HEADER TRANSPORT PROTEIN 02-AUG-12 4GF4 TITLE LOW PH STRUCTURE OF PSEUDOMONAS PUTIDA OPRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORIN B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-447; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 931281; SOURCE 4 STRAIN: PSEUDOMONAS PUTIDA F1; SOURCE 5 GENE: PPUBIRD1_1069; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS BETA-BARREL TRANSPORT OUTER MEMBRANE CHANNEL, BETA-BARREL, KEYWDS 2 CARBOHYDRATE TRANSPORT, BACTERIAL OUTER MEMBRANE, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.VAN DEN BERG REVDAT 4 15-NOV-17 4GF4 1 REMARK REVDAT 3 02-JAN-13 4GF4 1 JRNL REVDAT 2 07-NOV-12 4GF4 1 JRNL REVDAT 1 24-OCT-12 4GF4 0 JRNL AUTH B.VAN DEN BERG JRNL TITL STRUCTURAL BASIS FOR OUTER MEMBRANE SUGAR UPTAKE IN JRNL TITL 2 PSEUDOMONADS. JRNL REF J.BIOL.CHEM. V. 287 41044 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 23066028 JRNL DOI 10.1074/JBC.M112.408518 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 22812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1157 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 19.7656 - 7.6684 0.99 1275 146 0.2347 0.2601 REMARK 3 2 7.6684 - 6.1468 1.00 1305 148 0.2377 0.2959 REMARK 3 3 6.1468 - 5.3878 1.00 1290 145 0.2100 0.2704 REMARK 3 4 5.3878 - 4.9034 1.00 1296 147 0.1911 0.2215 REMARK 3 5 4.9034 - 4.5566 1.00 1270 148 0.1589 0.2037 REMARK 3 6 4.5566 - 4.2908 1.00 1311 144 0.1670 0.2251 REMARK 3 7 4.2908 - 4.0779 1.00 1292 142 0.1886 0.2643 REMARK 3 8 4.0779 - 3.9018 1.00 1285 146 0.2213 0.3061 REMARK 3 9 3.9018 - 3.7527 1.00 1287 147 0.2100 0.2554 REMARK 3 10 3.7527 - 3.6240 1.00 1302 143 0.2231 0.3152 REMARK 3 11 3.6240 - 3.5113 1.00 1282 141 0.2041 0.3094 REMARK 3 12 3.5113 - 3.4115 0.99 1274 141 0.2516 0.2954 REMARK 3 13 3.4115 - 3.3221 1.00 1269 142 0.2411 0.3035 REMARK 3 14 3.3221 - 3.2414 1.00 1322 146 0.2528 0.3513 REMARK 3 15 3.2414 - 3.1680 1.00 1297 137 0.2888 0.3193 REMARK 3 16 3.1680 - 3.1008 0.91 1160 132 0.3483 0.4254 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.330 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 : 0.010 2447 REMARK 3 ANGLE : 1.466 3287 REMARK 3 CHIRALITY : 0.105 335 REMARK 3 PLANARITY : 0.006 414 REMARK 3 DIHEDRAL : 21.074 853 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -3.5832 27.6539 91.5865 REMARK 3 T TENSOR REMARK 3 T11: 0.1166 T22: 0.1184 REMARK 3 T33: 0.1262 T12: 0.0267 REMARK 3 T13: -0.0068 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.8909 L22: 1.1927 REMARK 3 L33: 0.9245 L12: 0.0169 REMARK 3 L13: 0.1314 L23: 0.4590 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: 0.1505 S13: -0.2281 REMARK 3 S21: -0.0733 S22: -0.0167 S23: -0.0806 REMARK 3 S31: -0.0351 S32: 0.0491 S33: 0.0023 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 4GF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22871 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11700 REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.81300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 63.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM-CITRATE, 0.2 M SODIUM REMARK 280 FORMATE, 35-40% PEG 400 , PH 4.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.51850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.29600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 67.79050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.51850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.29600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.79050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.51850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.29600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.79050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.51850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.29600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.79050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA A -14 REMARK 465 ASN A -13 REMARK 465 VAL A -12 REMARK 465 ARG A -11 REMARK 465 LEU A -10 REMARK 465 GLN 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 HIS A -3 REMARK 465 HIS A -2 REMARK 465 LEU A -1 REMARK 465 GLU A 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 42 REMARK 465 GLY A 43 REMARK 465 GLY A 44 REMARK 465 TYR A 45 REMARK 465 ASN A 46 REMARK 465 ILE A 93 REMARK 465 SER A 94 REMARK 465 ASP A 95 REMARK 465 PRO A 96 REMARK 465 ARG A 97 REMARK 465 ALA A 98 REMARK 465 GLY A 99 REMARK 465 GLN A 100 REMARK 465 PHE A 146 REMARK 465 PRO A 147 REMARK 465 CYS A 148 REMARK 465 ASP A 149 REMARK 465 PHE A 150 REMARK 465 GLN A 151 REMARK 465 ASN A 152 REMARK 465 LEU A 153 REMARK 465 ALA A 154 REMARK 465 PHE A 155 REMARK 465 CYS A 156 REMARK 465 GLY A 157 REMARK 465 SER A 158 REMARK 465 GLN A 159 REMARK 465 VAL A 160 REMARK 465 GLY A 161 REMARK 465 ASN A 162 REMARK 465 TRP A 163 REMARK 465 VAL A 164 REMARK 465 GLY A 165 REMARK 465 GLY A 166 REMARK 465 ILE A 167 REMARK 465 TRP A 168 REMARK 465 TYR A 169 REMARK 465 ASN A 198 REMARK 465 PRO A 199 REMARK 465 SER A 200 REMARK 465 ASN A 201 REMARK 465 LEU A 202 REMARK 465 GLU A 203 REMARK 465 THR A 204 REMARK 465 GLY A 205 REMARK 465 ASN A 206 REMARK 465 GLY A 207 REMARK 465 PHE A 208 REMARK 465 LYS A 209 REMARK 465 LEU A 210 REMARK 465 SER A 211 REMARK 465 GLY A 212 REMARK 465 SER A 213 REMARK 465 GLY A 214 REMARK 465 ALA A 246 REMARK 465 LYS A 247 REMARK 465 ALA A 248 REMARK 465 ASP A 249 REMARK 465 ASP A 250 REMARK 465 VAL A 251 REMARK 465 TYR A 252 REMARK 465 ASP A 253 REMARK 465 ASP A 254 REMARK 465 VAL A 255 REMARK 465 ASN A 256 REMARK 465 GLY A 257 REMARK 465 ASN A 258 REMARK 465 PRO A 259 REMARK 465 GLN A 260 REMARK 465 ALA A 261 REMARK 465 LEU A 262 REMARK 465 THR A 263 REMARK 465 GLY A 264 REMARK 465 GLU A 265 REMARK 465 ALA A 266 REMARK 465 PHE A 267 REMARK 465 LYS A 268 REMARK 465 SER A 269 REMARK 465 HIS A 270 REMARK 465 SER A 271 REMARK 465 ALA A 307 REMARK 465 THR A 308 REMARK 465 ASN A 309 REMARK 465 VAL A 310 REMARK 465 ASP A 344 REMARK 465 ASP A 345 REMARK 465 VAL A 346 REMARK 465 LYS A 347 REMARK 465 LYS A 348 REMARK 465 ARG A 349 REMARK 465 ALA A 350 REMARK 465 GLU A 351 REMARK 465 LEU A 352 REMARK 465 LEU A 353 REMARK 465 ASN A 354 REMARK 465 ALA A 355 REMARK 465 GLN A 356 REMARK 465 SER A 357 REMARK 465 GLY A 358 REMARK 465 ILE A 359 REMARK 465 ASN A 360 REMARK 465 ASP A 361 REMARK 465 TYR A 362 REMARK 465 ASP A 363 REMARK 465 ASN A 364 REMARK 465 PRO A 365 REMARK 465 GLY A 366 REMARK 465 PHE A 367 REMARK 465 VAL A 368 REMARK 465 PRO A 369 REMARK 465 LEU A 370 REMARK 465 PRO A 401 REMARK 465 GLY A 402 REMARK 465 GLY A 403 REMARK 465 VAL A 404 REMARK 465 ASP A 405 REMARK 465 GLU A 406 REMARK 465 VAL A 407 REMARK 465 ASP A 408 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 GLU A 7 CG CD OE1 OE2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 25 CE NZ REMARK 470 ARG A 52 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 67 NZ REMARK 470 ARG A 83 CZ NH1 NH2 REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 101 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 102 OG REMARK 470 SER A 103 OG REMARK 470 GLN A 105 CG CD OE1 NE2 REMARK 470 TRP A 108 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 REMARK 470 TRP A 108 CH2 REMARK 470 ARG A 110 CD NE CZ NH1 NH2 REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 LYS A 229 CE NZ REMARK 470 LYS A 273 CE NZ REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 ASN A 343 CG OD1 ND2 REMARK 470 GLN A 371 CG CD OE1 NE2 REMARK 470 ARG A 372 CD NE CZ NH1 NH2 REMARK 470 LYS A 416 CE NZ 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 TYR A 125 N ASP A 127 2.16 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 PRO A 172 C - N - CA ANGL. DEV. = 13.3 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 SER A 5 -150.85 -56.54 REMARK 500 SER A 6 14.20 -163.49 REMARK 500 GLU A 7 6.94 -150.25 REMARK 500 TRP A 71 87.32 -36.81 REMARK 500 SER A 102 92.62 83.95 REMARK 500 TYR A 125 -115.88 -104.90 REMARK 500 PHE A 126 51.19 -27.54 REMARK 500 ASN A 144 -124.18 89.01 REMARK 500 TRP A 171 110.43 84.20 REMARK 500 GLU A 196 -116.68 -48.66 REMARK 500 HIS A 287 63.60 -52.09 REMARK 500 ASP A 290 98.72 -62.81 REMARK 500 ALA A 324 -82.26 -58.17 REMARK 500 ARG A 328 72.92 -115.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 171 PRO A 172 -143.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 C8E A 501 REMARK 610 C8E A 502 REMARK 610 C8E A 503 REMARK 610 C8E A 504 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C8E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C8E A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C8E A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C8E A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GEY RELATED DB: PDB REMARK 900 OPRB HIGH PH CRYSTAL FORM DBREF 4GF4 A 1 421 UNP E4R6F8 E4R6F8_PSEPB 27 447 SEQADV 4GF4 ALA A -14 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 ASN A -13 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 VAL A -12 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 ARG A -11 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 LEU A -10 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 GLN A -9 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -8 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -7 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -6 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -5 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -4 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -3 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 HIS A -2 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 LEU A -1 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 GLU A 0 UNP E4R6F8 EXPRESSION TAG SEQADV 4GF4 MSE A 220 UNP E4R6F8 LEU 246 ENGINEERED MUTATION SEQADV 4GF4 MSE A 222 UNP E4R6F8 VAL 248 ENGINEERED MUTATION SEQADV 4GF4 MSE A 415 UNP E4R6F8 LEU 441 ENGINEERED MUTATION SEQADV 4GF4 MSE A 417 UNP E4R6F8 ILE 443 ENGINEERED MUTATION SEQRES 1 A 436 ALA ASN VAL ARG LEU GLN HIS HIS HIS HIS HIS HIS HIS SEQRES 2 A 436 LEU GLU ALA GLU ALA PHE SER SER GLU SER LYS TRP MSE SEQRES 3 A 436 THR GLY ASP TRP GLY GLY THR ARG THR GLU LEU LEU ASP SEQRES 4 A 436 LYS GLY TYR ASP PHE THR LEU ASP TYR VAL GLY GLU VAL SEQRES 5 A 436 ALA GLY ASN LEU HIS GLY GLY TYR ASN ASP ASP LYS THR SEQRES 6 A 436 ALA ARG TYR SER ASP GLN PHE ALA LEU GLY ALA HIS LEU SEQRES 7 A 436 ASP LEU GLN LYS ILE LEU GLY TRP HIS ASP ALA GLU PHE SEQRES 8 A 436 LYS LEU ALA ILE THR GLU ARG SER GLY ARG ASN LEU SER SEQRES 9 A 436 ASN ASP ARG ILE SER ASP PRO ARG ALA GLY GLN PHE SER SEQRES 10 A 436 SER VAL GLN GLU VAL TRP GLY ARG GLY GLN THR TRP ARG SEQRES 11 A 436 LEU THR GLN MSE TRP ILE LYS GLN LYS TYR PHE ASP GLY SEQRES 12 A 436 ALA LEU ASP VAL LYS PHE GLY ARG PHE GLY GLU GLY GLU SEQRES 13 A 436 ASP PHE ASN SER PHE PRO CYS ASP PHE GLN ASN LEU ALA SEQRES 14 A 436 PHE CYS GLY SER GLN VAL GLY ASN TRP VAL GLY GLY ILE SEQRES 15 A 436 TRP TYR ASN TRP PRO VAL SER GLN TRP ALA LEU ARG VAL SEQRES 16 A 436 LYS TYR ASN ILE THR PRO ALA PHE PHE VAL GLN VAL GLY SEQRES 17 A 436 ALA PHE GLU GLN ASN PRO SER ASN LEU GLU THR GLY ASN SEQRES 18 A 436 GLY PHE LYS LEU SER GLY SER GLY THR LYS GLY ALA ILE SEQRES 19 A 436 MSE PRO MSE GLU ALA VAL TRP SER PRO LYS VAL ASN GLY SEQRES 20 A 436 LEU PRO GLY GLU TYR ARG LEU GLY TYR TYR TYR SER THR SEQRES 21 A 436 ALA LYS ALA ASP ASP VAL TYR ASP ASP VAL ASN GLY ASN SEQRES 22 A 436 PRO GLN ALA LEU THR GLY GLU ALA PHE LYS SER HIS SER SEQRES 23 A 436 SER LYS HIS GLY TRP TRP VAL VAL ALA GLN GLN GLN VAL SEQRES 24 A 436 THR ALA HIS GLY GLY ASP VAL ASN ARG GLY LEU SER LEU SEQRES 25 A 436 PHE ALA ASN PHE THR VAL HIS ASP LYS ALA THR ASN VAL SEQRES 26 A 436 VAL ASP ASN TYR GLN GLN VAL GLY LEU VAL TYR LYS GLY SEQRES 27 A 436 ALA PHE ASP ALA ARG PRO LYS ASP ASP ILE GLY PHE GLY SEQRES 28 A 436 VAL ALA ARG ILE HIS VAL ASN ASP ASP VAL LYS LYS ARG SEQRES 29 A 436 ALA GLU LEU LEU ASN ALA GLN SER GLY ILE ASN ASP TYR SEQRES 30 A 436 ASP ASN PRO GLY PHE VAL PRO LEU GLN ARG THR GLU TYR SEQRES 31 A 436 ASN ALA GLU LEU TYR TYR GLY PHE HIS VAL THR ASN TRP SEQRES 32 A 436 LEU THR VAL ARG PRO ASN LEU GLN TYR ILE LYS SER PRO SEQRES 33 A 436 GLY GLY VAL ASP GLU VAL ASP ASN ALA LEU VAL ALA GLY SEQRES 34 A 436 MSE LYS MSE GLN SER SER PHE MODRES 4GF4 MSE A 11 MET SELENOMETHIONINE MODRES 4GF4 MSE A 119 MET SELENOMETHIONINE MODRES 4GF4 MSE A 220 MET SELENOMETHIONINE MODRES 4GF4 MSE A 222 MET SELENOMETHIONINE MODRES 4GF4 MSE A 415 MET SELENOMETHIONINE MODRES 4GF4 MSE A 417 MET SELENOMETHIONINE HET MSE A 11 8 HET MSE A 119 8 HET MSE A 220 8 HET MSE A 222 8 HET MSE A 415 8 HET MSE A 417 8 HET C8E A 501 18 HET C8E A 502 18 HET C8E A 503 20 HET C8E A 504 12 HETNAM MSE SELENOMETHIONINE HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 C8E 4(C16 H34 O5) HELIX 1 1 LEU A 65 LEU A 69 1 5 HELIX 2 2 PHE A 126 GLY A 128 5 3 HELIX 3 3 GLY A 138 ASP A 142 5 5 SHEET 1 A13 GLN A 105 GLY A 109 0 SHEET 2 A13 ASN A 87 ASP A 91 -1 N ASN A 87 O GLY A 109 SHEET 3 A13 ASP A 48 ASP A 64 -1 N LYS A 49 O ASN A 90 SHEET 4 A13 TYR A 27 ASN A 40 -1 N ALA A 38 O ARG A 52 SHEET 5 A13 ALA A 410 SER A 420 -1 O SER A 419 N TYR A 33 SHEET 6 A13 LEU A 389 LYS A 399 -1 N GLN A 396 O VAL A 412 SHEET 7 A13 ARG A 372 THR A 386 -1 N PHE A 383 O VAL A 391 SHEET 8 A13 ASP A 332 VAL A 342 -1 N GLY A 336 O GLU A 378 SHEET 9 A13 ASP A 312 LYS A 322 -1 N GLN A 315 O ARG A 339 SHEET 10 A13 GLY A 294 ASP A 305 -1 N HIS A 304 O ASP A 312 SHEET 11 A13 HIS A 274 GLN A 283 -1 N TRP A 276 O VAL A 303 SHEET 12 A13 LEU A 233 TYR A 243 -1 N GLU A 236 O GLN A 281 SHEET 13 A13 LYS A 229 VAL A 230 -1 N VAL A 230 O LEU A 233 SHEET 1 B11 GLN A 105 GLY A 109 0 SHEET 2 B11 ASN A 87 ASP A 91 -1 N ASN A 87 O GLY A 109 SHEET 3 B11 ASP A 48 ASP A 64 -1 N LYS A 49 O ASN A 90 SHEET 4 B11 ALA A 74 SER A 84 -1 O LEU A 78 N ALA A 61 SHEET 5 B11 GLN A 112 LYS A 124 -1 O THR A 113 N ARG A 83 SHEET 6 B11 LEU A 130 PHE A 137 -1 O ARG A 136 N MSE A 119 SHEET 7 B11 SER A 174 THR A 185 -1 O ALA A 177 N GLY A 135 SHEET 8 B11 PHE A 188 PHE A 195 -1 O VAL A 190 N TYR A 182 SHEET 9 B11 MSE A 220 TRP A 226 -1 O VAL A 225 N PHE A 189 SHEET 10 B11 LEU A 233 TYR A 243 -1 O TYR A 241 N MSE A 222 SHEET 11 B11 LYS A 229 VAL A 230 -1 N VAL A 230 O LEU A 233 LINK C GLN A 118 N MSE A 119 1555 1555 1.32 LINK C MSE A 119 N TRP A 120 1555 1555 1.32 LINK C ILE A 219 N MSE A 220 1555 1555 1.34 LINK C MSE A 220 N PRO A 221 1555 1555 1.33 LINK C PRO A 221 N MSE A 222 1555 1555 1.32 LINK C MSE A 222 N GLU A 223 1555 1555 1.33 LINK C GLY A 414 N MSE A 415 1555 1555 1.33 LINK C MSE A 415 N LYS A 416 1555 1555 1.32 LINK C LYS A 416 N MSE A 417 1555 1555 1.32 LINK C MSE A 417 N GLN A 418 1555 1555 1.32 LINK C TRP A 10 N MSE A 11 1555 1555 1.32 LINK C MSE A 11 N THR A 12 1555 1555 1.32 CISPEP 1 GLY A 288 GLY A 289 0 -11.34 SITE 1 AC1 10 VAL A 132 PHE A 134 LEU A 178 VAL A 230 SITE 2 AC1 10 GLN A 282 LEU A 297 VAL A 317 LEU A 319 SITE 3 AC1 10 PHE A 335 C8E A 502 SITE 1 AC2 4 PHE A 134 TRP A 226 TYR A 237 C8E A 501 SITE 1 AC3 6 ALA A 129 LEU A 130 VAL A 192 MSE A 220 SITE 2 AC3 6 LEU A 319 TYR A 397 SITE 1 AC4 4 TYR A 33 VAL A 37 ASP A 55 MSE A 417 CRYST1 79.037 122.592 135.581 90.00 90.00 90.00 I 2 2 2 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 0.012652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007376 0.00000