HEADER TRANSPORT PROTEIN 05-MAY-16 5JQM TITLE CRYSTAL STRUCTURE OF PHOSPHATIDIC ACID TRANSPORTER UPS1/MDM35 VOID OF TITLE 2 BOUND PHOSPHOLIPID FROM SACCHAROMYCES CEREVISIAE AT 1.5 ANGSTROMS TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN UPS1, MITOCHONDRIAL,MITOCHONDRIAL DISTRIBUTION AND COMPND 3 MORPHOLOGY PROTEIN 35; COMPND 4 CHAIN: A, B, C; COMPND 5 SYNONYM: UNPROCESSED MGM1 PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: FUSION PROTEIN OF PROTEIN UPS1, MITOCHONDRIAL, COMPND 8 MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 35 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: UPS1, YLR193C, MDM35, YKL053C-A; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LIPID TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LU,K.C.CHAN,Y.ZHAI,J.FAN,F.SUN REVDAT 3 08-NOV-23 5JQM 1 REMARK REVDAT 2 02-SEP-20 5JQM 1 JRNL REVDAT 1 12-JUL-17 5JQM 0 JRNL AUTH J.LU,C.CHAN,L.YU,J.FAN,F.SUN,Y.ZHAI JRNL TITL MOLECULAR MECHANISM OF MITOCHONDRIAL PHOSPHATIDATE TRANSFER JRNL TITL 2 BY UPS1 JRNL REF COMMUN BIOL 2020 JRNL REFN ESSN 2399-3642 JRNL DOI 10.1038/S42003-020-01121-X REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 29.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 129411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 6414 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 29.5657 - 4.6550 0.90 3908 185 0.2080 0.2251 REMARK 3 2 4.6550 - 3.6971 0.97 4111 206 0.1740 0.1747 REMARK 3 3 3.6971 - 3.2304 1.00 4185 207 0.1680 0.2225 REMARK 3 4 3.2304 - 2.9353 1.00 4174 228 0.1844 0.2189 REMARK 3 5 2.9353 - 2.7251 1.00 4160 206 0.1792 0.2199 REMARK 3 6 2.7251 - 2.5645 1.00 4180 207 0.1766 0.2130 REMARK 3 7 2.5645 - 2.4362 1.00 4153 217 0.1799 0.2245 REMARK 3 8 2.4362 - 2.3302 1.00 4187 213 0.1617 0.2070 REMARK 3 9 2.3302 - 2.2405 1.00 4147 213 0.1514 0.1893 REMARK 3 10 2.2405 - 2.1632 1.00 4202 199 0.1471 0.1910 REMARK 3 11 2.1632 - 2.0956 1.00 4151 232 0.1430 0.1970 REMARK 3 12 2.0956 - 2.0357 1.00 4142 217 0.1312 0.1870 REMARK 3 13 2.0357 - 1.9821 1.00 4166 214 0.1303 0.1701 REMARK 3 14 1.9821 - 1.9338 1.00 4120 218 0.1361 0.1840 REMARK 3 15 1.9338 - 1.8898 1.00 4145 210 0.1341 0.1769 REMARK 3 16 1.8898 - 1.8496 1.00 4108 203 0.1312 0.1910 REMARK 3 17 1.8496 - 1.8126 1.00 4186 212 0.1293 0.1644 REMARK 3 18 1.8126 - 1.7784 1.00 4190 215 0.1337 0.1855 REMARK 3 19 1.7784 - 1.7466 1.00 4111 220 0.1351 0.2037 REMARK 3 20 1.7466 - 1.7170 1.00 4088 228 0.1358 0.1781 REMARK 3 21 1.7170 - 1.6893 1.00 4156 205 0.1436 0.1957 REMARK 3 22 1.6893 - 1.6634 1.00 4099 206 0.1398 0.2012 REMARK 3 23 1.6634 - 1.6389 0.99 4157 224 0.1320 0.1939 REMARK 3 24 1.6389 - 1.6158 0.99 4038 250 0.1405 0.2240 REMARK 3 25 1.6158 - 1.5940 0.99 4027 236 0.1434 0.1937 REMARK 3 26 1.5940 - 1.5733 0.98 4117 217 0.1432 0.2009 REMARK 3 27 1.5733 - 1.5536 0.98 4020 220 0.1516 0.2143 REMARK 3 28 1.5536 - 1.5349 0.98 4074 205 0.1647 0.2213 REMARK 3 29 1.5349 - 1.5171 0.94 3853 212 0.1776 0.2262 REMARK 3 30 1.5171 - 1.5000 0.87 3642 189 0.2045 0.2575 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) : 18.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.76 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 : 0.007 5744 REMARK 3 ANGLE : 1.059 7757 REMARK 3 CHIRALITY : 0.070 864 REMARK 3 PLANARITY : 0.006 970 REMARK 3 DIHEDRAL : 12.122 2092 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 5JQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 129446 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 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 (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 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: 5JQL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% TACSIMATE, PH5.0, 20% PEG 3350, REMARK 280 200MM SODIUM THIOCYANATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 59.28150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.28150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.14500 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 SER A -3 REMARK 465 GLN A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 REMARK 465 PHE A 133 REMARK 465 ASN A 134 REMARK 465 MET A 135 REMARK 465 ARG A 171 REMARK 465 ASN A 172 REMARK 465 PRO A 173 REMARK 465 GLN A 174 REMARK 465 PHE A 175 REMARK 465 LEU A 176 REMARK 465 GLU A 177 REMARK 465 VAL A 178 REMARK 465 LEU A 179 REMARK 465 PHE A 180 REMARK 465 GLN A 181 REMARK 465 GLY A 182 REMARK 465 PRO A 183 REMARK 465 MET A 184 REMARK 465 GLY A 185 REMARK 465 ASN A 186 REMARK 465 VAL A 221 REMARK 465 GLU A 222 REMARK 465 ASN A 223 REMARK 465 GLU A 224 REMARK 465 GLU A 259 REMARK 465 ASN A 260 REMARK 465 GLY A 261 REMARK 465 GLY A 262 REMARK 465 LYS A 263 REMARK 465 LEU A 264 REMARK 465 LYS A 265 REMARK 465 GLU A 266 REMARK 465 VAL A 267 REMARK 465 ASP A 268 REMARK 465 LYS A 269 REMARK 465 MET B -13 REMARK 465 GLY B -12 REMARK 465 SER B -11 REMARK 465 SER B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 SER B -3 REMARK 465 GLN B -2 REMARK 465 ASP B -1 REMARK 465 PRO B 0 REMARK 465 GLU B 169 REMARK 465 ALA B 170 REMARK 465 ARG B 171 REMARK 465 ASN B 172 REMARK 465 PRO B 173 REMARK 465 GLN B 174 REMARK 465 PHE B 175 REMARK 465 LEU B 176 REMARK 465 GLU B 177 REMARK 465 VAL B 178 REMARK 465 LEU B 179 REMARK 465 PHE B 180 REMARK 465 GLN B 181 REMARK 465 GLY B 182 REMARK 465 PRO B 183 REMARK 465 MET B 184 REMARK 465 GLY B 185 REMARK 465 ASN B 186 REMARK 465 ILE B 187 REMARK 465 MET B 188 REMARK 465 SER B 220 REMARK 465 VAL B 221 REMARK 465 GLU B 222 REMARK 465 ASN B 223 REMARK 465 ASN B 260 REMARK 465 GLY B 261 REMARK 465 GLY B 262 REMARK 465 LYS B 263 REMARK 465 LEU B 264 REMARK 465 LYS B 265 REMARK 465 GLU B 266 REMARK 465 VAL B 267 REMARK 465 ASP B 268 REMARK 465 LYS B 269 REMARK 465 MET C -13 REMARK 465 GLY C -12 REMARK 465 SER C -11 REMARK 465 SER C -10 REMARK 465 HIS C -9 REMARK 465 HIS C -8 REMARK 465 HIS C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 SER C -3 REMARK 465 GLN C -2 REMARK 465 ASP C -1 REMARK 465 PRO C 0 REMARK 465 GLY C 132 REMARK 465 PHE C 133 REMARK 465 ASN C 134 REMARK 465 MET C 135 REMARK 465 GLY C 136 REMARK 465 ALA C 170 REMARK 465 ARG C 171 REMARK 465 ASN C 172 REMARK 465 PRO C 173 REMARK 465 GLN C 174 REMARK 465 PHE C 175 REMARK 465 LEU C 176 REMARK 465 GLU C 177 REMARK 465 VAL C 178 REMARK 465 LEU C 179 REMARK 465 PHE C 180 REMARK 465 GLN C 181 REMARK 465 GLY C 182 REMARK 465 PRO C 183 REMARK 465 MET C 184 REMARK 465 GLY C 185 REMARK 465 ASN C 186 REMARK 465 GLU C 259 REMARK 465 ASN C 260 REMARK 465 GLY C 261 REMARK 465 GLY C 262 REMARK 465 LYS C 263 REMARK 465 LEU C 264 REMARK 465 LYS C 265 REMARK 465 GLU C 266 REMARK 465 VAL C 267 REMARK 465 ASP C 268 REMARK 465 LYS C 269 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 113 CG CD OE1 NE2 REMARK 470 LYS A 138 CG CD CE NZ REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 ILE A 187 CG1 CG2 CD1 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 GLN B 113 CG CD OE1 NE2 REMARK 470 ARG B 126 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 133 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN B 134 CG OD1 ND2 REMARK 470 MET B 135 CG SD CE REMARK 470 LYS B 138 CG CD CE NZ REMARK 470 GLN B 165 CG CD OE1 NE2 REMARK 470 LYS B 219 CG CD CE NZ REMARK 470 GLU B 224 CG CD OE1 OE2 REMARK 470 GLU B 259 CG CD OE1 OE2 REMARK 470 THR C 118 OG1 CG2 REMARK 470 GLU C 168 CG CD OE1 OE2 REMARK 470 GLU C 169 CG CD OE1 OE2 REMARK 470 ILE C 187 CG1 CG2 CD1 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 470 O HOH B 475 1.99 REMARK 500 O ILE B 73 O HOH B 301 2.08 REMARK 500 O HOH A 489 O HOH A 498 2.09 REMARK 500 O HOH C 495 O HOH C 504 2.12 REMARK 500 OD1 ASN C 223 O HOH C 301 2.12 REMARK 500 O HOH C 545 O HOH C 563 2.15 REMARK 500 O HOH A 463 O HOH C 379 2.16 REMARK 500 O HOH A 377 O HOH A 494 2.16 REMARK 500 O HOH C 540 O HOH C 548 2.18 REMARK 500 O HOH A 542 O HOH A 556 2.18 REMARK 500 OE2 GLU C 209 O HOH C 302 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 556 O HOH C 545 3555 2.00 REMARK 500 O PHE C 258 O HOH B 560 3455 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 92 CD - CE - NZ ANGL. DEV. = 13.9 DEGREES 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 LYS A 214 -56.33 -122.85 REMARK 500 PHE B 133 -79.83 -111.10 REMARK 500 LYS B 214 -58.20 -121.42 REMARK 500 LYS C 214 -57.66 -123.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 577 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 578 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 579 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B 558 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B 559 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH B 560 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B 561 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH C 571 DISTANCE = 6.23 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JQL RELATED DB: PDB REMARK 900 RELATED ID: 5JQO RELATED DB: PDB DBREF 5JQM A 1 175 UNP Q05776 UPS1_YEAST 1 175 DBREF 5JQM A 184 269 UNP O60200 MDM35_YEAST 1 86 DBREF 5JQM B 1 175 UNP Q05776 UPS1_YEAST 1 175 DBREF 5JQM B 184 269 UNP O60200 MDM35_YEAST 1 86 DBREF 5JQM C 1 175 UNP Q05776 UPS1_YEAST 1 175 DBREF 5JQM C 184 269 UNP O60200 MDM35_YEAST 1 86 SEQADV 5JQM MET A -13 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLY A -12 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER A -11 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER A -10 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -9 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -8 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -7 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -6 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -5 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS A -4 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER A -3 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLN A -2 UNP Q05776 EXPRESSION TAG SEQADV 5JQM ASP A -1 UNP Q05776 EXPRESSION TAG SEQADV 5JQM PRO A 0 UNP Q05776 EXPRESSION TAG SEQADV 5JQM LEU A 176 UNP Q05776 LINKER SEQADV 5JQM GLU A 177 UNP Q05776 LINKER SEQADV 5JQM VAL A 178 UNP Q05776 LINKER SEQADV 5JQM LEU A 179 UNP Q05776 LINKER SEQADV 5JQM PHE A 180 UNP Q05776 LINKER SEQADV 5JQM GLN A 181 UNP Q05776 LINKER SEQADV 5JQM GLY A 182 UNP Q05776 LINKER SEQADV 5JQM PRO A 183 UNP Q05776 LINKER SEQADV 5JQM MET B -13 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLY B -12 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER B -11 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER B -10 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -9 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -8 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -7 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -6 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -5 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS B -4 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER B -3 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLN B -2 UNP Q05776 EXPRESSION TAG SEQADV 5JQM ASP B -1 UNP Q05776 EXPRESSION TAG SEQADV 5JQM PRO B 0 UNP Q05776 EXPRESSION TAG SEQADV 5JQM LEU B 176 UNP Q05776 LINKER SEQADV 5JQM GLU B 177 UNP Q05776 LINKER SEQADV 5JQM VAL B 178 UNP Q05776 LINKER SEQADV 5JQM LEU B 179 UNP Q05776 LINKER SEQADV 5JQM PHE B 180 UNP Q05776 LINKER SEQADV 5JQM GLN B 181 UNP Q05776 LINKER SEQADV 5JQM GLY B 182 UNP Q05776 LINKER SEQADV 5JQM PRO B 183 UNP Q05776 LINKER SEQADV 5JQM MET C -13 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLY C -12 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER C -11 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER C -10 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -9 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -8 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -7 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -6 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -5 UNP Q05776 EXPRESSION TAG SEQADV 5JQM HIS C -4 UNP Q05776 EXPRESSION TAG SEQADV 5JQM SER C -3 UNP Q05776 EXPRESSION TAG SEQADV 5JQM GLN C -2 UNP Q05776 EXPRESSION TAG SEQADV 5JQM ASP C -1 UNP Q05776 EXPRESSION TAG SEQADV 5JQM PRO C 0 UNP Q05776 EXPRESSION TAG SEQADV 5JQM LEU C 176 UNP Q05776 LINKER SEQADV 5JQM GLU C 177 UNP Q05776 LINKER SEQADV 5JQM VAL C 178 UNP Q05776 LINKER SEQADV 5JQM LEU C 179 UNP Q05776 LINKER SEQADV 5JQM PHE C 180 UNP Q05776 LINKER SEQADV 5JQM GLN C 181 UNP Q05776 LINKER SEQADV 5JQM GLY C 182 UNP Q05776 LINKER SEQADV 5JQM PRO C 183 UNP Q05776 LINKER SEQRES 1 A 283 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 283 PRO MET VAL LEU LEU HIS LYS SER THR HIS ILE PHE PRO SEQRES 3 A 283 THR ASP PHE ALA SER VAL SER ARG ALA PHE PHE ASN ARG SEQRES 4 A 283 TYR PRO ASN PRO TYR SER PRO HIS VAL LEU SER ILE ASP SEQRES 5 A 283 THR ILE SER ARG ASN VAL ASP GLN GLU GLY ASN LEU ARG SEQRES 6 A 283 THR THR ARG LEU LEU LYS LYS SER GLY LYS LEU PRO THR SEQRES 7 A 283 TRP VAL LYS PRO PHE LEU ARG GLY ILE THR GLU THR TRP SEQRES 8 A 283 ILE ILE GLU VAL SER VAL VAL ASN PRO ALA ASN SER THR SEQRES 9 A 283 MET LYS THR TYR THR ARG ASN LEU ASP HIS THR GLY ILE SEQRES 10 A 283 MET LYS VAL GLU GLU TYR THR THR TYR GLN PHE ASP SER SEQRES 11 A 283 ALA THR SER SER THR ILE ALA ASP SER ARG VAL LYS PHE SEQRES 12 A 283 SER SER GLY PHE ASN MET GLY ILE LYS SER LYS VAL GLU SEQRES 13 A 283 ASP TRP SER ARG THR LYS PHE ASP GLU ASN VAL LYS LYS SEQRES 14 A 283 SER ARG MET GLY MET ALA PHE VAL ILE GLN LYS LEU GLU SEQRES 15 A 283 GLU ALA ARG ASN PRO GLN PHE LEU GLU VAL LEU PHE GLN SEQRES 16 A 283 GLY PRO MET GLY ASN ILE MET SER ALA SER PHE ALA PRO SEQRES 17 A 283 GLU CYS THR ASP LEU LYS THR LYS TYR ASP SER CYS PHE SEQRES 18 A 283 ASN GLU TRP TYR SER GLU LYS PHE LEU LYS GLY LYS SER SEQRES 19 A 283 VAL GLU ASN GLU CYS SER LYS GLN TRP TYR ALA TYR THR SEQRES 20 A 283 THR CYS VAL ASN ALA ALA LEU VAL LYS GLN GLY ILE LYS SEQRES 21 A 283 PRO ALA LEU ASP GLU ALA ARG GLU GLU ALA PRO PHE GLU SEQRES 22 A 283 ASN GLY GLY LYS LEU LYS GLU VAL ASP LYS SEQRES 1 B 283 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 B 283 PRO MET VAL LEU LEU HIS LYS SER THR HIS ILE PHE PRO SEQRES 3 B 283 THR ASP PHE ALA SER VAL SER ARG ALA PHE PHE ASN ARG SEQRES 4 B 283 TYR PRO ASN PRO TYR SER PRO HIS VAL LEU SER ILE ASP SEQRES 5 B 283 THR ILE SER ARG ASN VAL ASP GLN GLU GLY ASN LEU ARG SEQRES 6 B 283 THR THR ARG LEU LEU LYS LYS SER GLY LYS LEU PRO THR SEQRES 7 B 283 TRP VAL LYS PRO PHE LEU ARG GLY ILE THR GLU THR TRP SEQRES 8 B 283 ILE ILE GLU VAL SER VAL VAL ASN PRO ALA ASN SER THR SEQRES 9 B 283 MET LYS THR TYR THR ARG ASN LEU ASP HIS THR GLY ILE SEQRES 10 B 283 MET LYS VAL GLU GLU TYR THR THR TYR GLN PHE ASP SER SEQRES 11 B 283 ALA THR SER SER THR ILE ALA ASP SER ARG VAL LYS PHE SEQRES 12 B 283 SER SER GLY PHE ASN MET GLY ILE LYS SER LYS VAL GLU SEQRES 13 B 283 ASP TRP SER ARG THR LYS PHE ASP GLU ASN VAL LYS LYS SEQRES 14 B 283 SER ARG MET GLY MET ALA PHE VAL ILE GLN LYS LEU GLU SEQRES 15 B 283 GLU ALA ARG ASN PRO GLN PHE LEU GLU VAL LEU PHE GLN SEQRES 16 B 283 GLY PRO MET GLY ASN ILE MET SER ALA SER PHE ALA PRO SEQRES 17 B 283 GLU CYS THR ASP LEU LYS THR LYS TYR ASP SER CYS PHE SEQRES 18 B 283 ASN GLU TRP TYR SER GLU LYS PHE LEU LYS GLY LYS SER SEQRES 19 B 283 VAL GLU ASN GLU CYS SER LYS GLN TRP TYR ALA TYR THR SEQRES 20 B 283 THR CYS VAL ASN ALA ALA LEU VAL LYS GLN GLY ILE LYS SEQRES 21 B 283 PRO ALA LEU ASP GLU ALA ARG GLU GLU ALA PRO PHE GLU SEQRES 22 B 283 ASN GLY GLY LYS LEU LYS GLU VAL ASP LYS SEQRES 1 C 283 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 C 283 PRO MET VAL LEU LEU HIS LYS SER THR HIS ILE PHE PRO SEQRES 3 C 283 THR ASP PHE ALA SER VAL SER ARG ALA PHE PHE ASN ARG SEQRES 4 C 283 TYR PRO ASN PRO TYR SER PRO HIS VAL LEU SER ILE ASP SEQRES 5 C 283 THR ILE SER ARG ASN VAL ASP GLN GLU GLY ASN LEU ARG SEQRES 6 C 283 THR THR ARG LEU LEU LYS LYS SER GLY LYS LEU PRO THR SEQRES 7 C 283 TRP VAL LYS PRO PHE LEU ARG GLY ILE THR GLU THR TRP SEQRES 8 C 283 ILE ILE GLU VAL SER VAL VAL ASN PRO ALA ASN SER THR SEQRES 9 C 283 MET LYS THR TYR THR ARG ASN LEU ASP HIS THR GLY ILE SEQRES 10 C 283 MET LYS VAL GLU GLU TYR THR THR TYR GLN PHE ASP SER SEQRES 11 C 283 ALA THR SER SER THR ILE ALA ASP SER ARG VAL LYS PHE SEQRES 12 C 283 SER SER GLY PHE ASN MET GLY ILE LYS SER LYS VAL GLU SEQRES 13 C 283 ASP TRP SER ARG THR LYS PHE ASP GLU ASN VAL LYS LYS SEQRES 14 C 283 SER ARG MET GLY MET ALA PHE VAL ILE GLN LYS LEU GLU SEQRES 15 C 283 GLU ALA ARG ASN PRO GLN PHE LEU GLU VAL LEU PHE GLN SEQRES 16 C 283 GLY PRO MET GLY ASN ILE MET SER ALA SER PHE ALA PRO SEQRES 17 C 283 GLU CYS THR ASP LEU LYS THR LYS TYR ASP SER CYS PHE SEQRES 18 C 283 ASN GLU TRP TYR SER GLU LYS PHE LEU LYS GLY LYS SER SEQRES 19 C 283 VAL GLU ASN GLU CYS SER LYS GLN TRP TYR ALA TYR THR SEQRES 20 C 283 THR CYS VAL ASN ALA ALA LEU VAL LYS GLN GLY ILE LYS SEQRES 21 C 283 PRO ALA LEU ASP GLU ALA ARG GLU GLU ALA PRO PHE GLU SEQRES 22 C 283 ASN GLY GLY LYS LEU LYS GLU VAL ASP LYS FORMUL 4 HOH *811(H2 O) HELIX 1 AA1 ASP A 14 ASN A 24 1 11 HELIX 2 AA2 LYS A 67 ARG A 71 5 5 HELIX 3 AA3 SER A 116 SER A 119 5 4 HELIX 4 AA4 ILE A 137 GLU A 169 1 33 HELIX 5 AA5 ALA A 193 GLU A 195 5 3 HELIX 6 AA6 CYS A 196 LYS A 214 1 19 HELIX 7 AA7 SER A 226 LYS A 242 1 17 HELIX 8 AA8 ILE A 245 GLU A 255 1 11 HELIX 9 AA9 ASP B 14 ASN B 24 1 11 HELIX 10 AB1 LYS B 67 ARG B 71 5 5 HELIX 11 AB2 ILE B 137 GLU B 168 1 32 HELIX 12 AB3 ALA B 193 GLU B 195 5 3 HELIX 13 AB4 CYS B 196 LYS B 214 1 19 HELIX 14 AB5 CYS B 225 LYS B 242 1 18 HELIX 15 AB6 ILE B 245 GLU B 254 1 10 HELIX 16 AB7 ASP C 14 ASN C 24 1 11 HELIX 17 AB8 LYS C 67 ARG C 71 5 5 HELIX 18 AB9 LYS C 138 GLU C 169 1 32 HELIX 19 AC1 ALA C 193 GLU C 195 5 3 HELIX 20 AC2 CYS C 196 LYS C 214 1 19 HELIX 21 AC3 CYS C 225 LYS C 242 1 18 HELIX 22 AC4 ILE C 245 GLU C 255 1 11 SHEET 1 AA1 7 VAL A 2 PHE A 11 0 SHEET 2 AA1 7 SER A 120 SER A 131 -1 O SER A 125 N SER A 7 SHEET 3 AA1 7 MET A 104 ASP A 115 -1 N ASP A 115 O SER A 120 SHEET 4 AA1 7 THR A 90 ASN A 97 -1 N MET A 91 O TYR A 112 SHEET 5 AA1 7 ILE A 73 ASN A 85 -1 N VAL A 81 O TYR A 94 SHEET 6 AA1 7 LEU A 50 LYS A 61 -1 N ARG A 54 O GLU A 80 SHEET 7 AA1 7 VAL A 34 VAL A 44 -1 N ASN A 43 O ARG A 51 SHEET 1 AA2 7 VAL B 2 PHE B 11 0 SHEET 2 AA2 7 SER B 120 SER B 131 -1 O SER B 125 N SER B 7 SHEET 3 AA2 7 MET B 104 ASP B 115 -1 N ASP B 115 O SER B 120 SHEET 4 AA2 7 THR B 90 ASN B 97 -1 N MET B 91 O TYR B 112 SHEET 5 AA2 7 ILE B 73 ASN B 85 -1 N VAL B 81 O TYR B 94 SHEET 6 AA2 7 LEU B 50 LYS B 61 -1 N ARG B 54 O GLU B 80 SHEET 7 AA2 7 VAL B 34 VAL B 44 -1 N ASN B 43 O ARG B 51 SHEET 1 AA3 7 VAL C 2 PHE C 11 0 SHEET 2 AA3 7 SER C 120 SER C 130 -1 O SER C 125 N SER C 7 SHEET 3 AA3 7 LYS C 105 ASP C 115 -1 N ASP C 115 O SER C 120 SHEET 4 AA3 7 THR C 90 ASN C 97 -1 N MET C 91 O TYR C 112 SHEET 5 AA3 7 ILE C 73 ASN C 85 -1 N VAL C 81 O TYR C 94 SHEET 6 AA3 7 LEU C 50 LYS C 61 -1 N ARG C 54 O GLU C 80 SHEET 7 AA3 7 VAL C 34 VAL C 44 -1 N ASN C 43 O ARG C 51 SSBOND 1 CYS A 196 CYS A 235 1555 1555 2.06 SSBOND 2 CYS A 206 CYS A 225 1555 1555 2.04 SSBOND 3 CYS B 196 CYS B 235 1555 1555 2.06 SSBOND 4 CYS B 206 CYS B 225 1555 1555 2.05 SSBOND 5 CYS C 196 CYS C 235 1555 1555 2.06 SSBOND 6 CYS C 206 CYS C 225 1555 1555 2.04 CISPEP 1 TYR A 26 PRO A 27 0 -0.86 CISPEP 2 TYR B 26 PRO B 27 0 -1.55 CISPEP 3 TYR C 26 PRO C 27 0 -0.81 CRYST1 118.563 68.290 105.137 90.00 102.10 90.00 C 1 2 1 12 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 0.008434 0.000000 0.001808 0.00000 SCALE2 0.000000 0.014643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009727 0.00000