PDB Short entry for 4GDL HEADER PROTEIN BINDING 31-JUL-12 4GDL TITLE CRYSTAL STRUCTURE OF HUMAN ATG12~ATG5 CONJUGATE IN COMPLEX WITH AN N- TITLE 2 TERMINAL FRAGMENT OF ATG16L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN ATG12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AUTOPHAGY-RELATED PROTEIN 12, APG12-LIKE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AUTOPHAGY PROTEIN 5; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: APG5-LIKE, APOPTOSIS-SPECIFIC PROTEIN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: AUTOPHAGY-RELATED PROTEIN 16-1; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: APG16-LIKE 1; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APG12, APG12L, ATG12; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PACYC DUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: APG5L, ASP, ATG5; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PACYC DUET-1; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: APG16L, ATG16L1, UNQ9393/PRO34307; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS PROTEIN-PROTEIN CONJUGATE, PROTEIN-PROTEIN COMPLEX, UBIQUITIN-LIKE KEYWDS 2 PROTEIN, AUTOPHAGY, E3 LIGASE, UBIQUITIN-LIKE FOLD, STRUCTURAL KEYWDS 3 PROTEIN, ISOPEPTIDE BOND, CYTOPLASM AND AUTOPHAGOSOMAL MEMBRANES, KEYWDS 4 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.OTOMO,Z.METLAGEL,G.TAKAESU,T.OTOMO REVDAT 4 15-NOV-17 4GDL 1 REMARK REVDAT 3 16-JAN-13 4GDL 1 JRNL REVDAT 2 02-JAN-13 4GDL 1 JRNL REVDAT 1 05-DEC-12 4GDL 0 JRNL AUTH C.OTOMO,Z.METLAGEL,G.TAKAESU,T.OTOMO JRNL TITL STRUCTURE OF THE HUMAN ATG12~ATG5 CONJUGATE REQUIRED FOR LC3 JRNL TITL 2 LIPIDATION IN AUTOPHAGY. JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 59 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 23202584 JRNL DOI 10.1038/NSMB.2431 REMARK 2 REMARK 2 RESOLUTION. 2.88 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) : 2.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 12465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1263 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 36.2267 - 5.9729 0.99 1308 151 0.2006 0.2450 REMARK 3 2 5.9729 - 4.7442 1.00 1287 148 0.2030 0.2265 REMARK 3 3 4.7442 - 4.1455 1.00 1267 142 0.1802 0.2081 REMARK 3 4 4.1455 - 3.7669 0.99 1269 141 0.2207 0.2620 REMARK 3 5 3.7669 - 3.4971 0.99 1258 145 0.2354 0.3062 REMARK 3 6 3.4971 - 3.2911 0.99 1253 133 0.2514 0.2919 REMARK 3 7 3.2911 - 3.1264 0.98 1257 141 0.2506 0.2864 REMARK 3 8 3.1264 - 2.9903 0.97 1222 136 0.3040 0.3126 REMARK 3 9 2.9903 - 2.8753 0.86 1081 126 0.3301 0.4281 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 138.7 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 : 0.006 3316 REMARK 3 ANGLE : 0.510 4482 REMARK 3 CHIRALITY : 0.037 479 REMARK 3 PLANARITY : 0.003 566 REMARK 3 DIHEDRAL : 9.914 1256 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 53:61) REMARK 3 ORIGIN FOR THE GROUP (A): 131.9098 14.7466 14.7212 REMARK 3 T TENSOR REMARK 3 T11: 0.8731 T22: 1.5639 REMARK 3 T33: 1.5721 T12: 0.5559 REMARK 3 T13: 0.1543 T23: 0.5159 REMARK 3 L TENSOR REMARK 3 L11: 3.6238 L22: 3.2452 REMARK 3 L33: 6.0662 L12: 2.7977 REMARK 3 L13: 0.6736 L23: 0.8570 REMARK 3 S TENSOR REMARK 3 S11: -0.9306 S12: 1.6393 S13: 1.6291 REMARK 3 S21: -1.4487 S22: 0.1603 S23: 1.6733 REMARK 3 S31: -0.2069 S32: -1.6583 S33: 0.8281 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 62:91) REMARK 3 ORIGIN FOR THE GROUP (A): 129.9928 6.0654 15.7652 REMARK 3 T TENSOR REMARK 3 T11: 0.6716 T22: 1.8883 REMARK 3 T33: 1.1547 T12: 0.1147 REMARK 3 T13: -0.2917 T23: -0.1696 REMARK 3 L TENSOR REMARK 3 L11: 7.2938 L22: 3.7272 REMARK 3 L33: 5.8908 L12: -3.3147 REMARK 3 L13: -4.1637 L23: -0.7557 REMARK 3 S TENSOR REMARK 3 S11: 0.3887 S12: 1.6713 S13: -0.3986 REMARK 3 S21: -0.4764 S22: -0.5727 S23: 0.9357 REMARK 3 S31: -0.0244 S32: -2.8717 S33: 0.0498 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 92:104) REMARK 3 ORIGIN FOR THE GROUP (A): 133.6834 -2.2909 12.3846 REMARK 3 T TENSOR REMARK 3 T11: 1.1311 T22: 1.3008 REMARK 3 T33: 1.5979 T12: -0.1251 REMARK 3 T13: 0.0261 T23: -0.1878 REMARK 3 L TENSOR REMARK 3 L11: 6.5054 L22: 3.8222 REMARK 3 L33: 3.2700 L12: 4.9979 REMARK 3 L13: -2.7965 L23: -1.8131 REMARK 3 S TENSOR REMARK 3 S11: -1.4633 S12: 0.6937 S13: -2.0906 REMARK 3 S21: -1.9660 S22: 1.1251 S23: -0.2622 REMARK 3 S31: 1.6633 S32: 0.6728 S33: 0.3787 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 105:134) REMARK 3 ORIGIN FOR THE GROUP (A): 140.0424 11.9384 13.0095 REMARK 3 T TENSOR REMARK 3 T11: 0.9782 T22: 1.6464 REMARK 3 T33: 1.2002 T12: 0.2414 REMARK 3 T13: -0.1224 T23: 0.1838 REMARK 3 L TENSOR REMARK 3 L11: 9.7311 L22: 8.8877 REMARK 3 L33: 3.3538 L12: 7.6172 REMARK 3 L13: -0.5108 L23: 2.8401 REMARK 3 S TENSOR REMARK 3 S11: -0.3554 S12: 1.6975 S13: 0.9582 REMARK 3 S21: -1.0900 S22: 0.8627 S23: 0.3778 REMARK 3 S31: -1.1970 S32: 0.2940 S33: -0.6039 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 135:140) REMARK 3 ORIGIN FOR THE GROUP (A): 140.1161 -0.3734 4.6258 REMARK 3 T TENSOR REMARK 3 T11: 1.5600 T22: 2.3461 REMARK 3 T33: 1.7240 T12: 0.3194 REMARK 3 T13: -0.2346 T23: -0.1557 REMARK 3 L TENSOR REMARK 3 L11: 3.7752 L22: 9.6962 REMARK 3 L33: 2.3201 L12: 5.6888 REMARK 3 L13: -0.1132 L23: 1.3887 REMARK 3 S TENSOR REMARK 3 S11: 0.0168 S12: 2.3705 S13: 0.7689 REMARK 3 S21: -1.8665 S22: 0.8880 S23: 0.5925 REMARK 3 S31: -0.1597 S32: -1.8648 S33: 0.0609 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 3:117) REMARK 3 ORIGIN FOR THE GROUP (A): 158.9248 -6.7631 28.9032 REMARK 3 T TENSOR REMARK 3 T11: 0.6411 T22: 0.9328 REMARK 3 T33: 0.9535 T12: -0.0160 REMARK 3 T13: 0.0173 T23: -0.2245 REMARK 3 L TENSOR REMARK 3 L11: 7.0139 L22: 6.3927 REMARK 3 L33: 7.1094 L12: -1.4957 REMARK 3 L13: 1.3425 L23: -2.9860 REMARK 3 S TENSOR REMARK 3 S11: 0.2765 S12: 0.2747 S13: -1.2077 REMARK 3 S21: -0.3156 S22: -0.0774 S23: 0.9176 REMARK 3 S31: 0.7319 S32: -0.3263 S33: 0.0475 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 118:173) REMARK 3 ORIGIN FOR THE GROUP (A): 157.4494 3.1499 6.6807 REMARK 3 T TENSOR REMARK 3 T11: 1.1155 T22: 2.5459 REMARK 3 T33: 0.9501 T12: 0.0125 REMARK 3 T13: -0.1655 T23: -0.2036 REMARK 3 L TENSOR REMARK 3 L11: 4.2388 L22: 3.7026 REMARK 3 L33: 6.3635 L12: -2.2128 REMARK 3 L13: 0.0823 L23: -3.8407 REMARK 3 S TENSOR REMARK 3 S11: 0.3081 S12: 3.5878 S13: -0.2294 REMARK 3 S21: -0.8773 S22: -0.0315 S23: 0.2101 REMARK 3 S31: 0.2615 S32: 1.0743 S33: -0.4028 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 174:274) REMARK 3 ORIGIN FOR THE GROUP (A): 158.9984 18.7852 20.0348 REMARK 3 T TENSOR REMARK 3 T11: 0.8807 T22: 0.9552 REMARK 3 T33: 1.0515 T12: -0.0844 REMARK 3 T13: -0.0671 T23: 0.4015 REMARK 3 L TENSOR REMARK 3 L11: 6.8884 L22: 4.0508 REMARK 3 L33: 2.8113 L12: -0.0630 REMARK 3 L13: 1.7123 L23: 1.5365 REMARK 3 S TENSOR REMARK 3 S11: -0.4282 S12: 1.7108 S13: 2.1212 REMARK 3 S21: -0.3057 S22: 0.1234 S23: 0.0233 REMARK 3 S31: -0.6817 S32: 0.4777 S33: 0.2267 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESSEQ 10:43) REMARK 3 ORIGIN FOR THE GROUP (A): 175.8442 3.7178 25.6581 REMARK 3 T TENSOR REMARK 3 T11: 0.7444 T22: 1.4281 REMARK 3 T33: 0.7622 T12: -0.0613 REMARK 3 T13: 0.2367 T23: 0.0818 REMARK 3 L TENSOR REMARK 3 L11: 7.7345 L22: 3.2343 REMARK 3 L33: 4.4717 L12: -4.1351 REMARK 3 L13: 4.4435 L23: -2.2397 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: 0.9326 S13: 1.0446 REMARK 3 S21: -0.1225 S22: -0.4194 S23: -0.4746 REMARK 3 S31: -0.1523 S32: 0.8516 S33: 0.7474 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 4GDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-09 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0092 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12548 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.875 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 : 4.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.54100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 10 MG/ML IN 0.01M HEPES PH REMARK 280 7.0, 0.3 M NACL, 0.001 M DTT; RESERVOIR: 0.1M BICINE PH9.0, 0.2 REMARK 280 M SODIUM PHOSPHATE DIBASIC, 18% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, HANGING DROP, REMARK 280 PH 6.5 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 68.30050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.19950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.30050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.19950 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 400 REMARK 400 COMPOUND REMARK 400 THERE IS AN ISOPEPTIDE LINKAGE BETWEEN RESIDUE GLY140 OF ATG12 AND REMARK 400 LYS130 OF ATG5. THE ATG12~ATG5 CONJUGATE WAS GENERATED BY CO- REMARK 400 EXPRESSING ATG12 AND ATG5 FROM PACYC DUET-1 AND ATG7 AND ATG10 FROM REMARK 400 PCDF DUET-1 IN E. COLI 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 50 REMARK 465 SER A 51 REMARK 465 LYS A 52 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 228 REMARK 465 PRO B 229 REMARK 465 GLU B 230 REMARK 465 ASP B 231 REMARK 465 GLY B 232 REMARK 465 GLU B 233 REMARK 465 LYS B 234 REMARK 465 ASP B 275 REMARK 465 SER C 8 REMARK 465 HIS C 9 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 107 -60.10 -133.91 REMARK 500 SER B 43 -164.54 -107.38 REMARK 500 SER B 66 -144.37 -146.50 REMARK 500 PHE B 104 -38.90 -140.11 REMARK 500 GLN B 191 118.20 -166.06 REMARK 500 CYS B 223 65.91 -156.28 REMARK 500 ALA B 226 17.75 -159.42 REMARK 500 LEU B 265 75.59 -101.67 REMARK 500 PRO B 273 -163.49 -61.62 REMARK 500 GLN C 28 -67.83 -108.70 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 NA B 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 95 O REMARK 620 2 ASN B 99 OD1 152.4 REMARK 620 3 PRO B 97 O 82.7 92.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GDK RELATED DB: PDB REMARK 900 THE STRUCTURE OF THE SAME COMPLEX IN A DIFFERENT SPACE GROUP. DBREF 4GDL A 52 140 UNP O94817 ATG12_HUMAN 52 140 DBREF 4GDL B 1 275 UNP Q9H1Y0 ATG5_HUMAN 1 275 DBREF 4GDL C 11 43 UNP Q676U5 A16L1_HUMAN 11 43 SEQADV 4GDL GLY A 50 UNP O94817 EXPRESSION TAG SEQADV 4GDL SER A 51 UNP O94817 EXPRESSION TAG SEQADV 4GDL SER C 8 UNP Q676U5 EXPRESSION TAG SEQADV 4GDL HIS C 9 UNP Q676U5 EXPRESSION TAG SEQADV 4GDL MET C 10 UNP Q676U5 EXPRESSION TAG SEQRES 1 A 91 GLY SER LYS LYS LYS ILE ASP ILE LEU LEU LYS ALA VAL SEQRES 2 A 91 GLY ASP THR PRO ILE MET LYS THR LYS LYS TRP ALA VAL SEQRES 3 A 91 GLU ARG THR ARG THR ILE GLN GLY LEU ILE ASP PHE ILE SEQRES 4 A 91 LYS LYS PHE LEU LYS LEU VAL ALA SER GLU GLN LEU PHE SEQRES 5 A 91 ILE TYR VAL ASN GLN SER PHE ALA PRO SER PRO ASP GLN SEQRES 6 A 91 GLU VAL GLY THR LEU TYR GLU CYS PHE GLY SER ASP GLY SEQRES 7 A 91 LYS LEU VAL LEU HIS TYR CYS LYS SER GLN ALA TRP GLY SEQRES 1 B 275 MET THR ASP ASP LYS ASP VAL LEU ARG ASP VAL TRP PHE SEQRES 2 B 275 GLY ARG ILE PRO THR CYS PHE THR LEU TYR GLN ASP GLU SEQRES 3 B 275 ILE THR GLU ARG GLU ALA GLU PRO TYR TYR LEU LEU LEU SEQRES 4 B 275 PRO ARG VAL SER TYR LEU THR LEU VAL THR ASP LYS VAL SEQRES 5 B 275 LYS LYS HIS PHE GLN LYS VAL MET ARG GLN GLU ASP ILE SEQRES 6 B 275 SER GLU ILE TRP PHE GLU TYR GLU GLY THR PRO LEU LYS SEQRES 7 B 275 TRP HIS TYR PRO ILE GLY LEU LEU PHE ASP LEU LEU ALA SEQRES 8 B 275 SER SER SER ALA LEU PRO TRP ASN ILE THR VAL HIS PHE SEQRES 9 B 275 LYS SER PHE PRO GLU LYS ASP LEU LEU HIS CYS PRO SER SEQRES 10 B 275 LYS ASP ALA ILE GLU ALA HIS PHE MET SER CYS MET LYS SEQRES 11 B 275 GLU ALA ASP ALA LEU LYS HIS LYS SER GLN VAL ILE ASN SEQRES 12 B 275 GLU MET GLN LYS LYS ASP HIS LYS GLN LEU TRP MET GLY SEQRES 13 B 275 LEU GLN ASN ASP ARG PHE ASP GLN PHE TRP ALA ILE ASN SEQRES 14 B 275 ARG LYS LEU MET GLU TYR PRO ALA GLU GLU ASN GLY PHE SEQRES 15 B 275 ARG TYR ILE PRO PHE ARG ILE TYR GLN THR THR THR GLU SEQRES 16 B 275 ARG PRO PHE ILE GLN LYS LEU PHE ARG PRO VAL ALA ALA SEQRES 17 B 275 ASP GLY GLN LEU HIS THR LEU GLY ASP LEU LEU LYS GLU SEQRES 18 B 275 VAL CYS PRO SER ALA ILE ASP PRO GLU ASP GLY GLU LYS SEQRES 19 B 275 LYS ASN GLN VAL MET ILE HIS GLY ILE GLU PRO MET LEU SEQRES 20 B 275 GLU THR PRO LEU GLN TRP LEU SER GLU HIS LEU SER TYR SEQRES 21 B 275 PRO ASP ASN PHE LEU HIS ILE SER ILE ILE PRO GLN PRO SEQRES 22 B 275 THR ASP SEQRES 1 C 36 SER HIS MET PRO ARG TRP LYS ARG HIS ILE SER GLU GLN SEQRES 2 C 36 LEU ARG ARG ARG ASP ARG LEU GLN ARG GLN ALA PHE GLU SEQRES 3 C 36 GLU ILE ILE LEU GLN TYR ASN LYS LEU LEU HET NA B 301 1 HETNAM NA SODIUM ION FORMUL 4 NA NA 1+ HELIX 1 1 THR A 80 LEU A 92 1 13 HELIX 2 2 GLU A 115 GLY A 124 1 10 HELIX 3 3 ASP B 4 PHE B 13 1 10 HELIX 4 4 TYR B 44 VAL B 48 5 5 HELIX 5 5 ASP B 50 LYS B 58 1 9 HELIX 6 6 PRO B 82 ALA B 91 1 10 HELIX 7 7 SER B 117 LYS B 138 1 22 HELIX 8 8 GLN B 146 ASN B 159 1 14 HELIX 9 9 ARG B 161 ARG B 170 1 10 HELIX 10 10 LYS B 171 GLU B 174 5 4 HELIX 11 11 THR B 214 CYS B 223 1 10 HELIX 12 12 PRO B 250 LEU B 258 1 9 HELIX 13 13 PRO C 11 GLN C 28 1 18 HELIX 14 14 GLN C 28 LEU C 42 1 15 SHEET 1 A 4 LYS A 72 GLU A 76 0 SHEET 2 A 4 LYS A 54 ALA A 61 -1 N ILE A 57 O TRP A 73 SHEET 3 A 4 LYS A 128 CYS A 134 1 O LEU A 131 N LEU A 58 SHEET 4 A 4 PHE A 101 VAL A 104 -1 N PHE A 101 O CYS A 134 SHEET 1 B 5 TYR B 35 PRO B 40 0 SHEET 2 B 5 ARG B 15 LEU B 22 -1 N PHE B 20 O TYR B 35 SHEET 3 B 5 TRP B 98 HIS B 103 1 O TRP B 98 N PRO B 17 SHEET 4 B 5 TRP B 69 TYR B 72 -1 N GLU B 71 O THR B 101 SHEET 5 B 5 THR B 75 PRO B 76 -1 O THR B 75 N TYR B 72 SHEET 1 C 3 PHE B 187 TYR B 190 0 SHEET 2 C 3 LEU B 265 PRO B 271 1 O ILE B 267 N TYR B 190 SHEET 3 C 3 ASN B 236 MET B 239 -1 N GLN B 237 O ILE B 270 LINK O ALA B 95 NA NA B 301 1555 1555 2.25 LINK OD1 ASN B 99 NA NA B 301 1555 1555 2.41 LINK O PRO B 97 NA NA B 301 1555 1555 2.68 LINK C GLY A 140 NZ LYS B 130 1555 1555 1.33 CISPEP 1 GLY A 63 ASP A 64 0 2.84 CISPEP 2 LEU B 96 PRO B 97 0 -4.26 SITE 1 AC1 3 ALA B 95 PRO B 97 ASN B 99 CRYST1 136.601 58.399 91.802 90.00 130.04 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007321 0.000000 0.006151 0.00000 SCALE2 0.000000 0.017124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014228 0.00000