PDB Short entry for 5YWR HEADER SIGNALING PROTEIN 30-NOV-17 5YWR TITLE CRYSTAL STRUCTURE OF RING E3 LIGASE ZNRF1 IN COMPLEX WITH UBE2N TITLE 2 (UBC13) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 N; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BENDLESS-LIKE UBIQUITIN-CONJUGATING ENZYME,E2 UBIQUITIN- COMPND 5 CONJUGATING ENZYME N,UBC13,UBCH13,UBIQUITIN CARRIER PROTEIN N, COMPND 6 UBIQUITIN-PROTEIN LIGASE N; COMPND 7 EC: 2.3.2.23; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE ZNRF1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: NERVE INJURY-INDUCED GENE 283 PROTEIN,RING-TYPE E3 UBIQUITIN COMPND 13 TRANSFERASE ZNRF1,ZINC/RING FINGER PROTEIN 1; COMPND 14 EC: 2.3.2.27; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: FIRST 137 AMINO ACIDS DELETED FROM THE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2N, BLU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETSUMO2; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: ZNRF1, NIN283; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETSUMO2 KEYWDS UBIQUITIN E3 LIGASE, ZNRF1, UBIQUITIN CONJUGATING E2, UBE2N, UBC13, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.P.BEHERA,P.NASKAR,A.B.DATTA REVDAT 2 27-MAR-24 5YWR 1 REMARK REVDAT 1 06-JUN-18 5YWR 0 JRNL AUTH A.P.BEHERA,P.NASKAR,S.AGARWAL,P.A.BANKA,A.PODDAR,A.B.DATTA JRNL TITL STRUCTURAL INSIGHTS INTO THE NANOMOLAR AFFINITY OF RING E3 JRNL TITL 2 LIGASE ZNRF1 FOR UBE2N AND ITS FUNCTIONAL IMPLICATIONS. JRNL REF BIOCHEM. J. V. 475 1569 2018 JRNL REFN ESSN 1470-8728 JRNL PMID 29626159 JRNL DOI 10.1042/BCJ20170909 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 46000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 2368 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 42.4342 - 3.7791 0.99 2755 161 0.1518 0.1762 REMARK 3 2 3.7791 - 2.9998 1.00 2640 163 0.1438 0.1511 REMARK 3 3 2.9998 - 2.6207 1.00 2629 124 0.1623 0.1872 REMARK 3 4 2.6207 - 2.3811 1.00 2608 131 0.1577 0.1780 REMARK 3 5 2.3811 - 2.2104 1.00 2610 130 0.1549 0.1570 REMARK 3 6 2.2104 - 2.0801 1.00 2594 146 0.1533 0.1751 REMARK 3 7 2.0801 - 1.9759 1.00 2576 136 0.1619 0.1968 REMARK 3 8 1.9759 - 1.8899 1.00 2591 136 0.1706 0.2172 REMARK 3 9 1.8899 - 1.8172 1.00 2531 160 0.1764 0.1772 REMARK 3 10 1.8172 - 1.7545 1.00 2561 141 0.1824 0.2195 REMARK 3 11 1.7545 - 1.6996 1.00 2560 138 0.1856 0.1990 REMARK 3 12 1.6996 - 1.6510 1.00 2572 143 0.1856 0.2153 REMARK 3 13 1.6510 - 1.6075 1.00 2538 135 0.1949 0.2014 REMARK 3 14 1.6075 - 1.5683 1.00 2558 140 0.2063 0.2188 REMARK 3 15 1.5683 - 1.5327 1.00 2548 121 0.2240 0.2315 REMARK 3 16 1.5327 - 1.5001 0.97 2492 133 0.2540 0.2991 REMARK 3 17 1.5001 - 1.4700 0.89 2269 130 0.2851 0.3421 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.060 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 : 0.005 2052 REMARK 3 ANGLE : 0.683 2780 REMARK 3 CHIRALITY : 0.075 302 REMARK 3 PLANARITY : 0.005 370 REMARK 3 DIHEDRAL : 16.219 799 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.7450 23.9811 23.6602 REMARK 3 T TENSOR REMARK 3 T11: 0.1362 T22: 0.1077 REMARK 3 T33: 0.0553 T12: 0.0002 REMARK 3 T13: 0.0065 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 6.9317 L22: 8.1536 REMARK 3 L33: 7.3835 L12: 1.5276 REMARK 3 L13: -0.8858 L23: -0.7396 REMARK 3 S TENSOR REMARK 3 S11: 0.1984 S12: -0.4451 S13: 0.1596 REMARK 3 S21: 0.5991 S22: -0.0430 S23: 0.1483 REMARK 3 S31: -0.0365 S32: -0.0224 S33: -0.0808 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.9728 33.2293 18.4815 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.1556 REMARK 3 T33: 0.1861 T12: -0.0529 REMARK 3 T13: -0.0188 T23: -0.0423 REMARK 3 L TENSOR REMARK 3 L11: 2.7942 L22: 4.4238 REMARK 3 L33: 7.0703 L12: 3.1441 REMARK 3 L13: -3.0735 L23: -2.3305 REMARK 3 S TENSOR REMARK 3 S11: 0.1911 S12: -0.2388 S13: 0.4079 REMARK 3 S21: 0.3102 S22: -0.2451 S23: -0.5839 REMARK 3 S31: -0.0735 S32: 0.4097 S33: -0.0135 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.0920 36.7875 10.5088 REMARK 3 T TENSOR REMARK 3 T11: 0.0882 T22: 0.0730 REMARK 3 T33: 0.1520 T12: 0.0068 REMARK 3 T13: 0.0152 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 4.2045 L22: 2.4014 REMARK 3 L33: 3.4905 L12: 2.0600 REMARK 3 L13: -2.8290 L23: -1.6297 REMARK 3 S TENSOR REMARK 3 S11: 0.0382 S12: -0.1234 S13: 0.0764 REMARK 3 S21: -0.0544 S22: -0.0448 S23: -0.1397 REMARK 3 S31: -0.0660 S32: 0.1655 S33: -0.0380 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6805 21.1134 12.6913 REMARK 3 T TENSOR REMARK 3 T11: 0.1204 T22: 0.1059 REMARK 3 T33: 0.1412 T12: -0.0032 REMARK 3 T13: 0.0007 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 7.0906 L22: 3.4649 REMARK 3 L33: 3.3550 L12: 1.4367 REMARK 3 L13: -0.1421 L23: -3.2761 REMARK 3 S TENSOR REMARK 3 S11: -0.0947 S12: -0.0875 S13: 0.0200 REMARK 3 S21: -0.1872 S22: 0.0634 S23: 0.4961 REMARK 3 S31: 0.3056 S32: -0.2426 S33: 0.0688 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 68 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8267 30.0430 2.0429 REMARK 3 T TENSOR REMARK 3 T11: 0.1291 T22: 0.1066 REMARK 3 T33: 0.1253 T12: -0.0033 REMARK 3 T13: -0.0105 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.9312 L22: 5.7756 REMARK 3 L33: 2.5101 L12: 0.2834 REMARK 3 L13: -0.6036 L23: -2.6365 REMARK 3 S TENSOR REMARK 3 S11: 0.0161 S12: 0.1116 S13: 0.0790 REMARK 3 S21: -0.5718 S22: 0.0321 S23: 0.1654 REMARK 3 S31: 0.2431 S32: -0.1350 S33: -0.0588 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1858 29.3733 0.3740 REMARK 3 T TENSOR REMARK 3 T11: 0.2136 T22: 0.1722 REMARK 3 T33: 0.1752 T12: 0.0261 REMARK 3 T13: -0.0106 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 2.7108 L22: 4.1986 REMARK 3 L33: 3.0522 L12: -0.2789 REMARK 3 L13: -2.0549 L23: -2.0645 REMARK 3 S TENSOR REMARK 3 S11: 0.1664 S12: 0.4430 S13: 0.0955 REMARK 3 S21: -0.6509 S22: -0.0695 S23: 0.0749 REMARK 3 S31: 0.2072 S32: -0.3005 S33: -0.0907 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 152 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.7692 43.7774 -5.2243 REMARK 3 T TENSOR REMARK 3 T11: 0.2869 T22: 0.1592 REMARK 3 T33: 0.2703 T12: 0.0151 REMARK 3 T13: 0.0858 T23: 0.0893 REMARK 3 L TENSOR REMARK 3 L11: 4.0620 L22: 4.9509 REMARK 3 L33: 4.3740 L12: 0.2530 REMARK 3 L13: -0.7609 L23: 1.1599 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: 0.3288 S13: 0.3359 REMARK 3 S21: -0.6754 S22: -0.1039 S23: -0.2919 REMARK 3 S31: -0.1685 S32: 0.3228 S33: 0.0865 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 141 THROUGH 171 ) OR CHAIN 'B' REMARK 3 AND (RESID 302) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0323 5.7622 -4.7667 REMARK 3 T TENSOR REMARK 3 T11: 0.1049 T22: 0.1144 REMARK 3 T33: 0.1659 T12: -0.0083 REMARK 3 T13: -0.0099 T23: -0.0187 REMARK 3 L TENSOR REMARK 3 L11: 3.4972 L22: 2.5058 REMARK 3 L33: 7.6142 L12: -1.0474 REMARK 3 L13: 2.7454 L23: -1.1901 REMARK 3 S TENSOR REMARK 3 S11: -0.0712 S12: 0.2350 S13: 0.0866 REMARK 3 S21: 0.0448 S22: -0.0274 S23: -0.2907 REMARK 3 S31: -0.1524 S32: 0.2183 S33: 0.0776 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 172 THROUGH 227) OR CHAIN 'B' REMARK 3 AND (RESID 301 AND RESID 303) REMARK 3 ORIGIN FOR THE GROUP (A): 32.7539 6.2039 15.3719 REMARK 3 T TENSOR REMARK 3 T11: 0.0549 T22: 0.0783 REMARK 3 T33: 0.1473 T12: 0.0090 REMARK 3 T13: 0.0114 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 2.3332 L22: 3.7276 REMARK 3 L33: 4.6475 L12: -0.4896 REMARK 3 L13: 0.6015 L23: -0.9380 REMARK 3 S TENSOR REMARK 3 S11: 0.0194 S12: -0.0009 S13: -0.1435 REMARK 3 S21: -0.0727 S22: -0.0662 S23: -0.2044 REMARK 3 S31: 0.1607 S32: 0.2753 S33: 0.0174 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 5YWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979470 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46073 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 47.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.87200 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: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM FROMATE DIHYDRATE, 20% REMARK 280 PEG 3350 (W/V), PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 23.71500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.39600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.77400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.39600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.77400 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: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 23.71500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 29.77400 REMARK 350 BIOMT3 2 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 ALA A 2 REMARK 465 SER B 139 REMARK 465 HIS B 140 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 304 O HOH A 448 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 154 OE2 GLU B 223 4455 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 92 -106.15 -132.67 REMARK 500 SER B 149 -1.51 74.63 REMARK 500 ALA B 181 31.69 -140.60 REMARK 500 LEU B 203 -1.01 83.69 REMARK 500 ASN B 218 110.16 -162.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 499 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 500 DISTANCE = 5.88 ANGSTROMS 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 B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 145 SG REMARK 620 2 CYS B 148 SG 116.5 REMARK 620 3 HIS B 160 NE2 103.4 98.3 REMARK 620 4 CYS B 164 SG 118.5 109.1 108.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 184 SG REMARK 620 2 CYS B 187 SG 113.5 REMARK 620 3 HIS B 207 ND1 101.3 99.6 REMARK 620 4 CYS B 210 SG 120.1 104.2 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 202 SG REMARK 620 2 CYS B 204 SG 116.8 REMARK 620 3 CYS B 221 SG 107.8 100.3 REMARK 620 4 HIS B 224 ND1 112.2 100.8 118.7 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 PGE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 303 DBREF 5YWR A 1 152 UNP P61088 UBE2N_HUMAN 1 152 DBREF 5YWR B 139 227 UNP Q8ND25 ZNRF1_HUMAN 139 227 SEQRES 1 A 152 MET ALA GLY LEU PRO ARG ARG ILE ILE LYS GLU THR GLN SEQRES 2 A 152 ARG LEU LEU ALA GLU PRO VAL PRO GLY ILE LYS ALA GLU SEQRES 3 A 152 PRO ASP GLU SER ASN ALA ARG TYR PHE HIS VAL VAL ILE SEQRES 4 A 152 ALA GLY PRO GLN ASP SER PRO PHE GLU GLY GLY THR PHE SEQRES 5 A 152 LYS LEU GLU LEU PHE LEU PRO GLU GLU TYR PRO MET ALA SEQRES 6 A 152 ALA PRO LYS VAL ARG PHE MET THR LYS ILE TYR HIS PRO SEQRES 7 A 152 ASN VAL ASP LYS LEU GLY ARG ILE CYS LEU ASP ILE LEU SEQRES 8 A 152 LYS ASP LYS TRP SER PRO ALA LEU GLN ILE ARG THR VAL SEQRES 9 A 152 LEU LEU SER ILE GLN ALA LEU LEU SER ALA PRO ASN PRO SEQRES 10 A 152 ASP ASP PRO LEU ALA ASN ASP VAL ALA GLU GLN TRP LYS SEQRES 11 A 152 THR ASN GLU ALA GLN ALA ILE GLU THR ALA ARG ALA TRP SEQRES 12 A 152 THR ARG LEU TYR ALA MET ASN ASN ILE SEQRES 1 B 89 SER HIS SER GLY PHE LYS CYS PRO ILE CYS SER LYS SER SEQRES 2 B 89 VAL ALA SER ASP GLU MET GLU MET HIS PHE ILE MET CYS SEQRES 3 B 89 LEU SER LYS PRO ARG LEU SER TYR ASN ASP ASP VAL LEU SEQRES 4 B 89 THR LYS ASP ALA GLY GLU CYS VAL ILE CYS LEU GLU GLU SEQRES 5 B 89 LEU LEU GLN GLY ASP THR ILE ALA ARG LEU PRO CYS LEU SEQRES 6 B 89 CYS ILE TYR HIS LYS SER CYS ILE ASP SER TRP PHE GLU SEQRES 7 B 89 VAL ASN ARG SER CYS PRO GLU HIS PRO ALA ASP HET PGE A 201 10 HET FMT A 202 3 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HETNAM PGE TRIETHYLENE GLYCOL HETNAM FMT FORMIC ACID HETNAM ZN ZINC ION FORMUL 3 PGE C6 H14 O4 FORMUL 4 FMT C H2 O2 FORMUL 5 ZN 3(ZN 2+) FORMUL 8 HOH *364(H2 O) HELIX 1 AA1 PRO A 5 GLU A 18 1 14 HELIX 2 AA2 LEU A 88 LYS A 92 5 5 HELIX 3 AA3 GLN A 100 ALA A 114 1 15 HELIX 4 AA4 ASN A 123 ASN A 132 1 10 HELIX 5 AA5 ASN A 132 ALA A 148 1 17 HELIX 6 AA6 ALA B 153 ASP B 155 5 3 HELIX 7 AA7 GLU B 156 LEU B 165 1 10 HELIX 8 AA8 LYS B 208 GLU B 216 1 9 SHEET 1 AA1 4 ILE A 23 PRO A 27 0 SHEET 2 AA1 4 TYR A 34 ALA A 40 -1 O VAL A 38 N LYS A 24 SHEET 3 AA1 4 THR A 51 PHE A 57 -1 O LEU A 56 N PHE A 35 SHEET 4 AA1 4 LYS A 68 PHE A 71 -1 O LYS A 68 N PHE A 57 SHEET 1 AA2 2 PHE B 143 LYS B 144 0 SHEET 2 AA2 2 SER B 151 VAL B 152 -1 O VAL B 152 N PHE B 143 SHEET 1 AA3 3 ASN B 173 VAL B 176 0 SHEET 2 AA3 3 THR B 196 ARG B 199 -1 O ARG B 199 N ASN B 173 SHEET 3 AA3 3 ILE B 205 HIS B 207 -1 O TYR B 206 N ALA B 198 LINK SG CYS B 145 ZN ZN B 302 1555 1555 2.33 LINK SG CYS B 148 ZN ZN B 302 1555 1555 2.32 LINK NE2 HIS B 160 ZN ZN B 302 1555 1555 2.10 LINK SG CYS B 164 ZN ZN B 302 1555 1555 2.29 LINK SG CYS B 184 ZN ZN B 301 1555 1555 2.34 LINK SG CYS B 187 ZN ZN B 301 1555 1555 2.29 LINK SG CYS B 202 ZN ZN B 303 1555 1555 2.25 LINK SG CYS B 204 ZN ZN B 303 1555 1555 2.34 LINK ND1 HIS B 207 ZN ZN B 301 1555 1555 2.13 LINK SG CYS B 210 ZN ZN B 301 1555 1555 2.30 LINK SG CYS B 221 ZN ZN B 303 1555 1555 2.32 LINK ND1 HIS B 224 ZN ZN B 303 1555 1555 2.01 CISPEP 1 TYR A 62 PRO A 63 0 8.82 SITE 1 AC1 4 GLY A 22 ILE A 23 VAL A 38 HOH A 364 SITE 1 AC2 2 ILE A 86 LYS A 92 SITE 1 AC3 4 CYS B 184 CYS B 187 HIS B 207 CYS B 210 SITE 1 AC4 4 CYS B 145 CYS B 148 HIS B 160 CYS B 164 SITE 1 AC5 4 CYS B 202 CYS B 204 CYS B 221 HIS B 224 CRYST1 47.430 59.548 94.792 90.00 90.00 90.00 P 21 21 21 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 0.021084 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010549 0.00000