HEADER RNA BINDING PROTEIN 05-AUG-16 5SVD TITLE NOP9, A NEW PUF-LIKE PROTEIN, PREVENTS PREMATURE PRE-RRNA CLEAVAGE TO TITLE 2 CORRECTLY PROCESS MATURE 18S RRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOLAR PROTEIN 9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 46-645; COMPND 5 SYNONYM: PUMILIO DOMAIN-CONTAINING PROTEIN NOP9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: NOP9, YJL010C, J1357; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PSMT3 KEYWDS NOP9, PUF-LIKE PROTEINS, ITS1 RIBOSOME BIOGENESIS, RNA-BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,C.QIU,T.HALL REVDAT 4 06-MAR-24 5SVD 1 REMARK REVDAT 3 18-DEC-19 5SVD 1 REMARK REVDAT 2 20-SEP-17 5SVD 1 REMARK REVDAT 1 26-OCT-16 5SVD 0 JRNL AUTH J.ZHANG,K.L.MCCANN,C.QIU,L.E.GONZALEZ,S.J.BASERGA,T.M.HALL JRNL TITL NOP9 IS A PUF-LIKE PROTEIN THAT PREVENTS PREMATURE CLEAVAGE JRNL TITL 2 TO CORRECTLY PROCESS PRE-18S RRNA. JRNL REF NAT COMMUN V. 7 13085 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27725644 JRNL DOI 10.1038/NCOMMS13085 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 94387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1985 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 32.0259 - 5.0485 0.97 6805 145 0.1545 0.1995 REMARK 3 2 5.0485 - 4.0096 1.00 6910 147 0.1430 0.1663 REMARK 3 3 4.0096 - 3.5035 1.00 6873 150 0.1682 0.2009 REMARK 3 4 3.5035 - 3.1835 0.99 6836 142 0.2003 0.2440 REMARK 3 5 3.1835 - 2.9555 0.99 6815 151 0.2158 0.2323 REMARK 3 6 2.9555 - 2.7813 0.99 6817 145 0.2185 0.2444 REMARK 3 7 2.7813 - 2.6421 0.98 6766 141 0.2222 0.2753 REMARK 3 8 2.6421 - 2.5271 0.98 6736 147 0.2153 0.2690 REMARK 3 9 2.5271 - 2.4299 0.97 6655 141 0.2208 0.2802 REMARK 3 10 2.4299 - 2.3461 0.97 6603 156 0.2155 0.2703 REMARK 3 11 2.3461 - 2.2727 0.96 6621 127 0.2160 0.2584 REMARK 3 12 2.2727 - 2.2078 0.95 6480 143 0.2318 0.2550 REMARK 3 13 2.2078 - 2.1497 0.90 6213 137 0.2434 0.2656 REMARK 3 14 2.1497 - 2.0972 0.77 5272 113 0.2639 0.2938 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.790 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 : 0.009 8975 REMARK 3 ANGLE : 1.112 12105 REMARK 3 CHIRALITY : 0.046 1387 REMARK 3 PLANARITY : 0.006 1511 REMARK 3 DIHEDRAL : 13.006 3376 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.8414 -5.4205 29.5817 REMARK 3 T TENSOR REMARK 3 T11: 0.3716 T22: 0.3681 REMARK 3 T33: 0.3879 T12: 0.0250 REMARK 3 T13: 0.0614 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: -0.1164 L22: 0.0127 REMARK 3 L33: 0.0327 L12: 0.0789 REMARK 3 L13: 0.2146 L23: 0.0101 REMARK 3 S TENSOR REMARK 3 S11: -0.0402 S12: 0.0247 S13: 0.0468 REMARK 3 S21: -0.0400 S22: 0.0245 S23: 0.0098 REMARK 3 S31: -0.1067 S32: -0.0332 S33: 0.0130 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 5SVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-13 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96076 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (W/V) PEG 3350, 0.2 M AMMONIUM REMARK 280 CITRATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 55.23300 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLU A 46 REMARK 465 THR A 47 REMARK 465 GLN A 48 REMARK 465 PRO A 49 REMARK 465 PRO A 164 REMARK 465 SER A 165 REMARK 465 PHE A 166 REMARK 465 ASP A 167 REMARK 465 ASN A 168 REMARK 465 ASN A 169 REMARK 465 GLU A 170 REMARK 465 LYS A 171 REMARK 465 GLU A 172 REMARK 465 GLY A 173 REMARK 465 PRO A 174 REMARK 465 ASN A 220 REMARK 465 SER A 221 REMARK 465 THR A 222 REMARK 465 LYS A 223 REMARK 465 ALA A 224 REMARK 465 ASN A 225 REMARK 465 SER A 226 REMARK 465 THR A 227 REMARK 465 LEU A 228 REMARK 465 ARG A 229 REMARK 465 SER A 230 REMARK 465 LYS A 231 REMARK 465 LYS A 232 REMARK 465 SER A 233 REMARK 465 LYS A 234 REMARK 465 ILE A 235 REMARK 465 ALA A 236 REMARK 465 ARG A 237 REMARK 465 LYS A 238 REMARK 465 MET A 239 REMARK 465 ILE A 240 REMARK 465 ASP A 241 REMARK 465 ILE A 242 REMARK 465 LYS A 243 REMARK 465 ASP A 244 REMARK 465 ASN A 245 REMARK 465 ASP A 246 REMARK 465 ASP A 247 REMARK 465 PHE A 248 REMARK 465 ASN A 249 REMARK 465 LYS A 250 REMARK 465 ASN A 635 REMARK 465 SER A 636 REMARK 465 LYS A 637 REMARK 465 PRO A 638 REMARK 465 LEU A 639 REMARK 465 GLN A 640 REMARK 465 PRO A 641 REMARK 465 LYS A 642 REMARK 465 PRO A 643 REMARK 465 GLU A 644 REMARK 465 LYS A 645 REMARK 465 GLU B 46 REMARK 465 THR B 47 REMARK 465 GLN B 48 REMARK 465 PRO B 49 REMARK 465 LEU B 161 REMARK 465 LEU B 162 REMARK 465 THR B 163 REMARK 465 PRO B 164 REMARK 465 SER B 165 REMARK 465 PHE B 166 REMARK 465 ASP B 167 REMARK 465 ASN B 168 REMARK 465 ASN B 169 REMARK 465 GLU B 170 REMARK 465 LYS B 171 REMARK 465 GLU B 172 REMARK 465 GLY B 173 REMARK 465 PRO B 174 REMARK 465 TYR B 175 REMARK 465 PRO B 219 REMARK 465 ASN B 220 REMARK 465 SER B 221 REMARK 465 THR B 222 REMARK 465 LYS B 223 REMARK 465 ALA B 224 REMARK 465 ASN B 225 REMARK 465 SER B 226 REMARK 465 THR B 227 REMARK 465 LEU B 228 REMARK 465 ARG B 229 REMARK 465 SER B 230 REMARK 465 LYS B 231 REMARK 465 LYS B 232 REMARK 465 SER B 233 REMARK 465 LYS B 234 REMARK 465 ILE B 235 REMARK 465 ALA B 236 REMARK 465 ARG B 237 REMARK 465 LYS B 238 REMARK 465 MET B 239 REMARK 465 ILE B 240 REMARK 465 ASP B 241 REMARK 465 ILE B 242 REMARK 465 LYS B 243 REMARK 465 ASP B 244 REMARK 465 ASN B 245 REMARK 465 ASP B 246 REMARK 465 ASP B 247 REMARK 465 PHE B 248 REMARK 465 ASN B 249 REMARK 465 LYS B 250 REMARK 465 VAL B 251 REMARK 465 TYR B 252 REMARK 465 GLN B 253 REMARK 465 THR B 254 REMARK 465 ASN B 635 REMARK 465 SER B 636 REMARK 465 LYS B 637 REMARK 465 PRO B 638 REMARK 465 LEU B 639 REMARK 465 GLN B 640 REMARK 465 PRO B 641 REMARK 465 LYS B 642 REMARK 465 PRO B 643 REMARK 465 GLU B 644 REMARK 465 LYS B 645 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 GLU A 256 CG CD OE1 OE2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 ASP A 282 CG OD1 OD2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 476 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 477 CG OD1 OD2 REMARK 470 GLN B 72 CG CD OE1 NE2 REMARK 470 ARG B 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 298 CG CD CE NZ REMARK 470 ARG B 316 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 332 CG OD1 OD2 REMARK 470 ASP B 456 CG OD1 OD2 REMARK 470 ASP B 478 CG OD1 OD2 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 877 O HOH A 935 2.17 REMARK 500 OD2 ASP A 620 O HOH A 701 2.18 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 MET A 185 CG - SD - CE ANGL. DEV. = -11.2 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 THR A 274 -163.20 -103.91 REMARK 500 SER A 279 -86.66 -118.11 REMARK 500 THR A 385 -92.84 -133.32 REMARK 500 TYR A 451 56.20 -151.98 REMARK 500 ASN A 459 117.13 -164.45 REMARK 500 ARG A 476 -163.66 -73.69 REMARK 500 ASP A 477 49.17 -107.84 REMARK 500 SER B 257 -32.04 65.27 REMARK 500 ALA B 277 -44.86 -146.41 REMARK 500 GLU B 278 -123.85 23.93 REMARK 500 MET B 372 -35.41 -130.24 REMARK 500 THR B 385 -91.29 -132.69 REMARK 500 ASN B 420 71.56 -150.63 REMARK 500 TYR B 451 61.13 -152.06 REMARK 500 GLU B 453 -11.37 71.51 REMARK 500 ASP B 456 12.52 54.96 REMARK 500 ASN B 459 116.32 -162.44 REMARK 500 TRP B 479 157.60 64.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 284 GLN A 285 140.75 REMARK 500 ALA B 328 ASP B 329 -33.49 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 988 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 989 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 990 DISTANCE = 6.08 ANGSTROMS DBREF 5SVD A 46 645 UNP P47077 NOP9_YEAST 46 645 DBREF 5SVD B 46 645 UNP P47077 NOP9_YEAST 46 645 SEQADV 5SVD THR A 430 UNP P47077 ALA 430 ENGINEERED MUTATION SEQADV 5SVD THR B 430 UNP P47077 ALA 430 ENGINEERED MUTATION SEQRES 1 A 600 GLU THR GLN PRO GLN MET PHE PHE GLY VAL LEU ASP ARG SEQRES 2 A 600 GLU GLU LEU GLU TYR PHE LYS GLN ALA GLU SER THR LEU SEQRES 3 A 600 GLN LEU ASP ALA PHE GLU ALA PRO GLU GLU LYS PHE GLN SEQRES 4 A 600 PHE VAL THR SER ILE ILE GLU GLU ALA LYS GLY LYS GLU SEQRES 5 A 600 LEU LYS LEU VAL THR SER GLN ILE THR SER LYS LEU MET SEQRES 6 A 600 GLU ARG VAL ILE LEU GLU CYS ASP GLU THR GLN LEU LYS SEQRES 7 A 600 ASP ILE PHE GLN SER PHE ASN GLY VAL PHE PHE GLY LEU SEQRES 8 A 600 SER CYS HIS LYS TYR ALA SER HIS VAL LEU GLU THR LEU SEQRES 9 A 600 PHE VAL ARG SER ALA ALA LEU VAL GLU ARG GLU LEU LEU SEQRES 10 A 600 THR PRO SER PHE ASP ASN ASN GLU LYS GLU GLY PRO TYR SEQRES 11 A 600 VAL THR MET GLU ASN MET PHE LEU PHE MET LEU ASN GLU SEQRES 12 A 600 LEU LYS PRO HIS LEU LYS THR MET MET ASN HIS GLN TYR SEQRES 13 A 600 ALA SER HIS VAL LEU ARG LEU LEU ILE LEU ILE LEU SER SEQRES 14 A 600 SER LYS THR LEU PRO ASN SER THR LYS ALA ASN SER THR SEQRES 15 A 600 LEU ARG SER LYS LYS SER LYS ILE ALA ARG LYS MET ILE SEQRES 16 A 600 ASP ILE LYS ASP ASN ASP ASP PHE ASN LYS VAL TYR GLN SEQRES 17 A 600 THR PRO GLU SER PHE LYS SER GLU LEU ARG ASP ILE ILE SEQRES 18 A 600 THR THR LEU TYR LYS GLY PHE THR ASN GLY ALA GLU SER SEQRES 19 A 600 ARG SER ASP ILE SER GLN SER THR ILE THR LYS PHE ARG SEQRES 20 A 600 GLU TYR SER VAL ASP LYS VAL ALA SER PRO VAL ILE GLN SEQRES 21 A 600 LEU ILE ILE GLN VAL GLU GLY ILE PHE ASP ARG ASP ARG SEQRES 22 A 600 SER PHE TRP ARG LEU VAL PHE ASN THR ALA ASP GLU LYS SEQRES 23 A 600 ASP PRO LYS GLU GLU SER PHE LEU GLU TYR LEU LEU SER SEQRES 24 A 600 ASP PRO VAL GLY SER HIS PHE LEU GLU ASN VAL ILE GLY SEQRES 25 A 600 SER ALA ARG LEU LYS TYR VAL GLU ARG LEU TYR ARG LEU SEQRES 26 A 600 TYR MET LYS ASP ARG ILE VAL LYS LEU ALA LYS ARG ASP SEQRES 27 A 600 THR THR GLY ALA PHE VAL VAL ARG ALA LEU LEU GLU HIS SEQRES 28 A 600 LEU LYS GLU LYS ASP VAL LYS GLN ILE LEU ASP ALA VAL SEQRES 29 A 600 VAL PRO GLU LEU SER MET LEU LEU ASN SER ASN MET ASP SEQRES 30 A 600 PHE GLY THR ALA ILE ILE ASN THR SER ASN LYS GLN GLY SEQRES 31 A 600 GLY TYR LEU ARG ASP ASP VAL ILE ALA GLN LEU ILE GLN SEQRES 32 A 600 LYS TYR TYR PRO GLU LYS SER ASP ALA LYS ASN ILE LEU SEQRES 33 A 600 GLU SER CYS LEU LEU LEU SER ALA SER THR LEU GLY ASN SEQRES 34 A 600 THR ARG ASP ASP TRP PRO THR ALA GLU GLU ARG ARG ARG SEQRES 35 A 600 SER VAL PHE LEU GLU GLN LEU ILE ASP TYR ASP ASP LYS SEQRES 36 A 600 PHE LEU ASN ILE THR ILE ASP SER MET LEU ALA LEU PRO SEQRES 37 A 600 GLU GLU ARG LEU ILE GLN MET CYS TYR HIS GLY VAL PHE SEQRES 38 A 600 SER HIS VAL VAL GLU HIS VAL LEU GLN THR THR ARG VAL SEQRES 39 A 600 ASP ILE ILE LYS ARG LYS MET LEU LEU ASN ILE LEU SER SEQRES 40 A 600 LYS GLU SER VAL ASN LEU ALA CYS ASN VAL TYR GLY SER SEQRES 41 A 600 HIS ILE MET ASP LYS LEU TRP GLU PHE THR ALA LYS LEU SEQRES 42 A 600 THR LEU TYR LYS GLU ARG ILE ALA ARG ALA LEU VAL LEU SEQRES 43 A 600 GLU THR GLU LYS VAL LYS ASN SER ILE TYR GLY ARG GLN SEQRES 44 A 600 VAL TRP LYS ASN TRP LYS LEU GLU LEU TYR VAL ARG LYS SEQRES 45 A 600 MET TRP ASP TRP LYS LYS LEU ILE LYS GLU GLN GLU PHE SEQRES 46 A 600 GLU ILE PHE PRO ASN SER LYS PRO LEU GLN PRO LYS PRO SEQRES 47 A 600 GLU LYS SEQRES 1 B 600 GLU THR GLN PRO GLN MET PHE PHE GLY VAL LEU ASP ARG SEQRES 2 B 600 GLU GLU LEU GLU TYR PHE LYS GLN ALA GLU SER THR LEU SEQRES 3 B 600 GLN LEU ASP ALA PHE GLU ALA PRO GLU GLU LYS PHE GLN SEQRES 4 B 600 PHE VAL THR SER ILE ILE GLU GLU ALA LYS GLY LYS GLU SEQRES 5 B 600 LEU LYS LEU VAL THR SER GLN ILE THR SER LYS LEU MET SEQRES 6 B 600 GLU ARG VAL ILE LEU GLU CYS ASP GLU THR GLN LEU LYS SEQRES 7 B 600 ASP ILE PHE GLN SER PHE ASN GLY VAL PHE PHE GLY LEU SEQRES 8 B 600 SER CYS HIS LYS TYR ALA SER HIS VAL LEU GLU THR LEU SEQRES 9 B 600 PHE VAL ARG SER ALA ALA LEU VAL GLU ARG GLU LEU LEU SEQRES 10 B 600 THR PRO SER PHE ASP ASN ASN GLU LYS GLU GLY PRO TYR SEQRES 11 B 600 VAL THR MET GLU ASN MET PHE LEU PHE MET LEU ASN GLU SEQRES 12 B 600 LEU LYS PRO HIS LEU LYS THR MET MET ASN HIS GLN TYR SEQRES 13 B 600 ALA SER HIS VAL LEU ARG LEU LEU ILE LEU ILE LEU SER SEQRES 14 B 600 SER LYS THR LEU PRO ASN SER THR LYS ALA ASN SER THR SEQRES 15 B 600 LEU ARG SER LYS LYS SER LYS ILE ALA ARG LYS MET ILE SEQRES 16 B 600 ASP ILE LYS ASP ASN ASP ASP PHE ASN LYS VAL TYR GLN SEQRES 17 B 600 THR PRO GLU SER PHE LYS SER GLU LEU ARG ASP ILE ILE SEQRES 18 B 600 THR THR LEU TYR LYS GLY PHE THR ASN GLY ALA GLU SER SEQRES 19 B 600 ARG SER ASP ILE SER GLN SER THR ILE THR LYS PHE ARG SEQRES 20 B 600 GLU TYR SER VAL ASP LYS VAL ALA SER PRO VAL ILE GLN SEQRES 21 B 600 LEU ILE ILE GLN VAL GLU GLY ILE PHE ASP ARG ASP ARG SEQRES 22 B 600 SER PHE TRP ARG LEU VAL PHE ASN THR ALA ASP GLU LYS SEQRES 23 B 600 ASP PRO LYS GLU GLU SER PHE LEU GLU TYR LEU LEU SER SEQRES 24 B 600 ASP PRO VAL GLY SER HIS PHE LEU GLU ASN VAL ILE GLY SEQRES 25 B 600 SER ALA ARG LEU LYS TYR VAL GLU ARG LEU TYR ARG LEU SEQRES 26 B 600 TYR MET LYS ASP ARG ILE VAL LYS LEU ALA LYS ARG ASP SEQRES 27 B 600 THR THR GLY ALA PHE VAL VAL ARG ALA LEU LEU GLU HIS SEQRES 28 B 600 LEU LYS GLU LYS ASP VAL LYS GLN ILE LEU ASP ALA VAL SEQRES 29 B 600 VAL PRO GLU LEU SER MET LEU LEU ASN SER ASN MET ASP SEQRES 30 B 600 PHE GLY THR ALA ILE ILE ASN THR SER ASN LYS GLN GLY SEQRES 31 B 600 GLY TYR LEU ARG ASP ASP VAL ILE ALA GLN LEU ILE GLN SEQRES 32 B 600 LYS TYR TYR PRO GLU LYS SER ASP ALA LYS ASN ILE LEU SEQRES 33 B 600 GLU SER CYS LEU LEU LEU SER ALA SER THR LEU GLY ASN SEQRES 34 B 600 THR ARG ASP ASP TRP PRO THR ALA GLU GLU ARG ARG ARG SEQRES 35 B 600 SER VAL PHE LEU GLU GLN LEU ILE ASP TYR ASP ASP LYS SEQRES 36 B 600 PHE LEU ASN ILE THR ILE ASP SER MET LEU ALA LEU PRO SEQRES 37 B 600 GLU GLU ARG LEU ILE GLN MET CYS TYR HIS GLY VAL PHE SEQRES 38 B 600 SER HIS VAL VAL GLU HIS VAL LEU GLN THR THR ARG VAL SEQRES 39 B 600 ASP ILE ILE LYS ARG LYS MET LEU LEU ASN ILE LEU SER SEQRES 40 B 600 LYS GLU SER VAL ASN LEU ALA CYS ASN VAL TYR GLY SER SEQRES 41 B 600 HIS ILE MET ASP LYS LEU TRP GLU PHE THR ALA LYS LEU SEQRES 42 B 600 THR LEU TYR LYS GLU ARG ILE ALA ARG ALA LEU VAL LEU SEQRES 43 B 600 GLU THR GLU LYS VAL LYS ASN SER ILE TYR GLY ARG GLN SEQRES 44 B 600 VAL TRP LYS ASN TRP LYS LEU GLU LEU TYR VAL ARG LYS SEQRES 45 B 600 MET TRP ASP TRP LYS LYS LEU ILE LYS GLU GLN GLU PHE SEQRES 46 B 600 GLU ILE PHE PRO ASN SER LYS PRO LEU GLN PRO LYS PRO SEQRES 47 B 600 GLU LYS FORMUL 3 HOH *377(H2 O) HELIX 1 AA1 ASP A 57 ASP A 74 1 18 HELIX 2 AA2 ALA A 78 LYS A 94 1 17 HELIX 3 AA3 LYS A 96 SER A 103 1 8 HELIX 4 AA4 THR A 106 CYS A 117 1 12 HELIX 5 AA5 ASP A 118 SER A 128 1 11 HELIX 6 AA6 VAL A 132 CYS A 138 1 7 HELIX 7 AA7 TYR A 141 GLU A 160 1 20 HELIX 8 AA8 THR A 177 LYS A 190 1 14 HELIX 9 AA9 HIS A 192 ASN A 198 1 7 HELIX 10 AB1 TYR A 201 SER A 214 1 14 HELIX 11 AB2 PRO A 255 THR A 274 1 20 HELIX 12 AB3 SER A 286 VAL A 296 1 11 HELIX 13 AB4 ALA A 300 GLU A 311 1 12 HELIX 14 AB5 GLY A 312 PHE A 314 5 3 HELIX 15 AB6 ARG A 318 PHE A 325 1 8 HELIX 16 AB7 ASP A 332 LEU A 343 1 12 HELIX 17 AB8 ASP A 345 GLY A 357 1 13 HELIX 18 AB9 ARG A 360 MET A 372 1 13 HELIX 19 AC1 ARG A 375 LYS A 381 1 7 HELIX 20 AC2 THR A 385 LEU A 397 1 13 HELIX 21 AC3 LYS A 398 VAL A 410 1 13 HELIX 22 AC4 GLU A 412 ASN A 420 1 9 HELIX 23 AC5 ASN A 420 GLN A 434 1 15 HELIX 24 AC6 LEU A 438 TYR A 451 1 14 HELIX 25 AC7 ASN A 459 LEU A 466 1 8 HELIX 26 AC8 LEU A 467 SER A 470 5 4 HELIX 27 AC9 THR A 481 ASP A 498 1 18 HELIX 28 AD1 ASP A 498 LEU A 512 1 15 HELIX 29 AD2 PRO A 513 TYR A 522 1 10 HELIX 30 AD3 VAL A 525 LEU A 534 1 10 HELIX 31 AD4 GLN A 535 VAL A 539 5 5 HELIX 32 AD5 ASP A 540 SER A 552 1 13 HELIX 33 AD6 GLU A 554 CYS A 560 1 7 HELIX 34 AD7 TYR A 563 THR A 575 1 13 HELIX 35 AD8 LEU A 578 GLU A 592 1 15 HELIX 36 AD9 GLU A 592 ASN A 598 1 7 HELIX 37 AE1 SER A 599 TRP A 609 1 11 HELIX 38 AE2 LYS A 610 LYS A 617 1 8 HELIX 39 AE3 LYS A 617 PHE A 633 1 17 HELIX 40 AE4 ASP B 57 ASP B 74 1 18 HELIX 41 AE5 ALA B 78 LYS B 94 1 17 HELIX 42 AE6 LYS B 96 SER B 103 1 8 HELIX 43 AE7 SER B 103 CYS B 117 1 15 HELIX 44 AE8 ASP B 118 SER B 128 1 11 HELIX 45 AE9 VAL B 132 CYS B 138 1 7 HELIX 46 AF1 TYR B 141 ARG B 159 1 19 HELIX 47 AF2 THR B 177 LYS B 190 1 14 HELIX 48 AF3 HIS B 192 HIS B 199 1 8 HELIX 49 AF4 TYR B 201 SER B 214 1 14 HELIX 50 AF5 SER B 257 THR B 274 1 18 HELIX 51 AF6 SER B 279 ILE B 283 5 5 HELIX 52 AF7 SER B 284 VAL B 296 1 13 HELIX 53 AF8 ALA B 300 GLU B 311 1 12 HELIX 54 AF9 GLY B 312 PHE B 314 5 3 HELIX 55 AG1 ARG B 318 PHE B 325 1 8 HELIX 56 AG2 ASP B 332 LEU B 343 1 12 HELIX 57 AG3 ASP B 345 GLY B 357 1 13 HELIX 58 AG4 ARG B 360 MET B 372 1 13 HELIX 59 AG5 ARG B 375 LYS B 381 1 7 HELIX 60 AG6 THR B 385 LEU B 397 1 13 HELIX 61 AG7 LYS B 398 VAL B 410 1 13 HELIX 62 AG8 GLU B 412 ASN B 420 1 9 HELIX 63 AG9 ASN B 420 GLN B 434 1 15 HELIX 64 AH1 LEU B 438 TYR B 451 1 14 HELIX 65 AH2 ASN B 459 LEU B 465 1 7 HELIX 66 AH3 LEU B 466 SER B 470 5 5 HELIX 67 AH4 THR B 481 ASP B 498 1 18 HELIX 68 AH5 ASP B 498 LEU B 512 1 15 HELIX 69 AH6 PRO B 513 HIS B 523 1 11 HELIX 70 AH7 VAL B 525 VAL B 533 1 9 HELIX 71 AH8 ASP B 540 SER B 552 1 13 HELIX 72 AH9 GLU B 554 CYS B 560 1 7 HELIX 73 AI1 TYR B 563 THR B 575 1 13 HELIX 74 AI2 LEU B 578 GLU B 592 1 15 HELIX 75 AI3 GLU B 592 SER B 599 1 8 HELIX 76 AI4 SER B 599 TRP B 609 1 11 HELIX 77 AI5 LYS B 610 LYS B 617 1 8 HELIX 78 AI6 LYS B 617 PHE B 633 1 17 CISPEP 1 SER A 279 ARG A 280 0 -0.89 CISPEP 2 ARG A 280 SER A 281 0 0.38 CISPEP 3 SER A 281 ASP A 282 0 17.56 CISPEP 4 GLN A 285 SER A 286 0 6.49 CISPEP 5 ARG B 159 GLU B 160 0 -20.01 CRYST1 67.501 110.466 114.846 90.00 92.22 90.00 P 1 21 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 0.014815 0.000000 0.000576 0.00000 SCALE2 0.000000 0.009053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008714 0.00000