 AA3 PRO A 273 ILE A 275 5 3 HELIX 4 AA4 ASN A 277 GLY A 307 1 31 SHEET 1 AA1 2 THR A 3 VAL A 5 0 SHEET 2 AA1 2 VAL A 12 ILE A 14 -1 O VAL A 12 N VAL A 5 CRYST1 43.271 43.271 59.477 90.00 90.00 90.00 P 43 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 0.023110 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016813 0.00000 CONECT 1928 1929 1930 1934 1935 CONECT 1929 1928 1936 CONECT 1930 1928 1931 1932 1937 CONECT 1931 1930 1938 CONECT 1932 1930 1933 1939 1940 CONECT 1933 1932 1941 CONECT 1934 1928 CONECT 1935 1928 CONECT 1936 1929 CONECT 1937 1930 CONECT 1938 1931 CONECT 1939 1932 CONECT 1940 1932 CONECT 1941 1933 CONECT 1942 1943 1944 1948 1949 CONECT 1943 1942 1950 CONECT 1944 1942 1945 1946 1951 CONECT 1945 1944 1952 CONECT 1946 1944 1947 1953 1954 CONECT 1947 1946 1955 CONECT 1948 1942 CONECT 1949 1942 CONECT 1950 1943 CONECT 1951 1944 CONECT 1952 1945 CONECT 1953 1946 CONECT 1954 1946 CONECT 1955 1947 MASTER 213 0 2 4 2 0 0 6 1026 1 28 10 END