HEADER TRANSFERASE 27-MAY-18 6DJX TITLE CRYSTAL STRUCTURE OF PPARKIN-PUB-UBCH7 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RBR-TYPE E3 UBIQUITIN TRANSFERASE,RBR-TYPE E3 UBIQUITIN COMPND 3 TRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 29-109,155-496; COMPND 6 SYNONYM: PARKIN; COMPND 7 EC: 2.3.2.31; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: UBIQUITIN; COMPND 12 CHAIN: B; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 L3; COMPND 15 CHAIN: C; COMPND 16 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME L3, L-UBC, UBCH7, UBIQUITIN COMPND 17 CARRIER PROTEIN L3, UBIQUITIN-CONJUGATING ENZYME E2-F1, UBIQUITIN- COMPND 18 PROTEIN LIGASE L3; COMPND 19 EC: 2.3.2.23; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTROCERA DORSALIS; SOURCE 3 ORGANISM_COMMON: ORIENTAL FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 27457; SOURCE 5 GENE: PRKN2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 12 ORGANISM_COMMON: BOVINE; SOURCE 13 ORGANISM_TAXID: 9913; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 GENE: UBE2L3, UBCE7, UBCH7; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1 KEYWDS UBIQUITIN, E3 LIGASE, E2 CONJUGATING ENZYME, PHOSPHORYLATION, KEYWDS 2 MITOPHAGY, PARKINSON DISEASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SAUVE,G.SUNG,J.F.TREMPE,K.GEHRING REVDAT 5 11-OCT-23 6DJX 1 REMARK REVDAT 4 08-JAN-20 6DJX 1 REMARK REVDAT 3 25-JUL-18 6DJX 1 JRNL REVDAT 2 18-JUL-18 6DJX 1 JRNL REVDAT 1 04-JUL-18 6DJX 0 JRNL AUTH V.SAUVE,G.SUNG,N.SOYA,G.KOZLOV,N.BLAIMSCHEIN,L.S.MIOTTO, JRNL AUTH 2 J.F.TREMPE,G.L.LUKACS,K.GEHRING JRNL TITL MECHANISM OF PARKIN ACTIVATION BY PHOSPHORYLATION. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 623 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29967542 JRNL DOI 10.1038/S41594-018-0088-7 REMARK 2 REMARK 2 RESOLUTION. 4.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 4778 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 239 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 48.8608 - 6.9206 0.99 2773 151 0.2166 0.2518 REMARK 3 2 6.9206 - 5.4955 1.00 2793 151 0.3334 0.3557 REMARK 3 3 5.4955 - 4.8015 1.00 2813 149 0.3293 0.3759 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.760 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 233.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 299.5 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 : 0.004 4458 REMARK 3 ANGLE : 0.765 6026 REMARK 3 CHIRALITY : 0.030 650 REMARK 3 PLANARITY : 0.004 782 REMARK 3 DIHEDRAL : 10.945 1703 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND ((RESID 172 THROUGH 363 ) OR (RESID REMARK 3 1001 THROUGH 1004)) REMARK 3 ORIGIN FOR THE GROUP (A): 41.6191 6.5969 7.5346 REMARK 3 T TENSOR REMARK 3 T11: 2.7602 T22: 2.8113 REMARK 3 T33: 2.4916 T12: 0.1104 REMARK 3 T13: -0.1899 T23: 0.2788 REMARK 3 L TENSOR REMARK 3 L11: 1.5645 L22: 7.0089 REMARK 3 L33: 0.0497 L12: 1.2708 REMARK 3 L13: 0.5106 L23: 0.1362 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: -0.2982 S13: -0.0021 REMARK 3 S21: -1.0698 S22: 0.1382 S23: 0.2642 REMARK 3 S31: 0.0479 S32: -0.3646 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESID 364 THROUGH 410 ) OR (RESID REMARK 3 1005 THROUGH 1006)) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8910 33.7429 31.6824 REMARK 3 T TENSOR REMARK 3 T11: 4.0925 T22: 3.2162 REMARK 3 T33: 3.2768 T12: 1.0272 REMARK 3 T13: 0.6251 T23: -0.5841 REMARK 3 L TENSOR REMARK 3 L11: 1.0774 L22: 2.7109 REMARK 3 L33: 0.9540 L12: 1.7670 REMARK 3 L13: -1.2933 L23: -0.1887 REMARK 3 S TENSOR REMARK 3 S11: -0.1707 S12: -0.6532 S13: 0.8365 REMARK 3 S21: -0.8344 S22: -0.1490 S23: -0.4981 REMARK 3 S31: -1.1533 S32: -3.2031 S33: -0.0015 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8658 11.3476 22.9891 REMARK 3 T TENSOR REMARK 3 T11: 1.9976 T22: 2.5212 REMARK 3 T33: 2.4813 T12: 0.0406 REMARK 3 T13: 0.0897 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 3.1808 L22: 5.3104 REMARK 3 L33: 9.4795 L12: 3.1704 REMARK 3 L13: -1.4763 L23: 3.4160 REMARK 3 S TENSOR REMARK 3 S11: 0.1967 S12: 1.6699 S13: -0.4192 REMARK 3 S21: 1.1190 S22: 0.6553 S23: -0.1772 REMARK 3 S31: -0.2367 S32: -1.0757 S33: 0.0007 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 0 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.0585 39.2996 3.9774 REMARK 3 T TENSOR REMARK 3 T11: 2.1887 T22: 2.5938 REMARK 3 T33: 2.3458 T12: 0.0963 REMARK 3 T13: 0.1547 T23: 0.1574 REMARK 3 L TENSOR REMARK 3 L11: 3.0635 L22: 8.2726 REMARK 3 L33: 3.2917 L12: 3.0601 REMARK 3 L13: -0.3135 L23: -4.0468 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.2561 S13: -0.0996 REMARK 3 S21: -0.4224 S22: -0.5786 S23: 0.0629 REMARK 3 S31: -0.0419 S32: 0.6508 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.4551 -23.6313 6.3630 REMARK 3 T TENSOR REMARK 3 T11: 4.1126 T22: 2.0511 REMARK 3 T33: 2.2549 T12: -0.1234 REMARK 3 T13: 0.3648 T23: -0.2514 REMARK 3 L TENSOR REMARK 3 L11: 2.8896 L22: 3.7517 REMARK 3 L33: 0.4931 L12: 1.8844 REMARK 3 L13: -0.4833 L23: -2.7184 REMARK 3 S TENSOR REMARK 3 S11: -0.8695 S12: -0.5550 S13: 0.4706 REMARK 3 S21: -1.3363 S22: -0.6949 S23: -0.9360 REMARK 3 S31: 2.1431 S32: 0.7158 S33: -0.0010 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 6DJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-17 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 : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.238 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4791 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.800 REMARK 200 RESOLUTION RANGE LOW (A) : 48.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.62100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.0 REMARK 200 STARTING MODEL: PDB ENTRIES 5N2W & 1C4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 6.5, 6% ISOPROPANOL, REMARK 280 50 MM MAGNESIUM CHLORIDE, 5% W/V PEG4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.33100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.66200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.66200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.33100 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 GLY A 20 REMARK 465 GLY A 21 REMARK 465 GLU A 22 REMARK 465 ASN A 23 REMARK 465 LEU A 24 REMARK 465 PRO A 148 REMARK 465 GLN A 149 REMARK 465 PRO A 150 REMARK 465 GLN A 151 REMARK 465 ARG A 152 REMARK 465 GLN A 153 REMARK 465 ARG A 154 REMARK 465 SER A 155 REMARK 465 GLU A 156 REMARK 465 GLU A 157 REMARK 465 ARG A 158 REMARK 465 ILE A 159 REMARK 465 ASN A 160 REMARK 465 ILE A 161 REMARK 465 THR A 162 REMARK 465 GLU A 163 REMARK 465 GLU A 164 REMARK 465 ASP A 165 REMARK 465 ARG A 166 REMARK 465 GLN A 167 REMARK 465 ARG A 168 REMARK 465 THR A 169 REMARK 465 LYS A 170 REMARK 465 ALA A 171 REMARK 465 GLU A 411 REMARK 465 GLY A 412 REMARK 465 THR A 413 REMARK 465 SER A 414 REMARK 465 THR A 415 REMARK 465 ASN A 416 REMARK 465 ALA A 417 REMARK 465 SER A 418 REMARK 465 GLY A 419 REMARK 465 SER A 420 REMARK 465 CYS A 421 REMARK 465 GLU A 422 REMARK 465 TYR A 423 REMARK 465 SER A 424 REMARK 465 VAL A 425 REMARK 465 ASP A 426 REMARK 465 PRO A 427 REMARK 465 ASN A 428 REMARK 465 ARG A 429 REMARK 465 ALA A 430 REMARK 465 ALA A 431 REMARK 465 GLU A 432 REMARK 465 ALA A 433 REMARK 465 ARG A 434 REMARK 465 TRP A 435 REMARK 465 ASP A 436 REMARK 465 GLU A 437 REMARK 465 ALA A 438 REMARK 465 SER A 439 REMARK 465 LYS A 440 REMARK 465 VAL A 441 REMARK 465 THR A 442 REMARK 465 ILE A 443 REMARK 465 LYS A 444 REMARK 465 VAL A 445 REMARK 465 MET A 446 REMARK 465 THR A 447 REMARK 465 LYS A 448 REMARK 465 PRO A 449 REMARK 465 CYS A 450 REMARK 465 PRO A 451 REMARK 465 LYS A 452 REMARK 465 CYS A 453 REMARK 465 ARG A 454 REMARK 465 THR A 455 REMARK 465 PRO A 456 REMARK 465 THR A 457 REMARK 465 GLU A 458 REMARK 465 ARG A 459 REMARK 465 ASP A 460 REMARK 465 GLY A 461 REMARK 465 GLY A 462 REMARK 465 ALA A 463 REMARK 465 MET A 464 REMARK 465 HIS A 465 REMARK 465 MET A 466 REMARK 465 VAL A 467 REMARK 465 CYS A 468 REMARK 465 THR A 469 REMARK 465 ARG A 470 REMARK 465 ALA A 471 REMARK 465 GLY A 472 REMARK 465 CYS A 473 REMARK 465 GLY A 474 REMARK 465 PHE A 475 REMARK 465 GLU A 476 REMARK 465 TRP A 477 REMARK 465 CYS A 478 REMARK 465 TRP A 479 REMARK 465 ILE A 480 REMARK 465 CYS A 481 REMARK 465 GLN A 482 REMARK 465 THR A 483 REMARK 465 GLU A 484 REMARK 465 TRP A 485 REMARK 465 THR A 486 REMARK 465 ARG A 487 REMARK 465 ASP A 488 REMARK 465 CYS A 489 REMARK 465 MET A 490 REMARK 465 GLY A 491 REMARK 465 ALA A 492 REMARK 465 HIS A 493 REMARK 465 TRP A 494 REMARK 465 PHE A 495 REMARK 465 GLY A 496 REMARK 465 GLY B 75 REMARK 465 GLY B 76 REMARK 465 GLY C -4 REMARK 465 PRO C -3 REMARK 465 LEU C -2 REMARK 465 GLY C -1 REMARK 465 VAL C 153 REMARK 465 ASP C 154 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 PRO A 48 -5.18 -59.55 REMARK 500 ALA A 75 12.85 59.63 REMARK 500 SER A 101 -57.20 -130.56 REMARK 500 ASP A 205 78.61 50.84 REMARK 500 GLU A 207 -78.80 -68.42 REMARK 500 ARG A 217 -68.60 -143.40 REMARK 500 THR A 321 -165.68 -115.46 REMARK 500 ILE A 333 105.89 -59.06 REMARK 500 SER A 343 -163.92 -78.73 REMARK 500 LEU A 377 93.56 -66.07 REMARK 500 ARG A 397 -21.20 76.72 REMARK 500 CYS A 399 -20.45 -151.78 REMARK 500 LYS B 11 94.76 -61.73 REMARK 500 SER C 91 129.60 -34.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 177 SG REMARK 620 2 CYS A 180 SG 114.7 REMARK 620 3 CYS A 246 SG 119.6 110.8 REMARK 620 4 HIS A 249 NE2 103.6 109.8 96.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 192 SG REMARK 620 2 CYS A 195 SG 116.1 REMARK 620 3 CYS A 222 SG 119.1 115.0 REMARK 620 4 CYS A 229 SG 96.7 104.6 100.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 273 SG REMARK 620 2 CYS A 276 SG 103.0 REMARK 620 3 CYS A 295 SG 109.6 103.8 REMARK 620 4 CYS A 298 SG 120.0 116.3 102.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 288 SG REMARK 620 2 HIS A 292 ND1 98.1 REMARK 620 3 CYS A 324 SG 113.1 97.2 REMARK 620 4 CYS A 328 SG 118.2 105.2 119.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 367 SG REMARK 620 2 CYS A 372 SG 96.6 REMARK 620 3 CYS A 387 SG 119.2 118.7 REMARK 620 4 CYS A 391 SG 89.8 119.8 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1005 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 396 SG REMARK 620 2 CYS A 399 SG 121.2 REMARK 620 3 HIS A 404 NE2 108.9 90.5 REMARK 620 4 CYS A 408 SG 118.0 113.0 98.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1006 DBREF1 6DJX A 29 154 UNP A0A034W4L8_BACDO DBREF2 6DJX A A0A034W4L8 29 109 DBREF1 6DJX A 155 496 UNP A0A034W4L8_BACDO DBREF2 6DJX A A0A034W4L8 155 496 DBREF 6DJX B 1 76 UNP P62992 RS27A_BOVIN 1 76 DBREF 6DJX C 1 154 UNP P68036 UB2L3_HUMAN 1 154 SEQADV 6DJX GLY A 20 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX GLY A 21 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX GLU A 22 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX ASN A 23 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX LEU A 24 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX TYR A 25 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX LEU A 26 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX GLY A 27 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX GLY A 28 UNP A0A034W4L EXPRESSION TAG SEQADV 6DJX ALA A 463 UNP A0A034W4L CYS 463 ENGINEERED MUTATION SEQADV 6DJX GLY C -4 UNP P68036 EXPRESSION TAG SEQADV 6DJX PRO C -3 UNP P68036 EXPRESSION TAG SEQADV 6DJX LEU C -2 UNP P68036 EXPRESSION TAG SEQADV 6DJX GLY C -1 UNP P68036 EXPRESSION TAG SEQADV 6DJX SER C 0 UNP P68036 EXPRESSION TAG SEQADV 6DJX LYS C 86 UNP P68036 CYS 86 ENGINEERED MUTATION SEQRES 1 A 432 GLY GLY GLU ASN LEU TYR LEU GLY GLY SER LEU SER ILE SEQRES 2 A 432 TYR ILE LYS THR ASN THR GLY ARG THR LEU SER VAL ASN SEQRES 3 A 432 LEU GLU PRO GLN TRP ASP ILE LYS ASN VAL LYS GLU ILE SEQRES 4 A 432 VAL ALA PRO GLN LEU GLY LEU GLN PRO GLU GLU VAL LYS SEQRES 5 A 432 ILE ILE PHE ALA GLY LYS GLU LEU SER ASP ALA THR THR SEQRES 6 A 432 ILE GLN GLU CYS ASP LEU GLY GLN GLN SEP ILE LEU HIS SEQRES 7 A 432 ALA ILE ARG SER ARG PRO GLN PRO GLN ARG GLN ARG SER SEQRES 8 A 432 GLU GLU ARG ILE ASN ILE THR GLU GLU ASP ARG GLN ARG SEQRES 9 A 432 THR LYS ALA HIS PHE PHE VAL HIS CYS ALA GLN CYS ASN SEQRES 10 A 432 LYS LEU CYS LYS GLY LYS LEU ARG VAL ARG CYS SER LEU SEQRES 11 A 432 CYS LYS GLY GLY ALA PHE THR VAL HIS ARG ASP PRO GLU SEQRES 12 A 432 CYS TRP ASP ASP VAL LEU LYS PRO ARG ARG ILE THR GLY SEQRES 13 A 432 HIS CYS GLU SER GLN GLU ILE ALA CYS PHE ASP ASN GLU SEQRES 14 A 432 THR GLY ASP PRO PRO PHE THR GLU PHE TYR PHE LYS CYS SEQRES 15 A 432 GLY GLU HIS VAL SER GLY GLY GLU LYS ASP PHE ALA ALA SEQRES 16 A 432 PRO LEU ASN LEU ILE LYS ILE ASN ILE LYS ASP VAL PRO SEQRES 17 A 432 CYS LEU ALA CYS THR GLU VAL SER GLU THR VAL LEU VAL SEQRES 18 A 432 PHE PRO CYS GLU SER LYS HIS VAL THR CYS LEU GLU CYS SEQRES 19 A 432 PHE GLU GLN TYR CYS ARG SER ARG LEU SER GLU ARG GLN SEQRES 20 A 432 PHE MET PRO HIS PRO ASP ILE GLY TYR THR LEU PRO CYS SEQRES 21 A 432 PRO ALA GLY CYS GLU ASN SER PHE ILE GLU GLU ILE HIS SEQRES 22 A 432 HIS PHE LYS LEU LEU SER ARG GLU GLU TYR ALA ARG TYR SEQRES 23 A 432 GLN ARG PHE ALA THR GLU GLU TYR VAL LEU GLN ALA GLY SEQRES 24 A 432 GLY VAL LEU CYS PRO GLN PRO GLY CYS GLY MET GLY LEU SEQRES 25 A 432 LEU VAL GLU PRO GLU CYS LYS LYS VAL THR CYS GLN ASN SEQRES 26 A 432 GLY CYS GLY TYR VAL PHE CYS ARG ASN CYS LEU GLN GLY SEQRES 27 A 432 TYR HIS LEU GLY ASP CYS LEU PRO GLU GLY THR SER THR SEQRES 28 A 432 ASN ALA SER GLY SER CYS GLU TYR SER VAL ASP PRO ASN SEQRES 29 A 432 ARG ALA ALA GLU ALA ARG TRP ASP GLU ALA SER LYS VAL SEQRES 30 A 432 THR ILE LYS VAL MET THR LYS PRO CYS PRO LYS CYS ARG SEQRES 31 A 432 THR PRO THR GLU ARG ASP GLY GLY ALA MET HIS MET VAL SEQRES 32 A 432 CYS THR ARG ALA GLY CYS GLY PHE GLU TRP CYS TRP ILE SEQRES 33 A 432 CYS GLN THR GLU TRP THR ARG ASP CYS MET GLY ALA HIS SEQRES 34 A 432 TRP PHE GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEP SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 159 GLY PRO LEU GLY SER MET ALA ALA SER ARG ARG LEU MET SEQRES 2 C 159 LYS GLU LEU GLU GLU ILE ARG LYS CYS GLY MET LYS ASN SEQRES 3 C 159 PHE ARG ASN ILE GLN VAL ASP GLU ALA ASN LEU LEU THR SEQRES 4 C 159 TRP GLN GLY LEU ILE VAL PRO ASP ASN PRO PRO TYR ASP SEQRES 5 C 159 LYS GLY ALA PHE ARG ILE GLU ILE ASN PHE PRO ALA GLU SEQRES 6 C 159 TYR PRO PHE LYS PRO PRO LYS ILE THR PHE LYS THR LYS SEQRES 7 C 159 ILE TYR HIS PRO ASN ILE ASP GLU LYS GLY GLN VAL LYS SEQRES 8 C 159 LEU PRO VAL ILE SER ALA GLU ASN TRP LYS PRO ALA THR SEQRES 9 C 159 LYS THR ASP GLN VAL ILE GLN SER LEU ILE ALA LEU VAL SEQRES 10 C 159 ASN ASP PRO GLN PRO GLU HIS PRO LEU ARG ALA ASP LEU SEQRES 11 C 159 ALA GLU GLU TYR SER LYS ASP ARG LYS LYS PHE CYS LYS SEQRES 12 C 159 ASN ALA GLU GLU PHE THR LYS LYS TYR GLY GLU LYS ARG SEQRES 13 C 159 PRO VAL ASP MODRES 6DJX SEP A 94 SER MODIFIED RESIDUE MODRES 6DJX SEP B 65 SER MODIFIED RESIDUE HET SEP A 94 10 HET SEP B 65 10 HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET ZN A1004 1 HET ZN A1005 1 HET ZN A1006 1 HETNAM SEP PHOSPHOSERINE HETNAM ZN ZINC ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 4 ZN 6(ZN 2+) HELIX 1 AA1 ASP A 51 GLY A 64 1 14 HELIX 2 AA2 ILE A 85 ASP A 89 5 5 HELIX 3 AA3 GLU A 223 ALA A 228 1 6 HELIX 4 AA4 LEU A 296 SER A 308 1 13 HELIX 5 AA5 GLU A 335 LEU A 342 5 8 HELIX 6 AA6 SER A 343 ALA A 362 1 20 HELIX 7 AA7 THR B 22 GLY B 35 1 14 HELIX 8 AA8 LEU B 56 ASN B 60 5 5 HELIX 9 AA9 ALA C 3 CYS C 17 1 15 HELIX 10 AB1 ASN C 43 ASP C 47 5 5 HELIX 11 AB2 GLU C 60 LYS C 64 5 5 HELIX 12 AB3 LYS C 100 ASP C 114 1 15 HELIX 13 AB4 ARG C 122 ASP C 132 1 11 HELIX 14 AB5 ARG C 133 TYR C 147 1 15 SHEET 1 AA1 5 THR A 41 LEU A 46 0 SHEET 2 AA1 5 LEU A 30 LYS A 35 -1 N ILE A 32 O VAL A 44 SHEET 3 AA1 5 SEP A 94 ARG A 100 1 O SEP A 94 N TYR A 33 SHEET 4 AA1 5 VAL A 70 PHE A 74 -1 N ILE A 73 O HIS A 97 SHEET 5 AA1 5 LYS A 77 GLU A 78 -1 O LYS A 77 N PHE A 74 SHEET 1 AA2 2 VAL A 175 HIS A 176 0 SHEET 2 AA2 2 ALA A 259 PRO A 260 -1 O ALA A 259 N HIS A 176 SHEET 1 AA3 2 GLY A 186 ARG A 191 0 SHEET 2 AA3 2 GLU A 241 CYS A 246 -1 O TYR A 243 N ARG A 189 SHEET 1 AA4 3 ILE A 264 ILE A 266 0 SHEET 2 AA4 3 THR A 282 VAL A 285 -1 O VAL A 283 N LYS A 265 SHEET 3 AA4 3 VAL A 293 CYS A 295 -1 O THR A 294 N LEU A 284 SHEET 1 AA5 2 MET A 313 HIS A 315 0 SHEET 2 AA5 2 GLY A 319 THR A 321 -1 O GLY A 319 N HIS A 315 SHEET 1 AA6 4 LEU A 376 LEU A 377 0 SHEET 2 AA6 4 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 377 SHEET 3 AA6 4 GLN B 2 THR B 7 1 N PHE B 4 O LEU B 67 SHEET 4 AA6 4 THR B 12 GLU B 16 -1 O ILE B 13 N VAL B 5 SHEET 1 AA7 4 LEU A 376 LEU A 377 0 SHEET 2 AA7 4 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 377 SHEET 3 AA7 4 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 4 AA7 4 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA8 4 PHE C 22 GLN C 26 0 SHEET 2 AA8 4 THR C 34 ILE C 39 -1 O GLN C 36 N GLN C 26 SHEET 3 AA8 4 GLY C 49 ASN C 56 -1 O ILE C 53 N GLY C 37 SHEET 4 AA8 4 LYS C 67 PHE C 70 -1 O THR C 69 N GLU C 54 SHEET 1 AA9 4 PHE C 22 GLN C 26 0 SHEET 2 AA9 4 THR C 34 ILE C 39 -1 O GLN C 36 N GLN C 26 SHEET 3 AA9 4 GLY C 49 ASN C 56 -1 O ILE C 53 N GLY C 37 SHEET 4 AA9 4 GLU C 149 LYS C 150 -1 O GLU C 149 N ALA C 50 LINK C GLN A 93 N SEP A 94 1555 1555 1.33 LINK C SEP A 94 N ILE A 95 1555 1555 1.33 LINK C GLU B 64 N SEP B 65 1555 1555 1.33 LINK C SEP B 65 N THR B 66 1555 1555 1.33 LINK SG CYS A 177 ZN ZN A1002 1555 1555 2.31 LINK SG CYS A 180 ZN ZN A1002 1555 1555 2.35 LINK SG CYS A 192 ZN ZN A1001 1555 1555 2.42 LINK SG CYS A 195 ZN ZN A1001 1555 1555 2.30 LINK SG CYS A 222 ZN ZN A1001 1555 1555 2.33 LINK SG CYS A 229 ZN ZN A1001 1555 1555 2.32 LINK SG CYS A 246 ZN ZN A1002 1555 1555 2.31 LINK NE2 HIS A 249 ZN ZN A1002 1555 1555 2.02 LINK SG CYS A 273 ZN ZN A1003 1555 1555 2.30 LINK SG CYS A 276 ZN ZN A1003 1555 1555 2.31 LINK SG CYS A 288 ZN ZN A1004 1555 1555 2.33 LINK ND1 HIS A 292 ZN ZN A1004 1555 1555 2.03 LINK SG CYS A 295 ZN ZN A1003 1555 1555 2.29 LINK SG CYS A 298 ZN ZN A1003 1555 1555 2.25 LINK SG CYS A 324 ZN ZN A1004 1555 1555 2.27 LINK SG CYS A 328 ZN ZN A1004 1555 1555 2.33 LINK SG CYS A 367 ZN ZN A1006 1555 1555 2.25 LINK SG CYS A 372 ZN ZN A1006 1555 1555 2.31 LINK SG CYS A 387 ZN ZN A1006 1555 1555 2.31 LINK SG CYS A 391 ZN ZN A1006 1555 1555 2.20 LINK SG CYS A 396 ZN ZN A1005 1555 1555 2.24 LINK SG CYS A 399 ZN ZN A1005 1555 1555 2.29 LINK NE2 HIS A 404 ZN ZN A1005 1555 1555 2.01 LINK SG CYS A 408 ZN ZN A1005 1555 1555 2.33 SITE 1 AC1 4 CYS A 192 CYS A 195 CYS A 222 CYS A 229 SITE 1 AC2 4 CYS A 177 CYS A 180 CYS A 246 HIS A 249 SITE 1 AC3 4 CYS A 273 CYS A 276 CYS A 295 CYS A 298 SITE 1 AC4 4 CYS A 288 HIS A 292 CYS A 324 CYS A 328 SITE 1 AC5 4 CYS A 396 CYS A 399 HIS A 404 CYS A 408 SITE 1 AC6 4 CYS A 367 CYS A 372 CYS A 387 CYS A 391 CRYST1 135.669 135.669 87.993 90.00 90.00 120.00 P 31 2 1 6 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 0.007371 0.004256 0.000000 0.00000 SCALE2 0.000000 0.008511 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011365 0.00000