HEADER VIRAL PROTEIN/RNA 27-JUL-11 3T5N TITLE 1.8A CRYSTAL STRUCTURE OF LASSA VIRUS NUCLEOPROTEIN IN COMPLEX WITH TITLE 2 SSRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3'); COMPND 9 CHAIN: C; COMPND 10 OTHER_DETAILS: H20 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MOPEIA LASSA REASSORTANT 29; SOURCE 3 ORGANISM_TAXID: 300180; SOURCE 4 GENE: NP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET46; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS SSRNA, SINGLE STRANDED RNA, VIRAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.HASTIE,T.LIU,L.B.KING,N.NGO,M.A.ZANDONATTI,V.L.WOODS,J.C.DE LA AUTHOR 2 TORRE,E.O.SAPHIRE REVDAT 2 28-FEB-24 3T5N 1 REMARK SEQADV LINK REVDAT 1 11-JAN-12 3T5N 0 JRNL AUTH K.M.HASTIE,T.LIU,S.LI,L.B.KING,N.NGO,M.A.ZANDONATTI, JRNL AUTH 2 V.L.WOODS,J.C.DE LA TORRE,E.O.SAPHIRE JRNL TITL CRYSTAL STRUCTURE OF THE LASSA VIRUS NUCLEOPROTEIN-RNA JRNL TITL 2 COMPLEX REVEALS A GATING MECHANISM FOR RNA BINDING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 19365 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22084115 JRNL DOI 10.1073/PNAS.1108515108 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1491 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 45.1509 - 3.8500 1.00 2972 153 0.1737 0.1748 REMARK 3 2 3.8500 - 3.0561 1.00 2819 163 0.1736 0.2204 REMARK 3 3 3.0561 - 2.6698 1.00 2805 142 0.1980 0.2299 REMARK 3 4 2.6698 - 2.4257 1.00 2790 155 0.1810 0.2367 REMARK 3 5 2.4257 - 2.2519 1.00 2756 153 0.1726 0.1820 REMARK 3 6 2.2519 - 2.1191 1.00 2781 132 0.1696 0.1809 REMARK 3 7 2.1191 - 2.0130 1.00 2767 144 0.1768 0.2348 REMARK 3 8 2.0130 - 1.9254 1.00 2753 154 0.1788 0.2490 REMARK 3 9 1.9254 - 1.8512 1.00 2719 157 0.2250 0.2373 REMARK 3 10 1.8512 - 1.7873 0.97 2673 138 0.3027 0.3189 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 43.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.340 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) : 3.15480 REMARK 3 B22 (A**2) : -0.89560 REMARK 3 B33 (A**2) : -2.25910 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 2349 REMARK 3 ANGLE : 0.998 3201 REMARK 3 CHIRALITY : 0.064 386 REMARK 3 PLANARITY : 0.005 386 REMARK 3 DIHEDRAL : 13.728 901 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 8:107) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5562 17.7518 19.4801 REMARK 3 T TENSOR REMARK 3 T11: 0.0962 T22: 0.1719 REMARK 3 T33: 0.1258 T12: 0.0201 REMARK 3 T13: 0.0034 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.1646 L22: 4.2720 REMARK 3 L33: 1.6566 L12: -1.0488 REMARK 3 L13: 0.3199 L23: -1.0499 REMARK 3 S TENSOR REMARK 3 S11: 0.1225 S12: 0.1965 S13: 0.0254 REMARK 3 S21: -0.2692 S22: -0.2083 S23: -0.1970 REMARK 3 S31: 0.0330 S32: 0.1993 S33: 0.1130 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 108:170) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4134 2.2616 17.1735 REMARK 3 T TENSOR REMARK 3 T11: 0.4409 T22: 0.2646 REMARK 3 T33: 0.2807 T12: 0.2004 REMARK 3 T13: 0.1337 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.6988 L22: 0.7373 REMARK 3 L33: 1.3497 L12: -0.6881 REMARK 3 L13: 0.5797 L23: -0.4437 REMARK 3 S TENSOR REMARK 3 S11: 0.2172 S12: -0.0673 S13: -0.1684 REMARK 3 S21: -0.6231 S22: -0.3035 S23: -0.3929 REMARK 3 S31: 1.0941 S32: 0.9277 S33: 0.2224 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 171:296) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2003 18.7704 16.8915 REMARK 3 T TENSOR REMARK 3 T11: 0.1521 T22: 0.1444 REMARK 3 T33: 0.1644 T12: 0.0294 REMARK 3 T13: -0.0521 T23: -0.0487 REMARK 3 L TENSOR REMARK 3 L11: 1.4525 L22: 3.9253 REMARK 3 L33: 1.8296 L12: -1.1683 REMARK 3 L13: 0.4078 L23: -0.9831 REMARK 3 S TENSOR REMARK 3 S11: 0.1590 S12: 0.2191 S13: -0.1501 REMARK 3 S21: -0.5338 S22: -0.1804 S23: 0.4274 REMARK 3 S31: 0.0805 S32: -0.0403 S33: 0.0157 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 297:339) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7267 12.5247 27.2169 REMARK 3 T TENSOR REMARK 3 T11: 0.0927 T22: 0.1581 REMARK 3 T33: 0.1502 T12: 0.0149 REMARK 3 T13: -0.0018 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.9746 L22: 1.7284 REMARK 3 L33: 0.4331 L12: -0.2370 REMARK 3 L13: -0.1526 L23: -0.0446 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: 0.0448 S13: -0.0727 REMARK 3 S21: 0.0698 S22: -0.0918 S23: -0.0570 REMARK 3 S31: 0.0866 S32: 0.0707 S33: 0.0684 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN C AND RESID 0:4) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6443 8.6755 17.0992 REMARK 3 T TENSOR REMARK 3 T11: 0.2695 T22: 0.1938 REMARK 3 T33: 0.1703 T12: 0.0875 REMARK 3 T13: -0.0233 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 2.7390 L22: 1.3796 REMARK 3 L33: 3.1255 L12: 0.5882 REMARK 3 L13: 1.8960 L23: -1.0837 REMARK 3 S TENSOR REMARK 3 S11: 0.4841 S12: 0.1499 S13: -0.0431 REMARK 3 S21: -0.7157 S22: -0.5376 S23: 0.2003 REMARK 3 S31: 0.5289 S32: -0.3086 S33: 0.1494 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 3T5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-10; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : ALS; NULL REMARK 200 BEAMLINE : 5.0.2; 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795, 1.0; NULL REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) LIQUID REMARK 200 N2 COOLED; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.787 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.0, 18% PEG 3350, REMARK 280 12.5MM MGCL 2 AND 7.5MM NICL2, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 37.07950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.86850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.07950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.86850 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: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 -13 REMARK 465 ALA A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 VAL A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 LYS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 ILE A 7 REMARK 465 VAL A 113 REMARK 465 ILE A 114 REMARK 465 ARG A 115 REMARK 465 THR A 116 REMARK 465 GLU A 117 REMARK 465 ARG A 118 REMARK 465 PRO A 119 REMARK 465 LEU A 120 REMARK 465 SER A 121 REMARK 465 ALA A 122 REMARK 465 GLY A 123 REMARK 465 VAL A 124 REMARK 465 TYR A 125 REMARK 465 MET A 126 REMARK 465 GLY A 127 REMARK 465 ASN A 128 REMARK 465 LEU A 129 REMARK 465 SER A 130 REMARK 465 SER A 131 REMARK 465 GLN A 132 REMARK 465 GLN A 133 REMARK 465 LEU A 134 REMARK 465 ASP A 135 REMARK 465 GLN A 136 REMARK 465 ARG A 137 REMARK 465 ARG A 138 REMARK 465 ALA A 139 REMARK 465 LEU A 140 REMARK 465 LEU A 141 REMARK 465 ASN A 142 REMARK 465 MET A 143 REMARK 465 ILE A 144 REMARK 465 GLY A 145 REMARK 465 MET A 146 REMARK 465 SER A 147 REMARK 465 GLY A 148 REMARK 465 GLY A 149 REMARK 465 ASN A 150 REMARK 465 GLN A 151 REMARK 465 GLY A 152 REMARK 465 ALA A 153 REMARK 465 ARG A 154 REMARK 465 ALA A 155 REMARK 465 GLY A 156 REMARK 465 ARG A 157 REMARK 465 ASP A 158 REMARK 465 GLY A 159 REMARK 465 VAL A 160 REMARK 465 VAL A 161 REMARK 465 ARG A 162 REMARK 465 SER A 340 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 VAL A 163 CG1 CG2 REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 ASP A 220 CG OD1 OD2 REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 GLU A 299 CG CD OE1 OE2 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 NE ARG A 52 O HOH A 512 2.15 REMARK 500 NZ LYS A 269 O HOH A 484 2.19 REMARK 500 O SER A 48 O HOH A 490 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 U C 4 P U C 4 OP1 -0.132 REMARK 500 U C 4 P U C 4 OP2 -0.126 REMARK 500 U C 4 O5' U C 4 C5' -0.090 REMARK 500 U C 4 N1 U C 4 C2 -0.060 REMARK 500 C C 5 O5' C C 5 C5' -0.085 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U C 4 C2 - N3 - C4 ANGL. DEV. = -4.5 DEGREES REMARK 500 U C 4 N1 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 242 162.31 83.19 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 NI A 341 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 204 OD2 REMARK 620 2 HIS A 226 NE2 77.8 REMARK 620 3 HOH A 429 O 88.9 81.1 REMARK 620 4 HOH A 485 O 85.0 101.5 172.7 REMARK 620 5 HOH A 488 O 163.2 85.4 89.1 97.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 342 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3T5Q RELATED DB: PDB DBREF 3T5N A 1 340 UNP Q5S585 Q5S585_9VIRU 1 340 DBREF 3T5N C 2 7 PDB 3T5N 3T5N 2 7 SEQADV 3T5N MET A -13 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N ALA A -12 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -11 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -10 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -9 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -8 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -7 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N HIS A -6 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N VAL A -5 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N ASP A -4 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N ASP A -3 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N ASP A -2 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N ASP A -1 UNP Q5S585 EXPRESSION TAG SEQADV 3T5N LYS A 0 UNP Q5S585 EXPRESSION TAG SEQRES 1 A 354 MET ALA HIS HIS HIS HIS HIS HIS VAL ASP ASP ASP ASP SEQRES 2 A 354 LYS MET SER ALA SER LYS GLU ILE LYS SER PHE LEU TRP SEQRES 3 A 354 THR GLN SER LEU ARG ARG GLU LEU SER GLY TYR CYS SER SEQRES 4 A 354 ASN ILE LYS LEU GLN VAL VAL LYS ASP ALA GLN ALA LEU SEQRES 5 A 354 LEU HIS GLY LEU ASP PHE SER GLU VAL SER ASN VAL GLN SEQRES 6 A 354 ARG LEU MET ARG LYS GLU ARG ARG ASP ASP ASN ASP LEU SEQRES 7 A 354 LYS ARG LEU ARG ASP LEU ASN GLN ALA VAL ASN ASN LEU SEQRES 8 A 354 VAL GLU LEU LYS SER THR GLN GLN LYS SER ILE LEU ARG SEQRES 9 A 354 VAL GLY THR LEU THR SER ASP ASP LEU LEU ILE LEU ALA SEQRES 10 A 354 ALA ASP LEU GLU LYS LEU LYS SER LYS VAL ILE ARG THR SEQRES 11 A 354 GLU ARG PRO LEU SER ALA GLY VAL TYR MET GLY ASN LEU SEQRES 12 A 354 SER SER GLN GLN LEU ASP GLN ARG ARG ALA LEU LEU ASN SEQRES 13 A 354 MET ILE GLY MET SER GLY GLY ASN GLN GLY ALA ARG ALA SEQRES 14 A 354 GLY ARG ASP GLY VAL VAL ARG VAL TRP ASP VAL LYS ASN SEQRES 15 A 354 ALA GLU LEU LEU SER ASN GLN PHE GLY THR MET PRO SER SEQRES 16 A 354 LEU THR LEU ALA CYS LEU THR LYS GLN GLY GLN VAL ASP SEQRES 17 A 354 LEU ASN ASP ALA VAL GLN ALA LEU THR ASP LEU GLY LEU SEQRES 18 A 354 ILE TYR THR ALA LYS TYR PRO ASN THR SER ASP LEU ASP SEQRES 19 A 354 ARG LEU THR GLN SER HIS PRO ILE LEU ASN MET ILE ASP SEQRES 20 A 354 THR LYS LYS SER SER LEU ASN ILE SER GLY TYR ASN PHE SEQRES 21 A 354 SER LEU GLY ALA ALA VAL LYS ALA GLY ALA CYS MET LEU SEQRES 22 A 354 ASP GLY GLY ASN MET LEU GLU THR ILE LYS VAL SER PRO SEQRES 23 A 354 GLN THR MET ASP GLY ILE LEU LYS SER ILE LEU LYS VAL SEQRES 24 A 354 LYS LYS ALA LEU GLY MET PHE ILE SER ASP THR PRO GLY SEQRES 25 A 354 GLU ARG ASN PRO TYR GLU ASN ILE LEU TYR LYS ILE CYS SEQRES 26 A 354 LEU SER GLY ASP GLY TRP PRO TYR ILE ALA SER ARG THR SEQRES 27 A 354 SER ILE THR GLY ARG ALA TRP GLU ASN THR VAL VAL ASP SEQRES 28 A 354 LEU GLU SER SEQRES 1 C 6 U A U C U C HET NI A 341 1 HET NI A 342 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *184(H2 O) HELIX 1 1 LYS A 8 LEU A 20 1 13 HELIX 2 2 SER A 21 CYS A 24 5 4 HELIX 3 3 ILE A 27 LEU A 42 1 16 HELIX 4 4 ASP A 43 ARG A 55 1 13 HELIX 5 5 ASP A 61 VAL A 78 1 18 HELIX 6 6 THR A 95 LYS A 112 1 18 HELIX 7 7 ASN A 168 SER A 173 5 6 HELIX 8 8 MET A 179 GLY A 191 1 13 HELIX 9 9 ASP A 194 THR A 210 1 17 HELIX 10 10 ASN A 215 GLN A 224 1 10 HELIX 11 11 SER A 225 ILE A 232 5 8 HELIX 12 12 SER A 247 CYS A 257 1 11 HELIX 13 13 MET A 264 ILE A 268 5 5 HELIX 14 14 THR A 274 GLY A 290 1 17 HELIX 15 15 ASN A 301 LEU A 312 1 12 HELIX 16 16 ARG A 329 ASN A 333 1 5 SHEET 1 A 2 ARG A 59 ASP A 60 0 SHEET 2 A 2 TRP A 164 ASP A 165 1 O ASP A 165 N ARG A 59 SHEET 1 B 2 SER A 87 LEU A 89 0 SHEET 2 B 2 THR A 334 VAL A 336 1 O VAL A 335 N LEU A 89 LINK OD2 ASP A 204 NI NI A 341 1555 1555 2.11 LINK NE2 HIS A 226 NI NI A 341 1555 1555 2.14 LINK NI NI A 341 O HOH A 429 1555 1555 2.28 LINK NI NI A 341 O HOH A 485 1555 1555 1.96 LINK NI NI A 341 O HOH A 488 1555 1555 2.21 LINK NI NI A 342 O HOH A 465 1555 1555 2.48 SITE 1 AC1 5 ASP A 204 HIS A 226 HOH A 429 HOH A 485 SITE 2 AC1 5 HOH A 488 SITE 1 AC2 3 HIS A 40 GLU A 57 HOH A 465 CRYST1 74.159 71.737 56.887 90.00 90.00 90.00 P 21 21 2 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 0.013485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017579 0.00000