HEADER MEMBRANE PROTEIN 07-JUN-14 4TPH TITLE SELECTIVITY MECHANISM OF A BACTERIAL HOMOLOGUE OF THE HUMAN DRUG TITLE 2 PEPTIDE TRANSPORTERS PEPT1 AND PEPT2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTON:OLIGOPEPTIDE SYMPORTER POT FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 211586; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: SO_1277; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN, SECONDARY ACTIVE TRANSPORTER, COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.GUETTOU,E.QUISTGAARD,M.RABA,P.MOBERG,C.LOW,P.NORDLUND REVDAT 8 20-DEC-23 4TPH 1 REMARK REVDAT 7 13-SEP-17 4TPH 1 REMARK REVDAT 6 17-DEC-14 4TPH 1 REMARK REVDAT 5 10-DEC-14 4TPH 1 REVDAT 4 27-AUG-14 4TPH 1 REMARK REVDAT 3 13-AUG-14 4TPH 1 JRNL REVDAT 2 06-AUG-14 4TPH 1 AUTHOR JRNL REVDAT 1 09-JUL-14 4TPH 0 JRNL AUTH F.GUETTOU,E.M.QUISTGAARD,M.RABA,P.MOBERG,C.LOW,P.NORDLUND JRNL TITL SELECTIVITY MECHANISM OF A BACTERIAL HOMOLOG OF THE HUMAN JRNL TITL 2 DRUG-PEPTIDE TRANSPORTERS PEPT1 AND PEPT2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 728 2014 JRNL REFN ESSN 1545-9985 JRNL PMID 25064511 JRNL DOI 10.1038/NSMB.2860 REMARK 2 REMARK 2 RESOLUTION. 3.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 3.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.2 REMARK 3 NUMBER OF REFLECTIONS : 24515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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 29.5442 - 6.5421 1.00 3499 177 0.2465 0.2876 REMARK 3 2 6.5421 - 5.2019 1.00 3324 187 0.2802 0.3471 REMARK 3 3 5.2019 - 4.5470 1.00 3341 165 0.2012 0.2272 REMARK 3 4 4.5470 - 4.1325 1.00 3284 174 0.2140 0.3003 REMARK 3 5 4.1325 - 3.8370 0.93 2993 182 0.2702 0.3763 REMARK 3 6 3.8370 - 3.6112 0.76 2494 143 0.3175 0.3404 REMARK 3 7 3.6112 - 3.4306 0.62 2036 102 0.3088 0.3843 REMARK 3 8 3.4306 - 3.2815 0.46 1488 86 0.3122 0.3598 REMARK 3 9 3.2815 - 3.1553 0.25 802 38 0.3321 0.2643 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.060 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 : 0.013 7146 REMARK 3 ANGLE : 1.794 9739 REMARK 3 CHIRALITY : 0.072 1156 REMARK 3 PLANARITY : 0.009 1165 REMARK 3 DIHEDRAL : 16.277 2329 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): -38.9390 -63.8608 24.0864 REMARK 3 T TENSOR REMARK 3 T11: 0.5575 T22: 0.7872 REMARK 3 T33: 0.6297 T12: 0.0609 REMARK 3 T13: 0.1549 T23: 0.0578 REMARK 3 L TENSOR REMARK 3 L11: 0.4053 L22: 6.6330 REMARK 3 L33: 3.1992 L12: 0.6969 REMARK 3 L13: 0.8637 L23: 0.2040 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: 0.2721 S13: 0.1363 REMARK 3 S21: -0.2517 S22: -0.1679 S23: 0.2010 REMARK 3 S31: 0.0213 S32: -0.2746 S33: 0.1398 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' REMARK 3 ORIGIN FOR THE GROUP (A): -23.2166 -16.7613 30.1976 REMARK 3 T TENSOR REMARK 3 T11: 0.6959 T22: 0.7990 REMARK 3 T33: 0.7644 T12: 0.0752 REMARK 3 T13: 0.2940 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.9236 L22: 4.5113 REMARK 3 L33: 2.2274 L12: 0.3196 REMARK 3 L13: -0.2008 L23: -0.0421 REMARK 3 S TENSOR REMARK 3 S11: 0.1325 S12: 0.1379 S13: -0.0640 REMARK 3 S21: -0.4146 S22: -0.1149 S23: -0.6006 REMARK 3 S31: -0.0573 S32: 0.4810 S33: -0.0107 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 4TPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24515 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.160 REMARK 200 RESOLUTION RANGE LOW (A) : 29.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.24 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4LEP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE CITRATE PH 4.0, 36% REMARK 280 PEG300, 0.12 M ZNCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 273K 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 40.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 102.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.84000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 ASN A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 134 REMARK 465 ASP A 135 REMARK 465 ASP A 136 REMARK 465 ILE A 263 REMARK 465 ARG A 264 REMARK 465 THR A 265 REMARK 465 SER A 266 REMARK 465 GLU A 267 REMARK 465 PRO A 268 REMARK 465 SER A 269 REMARK 465 SER A 343 REMARK 465 TYR A 344 REMARK 465 SER A 345 REMARK 465 TRP A 346 REMARK 465 ALA A 347 REMARK 465 GLY A 348 REMARK 465 ARG A 349 REMARK 465 ASN A 350 REMARK 465 ASN A 351 REMARK 465 LYS A 352 REMARK 465 ASP A 353 REMARK 465 PHE A 354 REMARK 465 SER A 355 REMARK 465 TYR A 416 REMARK 465 VAL A 417 REMARK 465 PRO A 418 REMARK 465 ALA A 419 REMARK 465 ARG A 420 REMARK 465 MET A 421 REMARK 465 GLY A 422 REMARK 465 GLY A 423 REMARK 465 PHE A 424 REMARK 465 GLU A 493 REMARK 465 SER A 494 REMARK 465 HIS A 495 REMARK 465 HIS A 496 REMARK 465 ALA A 497 REMARK 465 HIS A 498 REMARK 465 SER A 499 REMARK 465 SER A 500 REMARK 465 ILE A 501 REMARK 465 GLU A 502 REMARK 465 ASN A 503 REMARK 465 ASN A 504 REMARK 465 ALA A 505 REMARK 465 ALA A 506 REMARK 465 ALA A 507 REMARK 465 SER A 508 REMARK 465 LEU A 509 REMARK 465 ARG A 510 REMARK 465 ASP A 511 REMARK 465 VAL A 512 REMARK 465 LYS A 513 REMARK 465 ALA A 514 REMARK 465 GLU A 515 REMARK 465 GLN A 516 REMARK 465 ALA A 517 REMARK 465 GLU A 518 REMARK 465 ASN A 519 REMARK 465 LEU A 520 REMARK 465 TYR A 521 REMARK 465 PHE A 522 REMARK 465 GLN A 523 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LEU B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 ASN B 6 REMARK 465 GLN B 7 REMARK 465 GLY B 134 REMARK 465 ASP B 135 REMARK 465 ASP B 136 REMARK 465 ILE B 263 REMARK 465 ARG B 264 REMARK 465 THR B 265 REMARK 465 SER B 266 REMARK 465 GLU B 267 REMARK 465 PRO B 268 REMARK 465 SER B 269 REMARK 465 SER B 343 REMARK 465 TYR B 344 REMARK 465 SER B 345 REMARK 465 TRP B 346 REMARK 465 ALA B 347 REMARK 465 GLY B 348 REMARK 465 ARG B 349 REMARK 465 ASN B 350 REMARK 465 ASN B 351 REMARK 465 LYS B 352 REMARK 465 ASP B 353 REMARK 465 PHE B 354 REMARK 465 SER B 355 REMARK 465 TYR B 416 REMARK 465 VAL B 417 REMARK 465 PRO B 418 REMARK 465 ALA B 419 REMARK 465 ARG B 420 REMARK 465 MET B 421 REMARK 465 GLY B 422 REMARK 465 GLY B 423 REMARK 465 PHE B 424 REMARK 465 GLU B 493 REMARK 465 SER B 494 REMARK 465 HIS B 495 REMARK 465 HIS B 496 REMARK 465 ALA B 497 REMARK 465 HIS B 498 REMARK 465 SER B 499 REMARK 465 SER B 500 REMARK 465 ILE B 501 REMARK 465 GLU B 502 REMARK 465 ASN B 503 REMARK 465 ASN B 504 REMARK 465 ALA B 505 REMARK 465 ALA B 506 REMARK 465 ALA B 507 REMARK 465 SER B 508 REMARK 465 LEU B 509 REMARK 465 ARG B 510 REMARK 465 ASP B 511 REMARK 465 VAL B 512 REMARK 465 LYS B 513 REMARK 465 ALA B 514 REMARK 465 GLU B 515 REMARK 465 GLN B 516 REMARK 465 ALA B 517 REMARK 465 GLU B 518 REMARK 465 ASN B 519 REMARK 465 LEU B 520 REMARK 465 TYR B 521 REMARK 465 PHE B 522 REMARK 465 GLN B 523 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 ASN A 174 CG OD1 ND2 REMARK 470 GLU A 175 CG CD OE1 OE2 REMARK 470 PHE A 176 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 SER A 202 OG REMARK 470 LEU A 203 CG CD1 CD2 REMARK 470 ASN A 205 CG OD1 ND2 REMARK 470 TYR A 206 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 208 OG REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 PRO A 210 CG CD REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 THR A 212 OG1 CG2 REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 214 CG CD REMARK 470 VAL A 215 CG1 CG2 REMARK 470 GLU A 270 CG CD OE1 OE2 REMARK 470 ARG A 271 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 404 CG CD1 CD2 REMARK 470 ARG A 415 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 174 CG OD1 ND2 REMARK 470 GLU B 175 CG CD OE1 OE2 REMARK 470 PHE B 176 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 201 CG CD CE NZ REMARK 470 SER B 202 OG REMARK 470 LEU B 203 CG CD1 CD2 REMARK 470 ASN B 205 CG OD1 ND2 REMARK 470 TYR B 206 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER B 208 OG REMARK 470 GLU B 209 CG CD OE1 OE2 REMARK 470 PRO B 210 CG CD REMARK 470 ASP B 211 CG OD1 OD2 REMARK 470 THR B 212 OG1 CG2 REMARK 470 ARG B 213 CG CD NE CZ NH1 NH2 REMARK 470 PRO B 214 CG CD REMARK 470 VAL B 215 CG1 CG2 REMARK 470 GLU B 270 CG CD OE1 OE2 REMARK 470 ARG B 271 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 404 CG CD1 CD2 REMARK 470 ARG B 415 CG CD NE CZ NH1 NH2 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 LEU A 127 CA - CB - CG ANGL. DEV. = 17.8 DEGREES REMARK 500 LEU A 408 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 LEU B 408 CA - CB - CG ANGL. DEV. = 14.7 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 ILE A 75 -66.64 -128.06 REMARK 500 GLU A 101 30.52 -88.06 REMARK 500 ASN A 174 -40.70 67.00 REMARK 500 PHE A 176 -83.50 -79.18 REMARK 500 MET A 199 3.83 -69.20 REMARK 500 SER A 202 -71.59 -40.46 REMARK 500 ASN A 205 -92.42 25.59 REMARK 500 SER A 208 167.59 105.33 REMARK 500 THR A 296 -98.43 -111.60 REMARK 500 ASN A 305 37.50 -146.13 REMARK 500 TRP A 308 3.82 -62.27 REMARK 500 PHE A 313 103.00 4.35 REMARK 500 THR A 315 -142.00 -86.42 REMARK 500 TRP A 318 -140.94 -118.74 REMARK 500 GLN A 379 7.09 -62.88 REMARK 500 ALA A 381 75.70 50.75 REMARK 500 LYS A 385 78.47 -68.32 REMARK 500 SER A 387 -75.89 -179.03 REMARK 500 SER A 388 -68.57 71.33 REMARK 500 VAL A 405 55.48 -115.65 REMARK 500 ILE B 75 -64.80 -121.94 REMARK 500 ASN B 174 -38.69 67.45 REMARK 500 PHE B 176 -79.23 -78.52 REMARK 500 MET B 199 5.00 -68.79 REMARK 500 ASN B 205 -89.12 29.52 REMARK 500 SER B 208 -157.63 117.83 REMARK 500 GLU B 209 -55.07 -150.71 REMARK 500 THR B 296 -97.78 -114.96 REMARK 500 ASN B 305 36.56 -145.78 REMARK 500 TRP B 308 2.19 -63.11 REMARK 500 PHE B 313 99.02 -15.79 REMARK 500 TRP B 318 -143.42 -110.36 REMARK 500 SER B 387 -76.78 -178.23 REMARK 500 SER B 388 -73.37 70.10 REMARK 500 VAL B 405 60.93 -119.87 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 TYR A 132 GLU A 133 147.27 REMARK 500 LEU B 274 ILE B 275 149.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LMT A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LMT B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LMT B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TPG RELATED DB: PDB REMARK 900 RELATED ID: 4TPJ RELATED DB: PDB DBREF 4TPH A 1 516 UNP Q8EHE6 Q8EHE6_SHEON 1 516 DBREF 4TPH B 1 516 UNP Q8EHE6 Q8EHE6_SHEON 1 516 SEQADV 4TPH ALA A 517 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH GLU A 518 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH ASN A 519 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH LEU A 520 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH TYR A 521 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH PHE A 522 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH GLN A 523 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH ALA B 517 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH GLU B 518 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH ASN B 519 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH LEU B 520 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH TYR B 521 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH PHE B 522 UNP Q8EHE6 EXPRESSION TAG SEQADV 4TPH GLN B 523 UNP Q8EHE6 EXPRESSION TAG SEQRES 1 A 523 MET THR LEU GLY THR ASN GLN VAL SER LYS THR HIS SER SEQRES 2 A 523 PHE MET THR VAL SER LEU ILE GLU LEU TRP GLU ARG PHE SEQRES 3 A 523 GLY TYR TYR GLY MET GLN ALA LEU ILE VAL TYR PHE MET SEQRES 4 A 523 VAL GLN ARG LEU GLY PHE ASP ASP SER ARG ALA ASN LEU SEQRES 5 A 523 VAL TRP SER ALA CYS ALA ALA LEU ILE TYR VAL SER PRO SEQRES 6 A 523 ALA ILE GLY GLY TRP VAL GLY ASP LYS ILE LEU GLY THR SEQRES 7 A 523 LYS ARG THR MET LEU LEU GLY ALA GLY ILE LEU SER VAL SEQRES 8 A 523 GLY TYR ALA LEU MET THR VAL PRO THR GLU ASN THR TRP SEQRES 9 A 523 PHE MET PHE SER ALA LEU GLY VAL ILE VAL VAL GLY ASN SEQRES 10 A 523 GLY LEU PHE LYS PRO ASN ALA GLY ASN LEU VAL ARG LYS SEQRES 11 A 523 ILE TYR GLU GLY ASP ASP SER LYS ILE ASP SER ALA PHE SEQRES 12 A 523 THR ILE TYR TYR MET ALA VAL ASN VAL GLY SER THR PHE SEQRES 13 A 523 SER MET LEU LEU THR PRO TRP ILE LYS ASP TYR VAL ASN SEQRES 14 A 523 ALA GLN TYR GLY ASN GLU PHE GLY TRP HIS ALA ALA PHE SEQRES 15 A 523 ALA VAL CYS CYS VAL GLY ILE LEU VAL GLY LEU GLY ASN SEQRES 16 A 523 TYR ALA LEU MET HIS LYS SER LEU ALA ASN TYR GLY SER SEQRES 17 A 523 GLU PRO ASP THR ARG PRO VAL ASN LYS LYS SER LEU ALA SEQRES 18 A 523 ILE VAL LEU ALA LEU ALA ALA LEU SER VAL VAL ALA SER SEQRES 19 A 523 ALA ILE ILE LEU GLU TYR GLU ASP VAL ALA ARG VAL PHE SEQRES 20 A 523 VAL TYR ALA ALA GLY VAL ALA VAL LEU GLY ILE PHE PHE SEQRES 21 A 523 HIS LEU ILE ARG THR SER GLU PRO SER GLU ARG ALA GLY SEQRES 22 A 523 LEU ILE ALA ALA LEU ILE LEU THR VAL GLN THR VAL PHE SEQRES 23 A 523 PHE PHE ILE PHE TYR GLN GLN MET SER THR SER LEU ALA SEQRES 24 A 523 LEU PHE ALA LEU ARG ASN VAL ASP TRP ASP PHE GLN VAL SEQRES 25 A 523 PHE GLY THR HIS LEU TRP THR TRP SER PRO ALA GLN PHE SEQRES 26 A 523 GLN ALA LEU ASN PRO ILE TRP ILE MET VAL LEU SER PRO SEQRES 27 A 523 VAL LEU ALA TRP SER TYR SER TRP ALA GLY ARG ASN ASN SEQRES 28 A 523 LYS ASP PHE SER ILE ALA ALA LYS PHE ALA LEU GLY PHE SEQRES 29 A 523 ALA VAL VAL ALA ILE GLY PHE PHE ILE TYR GLY PHE ALA SEQRES 30 A 523 GLY GLN PHE ALA VAL ASN GLY LYS THR SER SER TRP VAL SEQRES 31 A 523 MET ILE TRP GLY TYR ALA SER TYR SER LEU GLY GLU LEU SEQRES 32 A 523 LEU VAL SER GLY LEU GLY LEU ALA MET ILE ALA ARG TYR SEQRES 33 A 523 VAL PRO ALA ARG MET GLY GLY PHE MET MET GLY ALA TYR SEQRES 34 A 523 PHE VAL ALA SER GLY ILE SER GLN TYR LEU GLY GLY VAL SEQRES 35 A 523 VAL ALA ASN PHE ALA SER VAL PRO GLN ASP LEU VAL ASP SEQRES 36 A 523 PRO LEU GLN THR LEU PRO VAL TYR THR ASN LEU PHE ASN SEQRES 37 A 523 LYS LEU GLY VAL ALA ALA VAL VAL CYS THR ILE ILE ALA SEQRES 38 A 523 LEU ALA VAL LEU PRO LEU MET ARG ARG LEU THR GLU SER SEQRES 39 A 523 HIS HIS ALA HIS SER SER ILE GLU ASN ASN ALA ALA ALA SEQRES 40 A 523 SER LEU ARG ASP VAL LYS ALA GLU GLN ALA GLU ASN LEU SEQRES 41 A 523 TYR PHE GLN SEQRES 1 B 523 MET THR LEU GLY THR ASN GLN VAL SER LYS THR HIS SER SEQRES 2 B 523 PHE MET THR VAL SER LEU ILE GLU LEU TRP GLU ARG PHE SEQRES 3 B 523 GLY TYR TYR GLY MET GLN ALA LEU ILE VAL TYR PHE MET SEQRES 4 B 523 VAL GLN ARG LEU GLY PHE ASP ASP SER ARG ALA ASN LEU SEQRES 5 B 523 VAL TRP SER ALA CYS ALA ALA LEU ILE TYR VAL SER PRO SEQRES 6 B 523 ALA ILE GLY GLY TRP VAL GLY ASP LYS ILE LEU GLY THR SEQRES 7 B 523 LYS ARG THR MET LEU LEU GLY ALA GLY ILE LEU SER VAL SEQRES 8 B 523 GLY TYR ALA LEU MET THR VAL PRO THR GLU ASN THR TRP SEQRES 9 B 523 PHE MET PHE SER ALA LEU GLY VAL ILE VAL VAL GLY ASN SEQRES 10 B 523 GLY LEU PHE LYS PRO ASN ALA GLY ASN LEU VAL ARG LYS SEQRES 11 B 523 ILE TYR GLU GLY ASP ASP SER LYS ILE ASP SER ALA PHE SEQRES 12 B 523 THR ILE TYR TYR MET ALA VAL ASN VAL GLY SER THR PHE SEQRES 13 B 523 SER MET LEU LEU THR PRO TRP ILE LYS ASP TYR VAL ASN SEQRES 14 B 523 ALA GLN TYR GLY ASN GLU PHE GLY TRP HIS ALA ALA PHE SEQRES 15 B 523 ALA VAL CYS CYS VAL GLY ILE LEU VAL GLY LEU GLY ASN SEQRES 16 B 523 TYR ALA LEU MET HIS LYS SER LEU ALA ASN TYR GLY SER SEQRES 17 B 523 GLU PRO ASP THR ARG PRO VAL ASN LYS LYS SER LEU ALA SEQRES 18 B 523 ILE VAL LEU ALA LEU ALA ALA LEU SER VAL VAL ALA SER SEQRES 19 B 523 ALA ILE ILE LEU GLU TYR GLU ASP VAL ALA ARG VAL PHE SEQRES 20 B 523 VAL TYR ALA ALA GLY VAL ALA VAL LEU GLY ILE PHE PHE SEQRES 21 B 523 HIS LEU ILE ARG THR SER GLU PRO SER GLU ARG ALA GLY SEQRES 22 B 523 LEU ILE ALA ALA LEU ILE LEU THR VAL GLN THR VAL PHE SEQRES 23 B 523 PHE PHE ILE PHE TYR GLN GLN MET SER THR SER LEU ALA SEQRES 24 B 523 LEU PHE ALA LEU ARG ASN VAL ASP TRP ASP PHE GLN VAL SEQRES 25 B 523 PHE GLY THR HIS LEU TRP THR TRP SER PRO ALA GLN PHE SEQRES 26 B 523 GLN ALA LEU ASN PRO ILE TRP ILE MET VAL LEU SER PRO SEQRES 27 B 523 VAL LEU ALA TRP SER TYR SER TRP ALA GLY ARG ASN ASN SEQRES 28 B 523 LYS ASP PHE SER ILE ALA ALA LYS PHE ALA LEU GLY PHE SEQRES 29 B 523 ALA VAL VAL ALA ILE GLY PHE PHE ILE TYR GLY PHE ALA SEQRES 30 B 523 GLY GLN PHE ALA VAL ASN GLY LYS THR SER SER TRP VAL SEQRES 31 B 523 MET ILE TRP GLY TYR ALA SER TYR SER LEU GLY GLU LEU SEQRES 32 B 523 LEU VAL SER GLY LEU GLY LEU ALA MET ILE ALA ARG TYR SEQRES 33 B 523 VAL PRO ALA ARG MET GLY GLY PHE MET MET GLY ALA TYR SEQRES 34 B 523 PHE VAL ALA SER GLY ILE SER GLN TYR LEU GLY GLY VAL SEQRES 35 B 523 VAL ALA ASN PHE ALA SER VAL PRO GLN ASP LEU VAL ASP SEQRES 36 B 523 PRO LEU GLN THR LEU PRO VAL TYR THR ASN LEU PHE ASN SEQRES 37 B 523 LYS LEU GLY VAL ALA ALA VAL VAL CYS THR ILE ILE ALA SEQRES 38 B 523 LEU ALA VAL LEU PRO LEU MET ARG ARG LEU THR GLU SER SEQRES 39 B 523 HIS HIS ALA HIS SER SER ILE GLU ASN ASN ALA ALA ALA SEQRES 40 B 523 SER LEU ARG ASP VAL LYS ALA GLU GLN ALA GLU ASN LEU SEQRES 41 B 523 TYR PHE GLN HET ZN A 601 1 HET LMT A 602 35 HET ALA A 603 5 HET DBY A 604 15 HET LMT B 601 35 HET LMT B 602 35 HETNAM ZN ZINC ION HETNAM LMT DODECYL-BETA-D-MALTOSIDE HETNAM ALA ALANINE HETNAM DBY 3,5 DIBROMOTYROSINE FORMUL 3 ZN ZN 2+ FORMUL 4 LMT 3(C24 H46 O11) FORMUL 5 ALA C3 H7 N O2 FORMUL 6 DBY C9 H9 BR2 N O3 HELIX 1 AA1 SER A 9 ARG A 42 1 34 HELIX 2 AA2 ASP A 46 SER A 64 1 19 HELIX 3 AA3 SER A 64 ILE A 75 1 12 HELIX 4 AA4 GLY A 77 VAL A 98 1 22 HELIX 5 AA5 ASN A 102 TYR A 132 1 31 HELIX 6 AA6 LYS A 138 TYR A 172 1 35 HELIX 7 AA7 GLY A 177 LEU A 203 1 27 HELIX 8 AA8 ASN A 216 TYR A 240 1 25 HELIX 9 AA9 TYR A 240 LEU A 262 1 23 HELIX 10 AB1 ARG A 271 MET A 294 1 24 HELIX 11 AB2 THR A 296 VAL A 306 1 11 HELIX 12 AB3 SER A 321 GLN A 326 5 6 HELIX 13 AB4 ALA A 327 TRP A 342 1 16 HELIX 14 AB5 ALA A 357 PHE A 376 1 20 HELIX 15 AB6 SER A 388 VAL A 405 1 18 HELIX 16 AB7 GLY A 409 ILE A 413 5 5 HELIX 17 AB8 MET A 426 ALA A 447 1 22 HELIX 18 AB9 ASP A 455 THR A 492 1 38 HELIX 19 AC1 SER B 9 ARG B 42 1 34 HELIX 20 AC2 ASP B 46 SER B 64 1 19 HELIX 21 AC3 SER B 64 ILE B 75 1 12 HELIX 22 AC4 GLY B 77 THR B 97 1 21 HELIX 23 AC5 ASN B 102 TYR B 132 1 31 HELIX 24 AC6 LYS B 138 TYR B 172 1 35 HELIX 25 AC7 GLY B 177 LEU B 203 1 27 HELIX 26 AC8 ASN B 216 TYR B 240 1 25 HELIX 27 AC9 TYR B 240 LEU B 262 1 23 HELIX 28 AD1 ARG B 271 MET B 294 1 24 HELIX 29 AD2 THR B 296 VAL B 306 1 11 HELIX 30 AD3 SER B 321 GLN B 326 5 6 HELIX 31 AD4 ALA B 327 ALA B 341 1 15 HELIX 32 AD5 ALA B 357 PHE B 376 1 20 HELIX 33 AD6 SER B 388 VAL B 405 1 18 HELIX 34 AD7 GLY B 409 ILE B 413 5 5 HELIX 35 AD8 MET B 426 ALA B 447 1 22 HELIX 36 AD9 ASP B 455 VAL B 484 1 30 HELIX 37 AE1 VAL B 484 THR B 492 1 9 LINK C ALA A 603 N DBY A 604 1555 1555 1.45 CISPEP 1 GLU A 175 PHE A 176 0 12.78 CISPEP 2 PHE A 313 GLY A 314 0 1.65 CISPEP 3 LEU A 317 TRP A 318 0 -1.19 CISPEP 4 GLU B 175 PHE B 176 0 11.77 CISPEP 5 PHE B 313 GLY B 314 0 7.83 CISPEP 6 LEU B 317 TRP B 318 0 4.65 SITE 1 AC1 6 PHE A 156 LEU A 159 TRP A 163 TRP A 318 SITE 2 AC1 6 THR A 319 GLN A 324 SITE 1 AC2 8 PHE B 156 LEU B 159 TRP B 163 ASP B 166 SITE 2 AC2 8 TRP B 318 THR B 319 SER B 321 GLN B 324 SITE 1 AC3 5 GLN A 458 ASN B 102 TRP B 104 SER B 108 SITE 2 AC3 5 VAL B 112 CRYST1 80.650 107.680 204.210 90.00 90.00 90.00 P 21 21 21 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 0.012399 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004897 0.00000