PDB Short entry for 6N6J HEADER RNA BINDING PROTEIN/RNA 26-NOV-18 6N6J TITLE HUMAN REXO2 BOUND TO PAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA EXONUCLEASE 2 HOMOLOG,SMALL FRAGMENT NUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: REXO2; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*AP*A)-3'); COMPND 9 CHAIN: D, C; COMPND 10 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: REXO2, SFN, SMFN, CGI-114; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS 3'-5' EXORIBONUCLEASE, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.LORMAND,H.SONDERMANN REVDAT 3 01-JAN-20 6N6J 1 REMARK REVDAT 2 16-OCT-19 6N6J 1 JRNL REVDAT 1 12-JUN-19 6N6J 0 JRNL AUTH S.K.KIM,J.D.LORMAND,C.A.WEISS,K.A.EGER,H.TURDIEV,A.TURDIEV, JRNL AUTH 2 W.C.WINKLER,H.SONDERMANN,V.T.LEE JRNL TITL A DEDICATED DIRIBONUCLEOTIDASE RESOLVES A KEY BOTTLENECK FOR JRNL TITL 2 THE TERMINAL STEP OF RNA DEGRADATION. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31225796 JRNL DOI 10.7554/ELIFE.46313 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 118555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2958 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 31.6782 - 3.6309 1.00 5872 149 0.1489 0.1649 REMARK 3 2 3.6309 - 2.8826 1.00 5647 146 0.1406 0.1661 REMARK 3 3 2.8826 - 2.5184 1.00 5626 143 0.1564 0.1969 REMARK 3 4 2.5184 - 2.2882 1.00 5557 143 0.1483 0.1611 REMARK 3 5 2.2882 - 2.1242 1.00 5573 142 0.1413 0.1464 REMARK 3 6 2.1242 - 1.9990 1.00 5532 141 0.1417 0.1487 REMARK 3 7 1.9990 - 1.8989 1.00 5502 143 0.1464 0.1789 REMARK 3 8 1.8989 - 1.8162 1.00 5532 140 0.1434 0.1596 REMARK 3 9 1.8162 - 1.7463 1.00 5502 141 0.1473 0.1534 REMARK 3 10 1.7463 - 1.6861 1.00 5502 141 0.1452 0.1422 REMARK 3 11 1.6861 - 1.6334 1.00 5480 141 0.1457 0.1691 REMARK 3 12 1.6334 - 1.5867 1.00 5473 141 0.1473 0.1460 REMARK 3 13 1.5867 - 1.5449 1.00 5480 140 0.1496 0.1664 REMARK 3 14 1.5449 - 1.5072 1.00 5496 140 0.1508 0.1680 REMARK 3 15 1.5072 - 1.4729 1.00 5472 139 0.1600 0.1673 REMARK 3 16 1.4729 - 1.4416 1.00 5466 140 0.1708 0.1682 REMARK 3 17 1.4416 - 1.4128 1.00 5485 141 0.1843 0.1988 REMARK 3 18 1.4128 - 1.3861 1.00 5448 139 0.1986 0.2075 REMARK 3 19 1.3861 - 1.3613 1.00 5489 140 0.2121 0.2415 REMARK 3 20 1.3613 - 1.3383 1.00 5450 140 0.2435 0.2422 REMARK 3 21 1.3383 - 1.3167 0.92 5013 128 0.2816 0.3222 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.69 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 4:86) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5738 8.1830 12.6855 REMARK 3 T TENSOR REMARK 3 T11: 0.0923 T22: 0.0901 REMARK 3 T33: 0.0611 T12: -0.0041 REMARK 3 T13: 0.0024 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.0433 L22: 1.7362 REMARK 3 L33: 0.6713 L12: 0.5658 REMARK 3 L13: 0.4913 L23: 0.1694 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: -0.0064 S13: 0.0042 REMARK 3 S21: -0.0974 S22: 0.0045 S23: 0.0579 REMARK 3 S31: 0.0371 S32: -0.0312 S33: -0.0298 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 87:184) REMARK 3 ORIGIN FOR THE GROUP (A): 5.9873 18.0447 15.7413 REMARK 3 T TENSOR REMARK 3 T11: 0.0916 T22: 0.1196 REMARK 3 T33: 0.0987 T12: 0.0012 REMARK 3 T13: 0.0030 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.3050 L22: 1.7230 REMARK 3 L33: 0.5662 L12: 0.1798 REMARK 3 L13: -0.1772 L23: -0.4785 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0194 S13: -0.0056 REMARK 3 S21: -0.1204 S22: -0.0074 S23: -0.0453 REMARK 3 S31: 0.0200 S32: 0.0072 S33: -0.0033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 185:198) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5009 31.2163 9.0880 REMARK 3 T TENSOR REMARK 3 T11: 0.5429 T22: 0.7371 REMARK 3 T33: 0.6190 T12: 0.0413 REMARK 3 T13: 0.1250 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 8.5667 L22: 7.3090 REMARK 3 L33: 3.1099 L12: -2.1198 REMARK 3 L13: 5.1386 L23: -0.8379 REMARK 3 S TENSOR REMARK 3 S11: 0.5136 S12: 0.8944 S13: 0.0756 REMARK 3 S21: -1.1788 S22: -0.3998 S23: -1.0394 REMARK 3 S31: -0.0112 S32: 1.0186 S33: -0.1072 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 2:7) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9840 43.2256 14.0536 REMARK 3 T TENSOR REMARK 3 T11: 0.5237 T22: 0.3900 REMARK 3 T33: 0.4514 T12: 0.1065 REMARK 3 T13: -0.0004 T23: 0.1766 REMARK 3 L TENSOR REMARK 3 L11: 3.7405 L22: 5.2706 REMARK 3 L33: 5.4465 L12: 2.6592 REMARK 3 L13: 2.0979 L23: -2.3058 REMARK 3 S TENSOR REMARK 3 S11: 0.2325 S12: 2.0514 S13: 1.7648 REMARK 3 S21: -1.4203 S22: -0.1114 S23: 0.2852 REMARK 3 S31: -1.9271 S32: -0.7241 S33: -0.1609 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 8:137) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6758 27.8407 33.7716 REMARK 3 T TENSOR REMARK 3 T11: 0.0797 T22: 0.1116 REMARK 3 T33: 0.0967 T12: -0.0176 REMARK 3 T13: 0.0069 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.9417 L22: 1.1423 REMARK 3 L33: 1.1278 L12: -0.1776 REMARK 3 L13: -0.1035 L23: 0.1003 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: -0.1203 S13: -0.0545 REMARK 3 S21: 0.1100 S22: -0.0175 S23: 0.0892 REMARK 3 S31: 0.0973 S32: -0.0966 S33: 0.0179 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 138:187) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5761 32.5621 26.9073 REMARK 3 T TENSOR REMARK 3 T11: 0.0809 T22: 0.0999 REMARK 3 T33: 0.1096 T12: -0.0146 REMARK 3 T13: -0.0116 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 3.0271 L22: 0.8136 REMARK 3 L33: 1.2436 L12: -0.2904 REMARK 3 L13: -1.5182 L23: 0.5462 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: -0.1945 S13: 0.1354 REMARK 3 S21: -0.0056 S22: 0.0689 S23: -0.1059 REMARK 3 S31: -0.0752 S32: 0.2050 S33: -0.0616 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 6N6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.317 REMARK 200 RESOLUTION RANGE LOW (A) : 45.863 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63400 REMARK 200 R SYM FOR SHELL (I) : 0.63400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6N6I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE (PH 5.5) AND 15 REMARK 280 -20% POLYETHYLENE GLYCOL 3350, 25% GLYCEROL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 22.93150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.11250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.78300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.11250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.93150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.78300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 REMARK 350 BIOMOLECULE: 2 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: 1670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 199 REMARK 465 ASN A 200 REMARK 465 GLU A 201 REMARK 465 LYS A 202 REMARK 465 THR A 203 REMARK 465 VAL A 204 REMARK 465 SER A 205 REMARK 465 MET B 1 REMARK 465 ASP B 188 REMARK 465 GLU B 189 REMARK 465 LYS B 190 REMARK 465 LYS B 191 REMARK 465 ARG B 192 REMARK 465 LYS B 193 REMARK 465 ILE B 194 REMARK 465 ILE B 195 REMARK 465 GLU B 196 REMARK 465 ASN B 197 REMARK 465 GLY B 198 REMARK 465 GLU B 199 REMARK 465 ASN B 200 REMARK 465 GLU B 201 REMARK 465 LYS B 202 REMARK 465 THR B 203 REMARK 465 VAL B 204 REMARK 465 SER B 205 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 LYS A 190 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ILE B 187 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A D 603 P A D 603 OP3 -0.120 REMARK 500 A D 603 P A D 603 OP3 -0.122 REMARK 500 A C 603 P A C 603 OP3 -0.117 REMARK 500 A C 603 P A C 603 OP3 -0.120 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 25 -37.30 -130.97 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 D 701 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 A D 603 O3' 157.7 REMARK 620 3 A D 603 O3' 157.6 0.2 REMARK 620 4 A D 604 OP1 101.8 57.1 57.1 REMARK 620 5 HOH A 476 O 81.7 101.1 101.3 83.4 REMARK 620 6 HOH A 507 O 86.2 89.6 89.5 98.0 167.9 REMARK 620 7 HOH D 802 O 122.2 77.5 77.5 134.2 112.8 74.7 REMARK 620 8 HOH D 802 O 89.0 113.0 113.0 166.8 90.7 90.2 38.6 REMARK 620 9 HOH A 476 O 104.5 87.2 87.4 98.6 30.8 157.8 83.1 71.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 702 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 15 OD1 REMARK 620 2 A C 603 O3' 156.6 REMARK 620 3 A C 603 O3' 156.9 0.6 REMARK 620 4 A C 604 OP1 103.1 57.0 57.0 REMARK 620 5 HOH B 472 O 84.2 87.5 88.1 100.4 REMARK 620 6 HOH C 802 O 119.9 77.9 78.0 134.9 72.6 REMARK 620 7 HOH C 802 O 91.2 110.1 110.0 164.8 86.1 34.3 REMARK 620 8 HOH C 805 O 105.2 90.9 90.2 97.9 157.0 84.6 72.9 REMARK 620 9 HOH C 805 O 86.0 102.5 101.9 84.1 169.9 110.6 91.7 26.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLI A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 702 DBREF 6N6J A 1 205 UNP Q9Y3B8 ORN_HUMAN 1 205 DBREF 6N6J D 603 604 PDB 6N6J 6N6J 603 604 DBREF 6N6J B 1 205 UNP Q9Y3B8 ORN_HUMAN 1 205 DBREF 6N6J C 603 604 PDB 6N6J 6N6J 603 604 SEQRES 1 A 205 MET ALA ALA GLY GLU SER MET ALA GLN ARG MET VAL TRP SEQRES 2 A 205 VAL ASP LEU GLU MET THR GLY LEU ASP ILE GLU LYS ASP SEQRES 3 A 205 GLN ILE ILE GLU MET ALA CYS LEU ILE THR ASP SER ASP SEQRES 4 A 205 LEU ASN ILE LEU ALA GLU GLY PRO ASN LEU ILE ILE LYS SEQRES 5 A 205 GLN PRO ASP GLU LEU LEU ASP SER MET SER ASP TRP CYS SEQRES 6 A 205 LYS GLU HIS HIS GLY LYS SER GLY LEU THR LYS ALA VAL SEQRES 7 A 205 LYS GLU SER THR ILE THR LEU GLN GLN ALA GLU TYR GLU SEQRES 8 A 205 PHE LEU SER PHE VAL ARG GLN GLN THR PRO PRO GLY LEU SEQRES 9 A 205 CYS PRO LEU ALA GLY ASN SER VAL HIS GLU ASP LYS LYS SEQRES 10 A 205 PHE LEU ASP LYS TYR MET PRO GLN PHE MET LYS HIS LEU SEQRES 11 A 205 HIS TYR ARG ILE ILE ASP VAL SER THR VAL LYS GLU LEU SEQRES 12 A 205 CYS ARG ARG TRP TYR PRO GLU GLU TYR GLU PHE ALA PRO SEQRES 13 A 205 LYS LYS ALA ALA SER HIS ARG ALA LEU ASP ASP ILE SER SEQRES 14 A 205 GLU SER ILE LYS GLU LEU GLN PHE TYR ARG ASN ASN ILE SEQRES 15 A 205 PHE LYS LYS LYS ILE ASP GLU LYS LYS ARG LYS ILE ILE SEQRES 16 A 205 GLU ASN GLY GLU ASN GLU LYS THR VAL SER SEQRES 1 D 2 A A SEQRES 1 B 205 MET ALA ALA GLY GLU SER MET ALA GLN ARG MET VAL TRP SEQRES 2 B 205 VAL ASP LEU GLU MET THR GLY LEU ASP ILE GLU LYS ASP SEQRES 3 B 205 GLN ILE ILE GLU MET ALA CYS LEU ILE THR ASP SER ASP SEQRES 4 B 205 LEU ASN ILE LEU ALA GLU GLY PRO ASN LEU ILE ILE LYS SEQRES 5 B 205 GLN PRO ASP GLU LEU LEU ASP SER MET SER ASP TRP CYS SEQRES 6 B 205 LYS GLU HIS HIS GLY LYS SER GLY LEU THR LYS ALA VAL SEQRES 7 B 205 LYS GLU SER THR ILE THR LEU GLN GLN ALA GLU TYR GLU SEQRES 8 B 205 PHE LEU SER PHE VAL ARG GLN GLN THR PRO PRO GLY LEU SEQRES 9 B 205 CYS PRO LEU ALA GLY ASN SER VAL HIS GLU ASP LYS LYS SEQRES 10 B 205 PHE LEU ASP LYS TYR MET PRO GLN PHE MET LYS HIS LEU SEQRES 11 B 205 HIS TYR ARG ILE ILE ASP VAL SER THR VAL LYS GLU LEU SEQRES 12 B 205 CYS ARG ARG TRP TYR PRO GLU GLU TYR GLU PHE ALA PRO SEQRES 13 B 205 LYS LYS ALA ALA SER HIS ARG ALA LEU ASP ASP ILE SER SEQRES 14 B 205 GLU SER ILE LYS GLU LEU GLN PHE TYR ARG ASN ASN ILE SEQRES 15 B 205 PHE LYS LYS LYS ILE ASP GLU LYS LYS ARG LYS ILE ILE SEQRES 16 B 205 GLU ASN GLY GLU ASN GLU LYS THR VAL SER SEQRES 1 C 2 A A HET GOL A 301 6 HET MLI A 302 7 HET NA D 701 1 HET GOL B 301 6 HET EDO C 701 8 HET NA C 702 1 HETNAM GOL GLYCEROL HETNAM MLI MALONATE ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 MLI C3 H2 O4 2- FORMUL 7 NA 2(NA 1+) FORMUL 9 EDO C2 H6 O2 FORMUL 11 HOH *455(H2 O) HELIX 1 AA1 GLY A 4 GLN A 9 1 6 HELIX 2 AA2 PRO A 54 SER A 60 1 7 HELIX 3 AA3 SER A 62 SER A 72 1 11 HELIX 4 AA4 GLY A 73 SER A 81 1 9 HELIX 5 AA5 THR A 84 THR A 100 1 17 HELIX 6 AA6 VAL A 112 MET A 123 1 12 HELIX 7 AA7 MET A 123 HIS A 129 1 7 HELIX 8 AA8 VAL A 137 TYR A 148 1 12 HELIX 9 AA9 TYR A 148 GLU A 153 1 6 HELIX 10 AB1 ARG A 163 PHE A 183 1 21 HELIX 11 AB2 ASP A 188 GLY A 198 1 11 HELIX 12 AB3 ALA B 3 GLN B 9 1 7 HELIX 13 AB4 PRO B 54 SER B 60 1 7 HELIX 14 AB5 SER B 62 SER B 72 1 11 HELIX 15 AB6 GLY B 73 SER B 81 1 9 HELIX 16 AB7 THR B 84 THR B 100 1 17 HELIX 17 AB8 VAL B 112 MET B 123 1 12 HELIX 18 AB9 MET B 123 HIS B 129 1 7 HELIX 19 AC1 VAL B 137 TYR B 148 1 12 HELIX 20 AC2 TYR B 148 GLU B 153 1 6 HELIX 21 AC3 ARG B 163 PHE B 183 1 21 SHEET 1 AA1 5 ILE A 42 ILE A 50 0 SHEET 2 AA1 5 ILE A 28 THR A 36 -1 N ILE A 35 O LEU A 43 SHEET 3 AA1 5 MET A 11 MET A 18 -1 N GLU A 17 O ILE A 29 SHEET 4 AA1 5 LEU A 107 GLY A 109 1 O ALA A 108 N VAL A 14 SHEET 5 AA1 5 ILE A 134 ASP A 136 1 O ILE A 135 N LEU A 107 SHEET 1 AA2 5 ILE B 42 ILE B 50 0 SHEET 2 AA2 5 ILE B 28 THR B 36 -1 N CYS B 33 O GLY B 46 SHEET 3 AA2 5 MET B 11 MET B 18 -1 N TRP B 13 O LEU B 34 SHEET 4 AA2 5 LEU B 107 GLY B 109 1 O ALA B 108 N VAL B 12 SHEET 5 AA2 5 ILE B 134 ASP B 136 1 O ILE B 135 N LEU B 107 LINK OD1 ASP A 15 NA NA D 701 1555 1555 2.34 LINK O3'A A D 603 NA NA D 701 1555 1555 2.60 LINK O3'B A D 603 NA NA D 701 1555 1555 2.60 LINK OP1 A D 604 NA NA D 701 1555 1555 2.47 LINK OD1 ASP B 15 NA NA C 702 1555 1555 2.31 LINK O3'A A C 603 NA NA C 702 1555 1555 2.56 LINK O3'B A C 603 NA NA C 702 1555 1555 2.63 LINK OP1 A C 604 NA NA C 702 1555 1555 2.48 LINK NA NA D 701 O BHOH A 476 1555 1555 2.49 LINK NA NA D 701 O HOH A 507 1555 1555 2.34 LINK NA NA D 701 O AHOH D 802 1555 1555 2.50 LINK NA NA D 701 O BHOH D 802 1555 1555 2.23 LINK NA NA D 701 O AHOH A 476 1555 1555 2.37 LINK NA NA C 702 O HOH B 472 1555 1555 2.38 LINK NA NA C 702 O AHOH C 802 1555 1555 2.57 LINK NA NA C 702 O BHOH C 802 1555 1555 2.28 LINK NA NA C 702 O AHOH C 805 1555 1555 2.32 LINK NA NA C 702 O BHOH C 805 1555 1555 2.43 SITE 1 AC1 10 ASN A 110 LYS A 158 ALA A 160 HIS A 162 SITE 2 AC1 10 ASP A 167 HOH A 426 HOH A 476 HOH A 556 SITE 3 AC1 10 A D 603 A D 604 SITE 1 AC2 6 LYS A 186 ILE A 187 HOH A 409 ARG B 97 SITE 2 AC2 6 PRO B 102 GLU B 151 SITE 1 AC3 6 ASP A 15 HOH A 476 HOH A 507 A D 603 SITE 2 AC3 6 A D 604 HOH D 802 SITE 1 AC4 8 GLN A 86 GLU A 89 PRO A 124 GLN A 125 SITE 2 AC4 8 GLU B 45 SER B 169 HOH B 424 HOH B 443 SITE 1 AC5 5 ASN B 110 ASP B 167 A C 603 A C 604 SITE 2 AC5 5 HOH C 805 SITE 1 AC6 6 ASP B 15 HOH B 472 A C 603 A C 604 SITE 2 AC6 6 HOH C 802 HOH C 805 CRYST1 45.863 87.566 124.225 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 0.021804 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008050 0.00000