HEADER RIBOSOMAL PROTEIN 19-AUG-10 3OIJ TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NEP1/EMG1 BOUND TO S- TITLE 2 ADENOSYLHOMOCYSTEINE AND 2 MOLECULES OF COGNATE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESSENTIAL FOR MITOTIC GROWTH 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEOLAR ESSENTIAL PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_TAXID: 4932; SOURCE 4 GENE: EMG1, NEP1, YLR186W, L9470.5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST527; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: COGNATE RNA FRAGMENT SYNTHESIZED TO MIMIC NATURAL RNA SOURCE 13 SUBSTRATE KEYWDS EMG1, SCNEP1, SPOUT, RIBOSOME BIOGENESIS, METHYLTRANSFERASE, RRNA KEYWDS 2 PROCESSING, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.R.THOMAS,N.LARONDE-LEBLANC REVDAT 4 06-SEP-23 3OIJ 1 REMARK SEQADV REVDAT 3 08-NOV-17 3OIJ 1 REMARK REVDAT 2 13-APR-11 3OIJ 1 JRNL REVDAT 1 01-DEC-10 3OIJ 0 JRNL AUTH S.R.THOMAS,C.A.KELLER,A.SZYK,J.R.CANNON,N.A.LARONDE-LEBLANC JRNL TITL STRUCTURAL INSIGHT INTO THE FUNCTIONAL MECHANISM OF JRNL TITL 2 NEP1/EMG1 N1-SPECIFIC PSEUDOURIDINE METHYLTRANSFERASE IN JRNL TITL 3 RIBOSOME BIOGENESIS. JRNL REF NUCLEIC ACIDS RES. V. 39 2445 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21087996 JRNL DOI 10.1093/NAR/GKQ1131 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 761 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 29.8871 - 5.1231 1.00 3044 168 0.2042 0.2695 REMARK 3 2 5.1231 - 4.0696 1.00 2952 144 0.1360 0.1994 REMARK 3 3 4.0696 - 3.5562 1.00 2918 132 0.1609 0.2256 REMARK 3 4 3.5562 - 3.2314 1.00 2866 175 0.2046 0.2981 REMARK 3 5 3.2314 - 3.0001 0.96 2780 142 0.2435 0.3749 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 : 0.27 REMARK 3 B_SOL : 21.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.48700 REMARK 3 B22 (A**2) : 1.09850 REMARK 3 B33 (A**2) : 0.38850 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 : 0.008 4125 REMARK 3 ANGLE : 1.290 5707 REMARK 3 CHIRALITY : 0.078 702 REMARK 3 PLANARITY : 0.004 609 REMARK 3 DIHEDRAL : 18.517 1647 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 27:252) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0349 4.4317 8.2072 REMARK 3 T TENSOR REMARK 3 T11: 0.1577 T22: 0.2105 REMARK 3 T33: 0.1272 T12: 0.1945 REMARK 3 T13: 0.0077 T23: 0.0724 REMARK 3 L TENSOR REMARK 3 L11: 2.0340 L22: 1.4533 REMARK 3 L33: 3.8348 L12: -0.0235 REMARK 3 L13: 1.4097 L23: 0.1694 REMARK 3 S TENSOR REMARK 3 S11: -0.0480 S12: -0.0188 S13: 0.2114 REMARK 3 S21: 0.1150 S22: 0.1047 S23: -0.1760 REMARK 3 S31: -0.3019 S32: -0.5095 S33: -0.0272 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 28:252) REMARK 3 ORIGIN FOR THE GROUP (A): 38.9785 -5.0658 21.4929 REMARK 3 T TENSOR REMARK 3 T11: 0.2378 T22: 0.2106 REMARK 3 T33: 0.2054 T12: 0.0466 REMARK 3 T13: -0.0676 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.0831 L22: 2.6614 REMARK 3 L33: 1.8752 L12: -0.3748 REMARK 3 L13: 0.7481 L23: 0.5361 REMARK 3 S TENSOR REMARK 3 S11: 0.0591 S12: -0.0959 S13: -0.0292 REMARK 3 S21: 0.1959 S22: -0.0912 S23: -0.2374 REMARK 3 S31: 0.0981 S32: 0.0794 S33: -0.0037 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C AND RESID 1:14) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0497 -21.3968 15.0301 REMARK 3 T TENSOR REMARK 3 T11: 0.6923 T22: 0.5293 REMARK 3 T33: 0.6637 T12: -0.2432 REMARK 3 T13: -0.1125 T23: -0.1493 REMARK 3 L TENSOR REMARK 3 L11: 2.4783 L22: 0.3807 REMARK 3 L33: 0.2074 L12: 0.9614 REMARK 3 L13: -0.8302 L23: -0.2711 REMARK 3 S TENSOR REMARK 3 S11: 0.2827 S12: -0.4377 S13: -0.9168 REMARK 3 S21: 0.2030 S22: -0.5737 S23: 0.3028 REMARK 3 S31: 0.6596 S32: -1.0623 S33: -0.0525 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN D AND RESID 1:14) REMARK 3 ORIGIN FOR THE GROUP (A): 42.5850 -7.7645 -4.6446 REMARK 3 T TENSOR REMARK 3 T11: 0.6372 T22: 0.7231 REMARK 3 T33: 0.5693 T12: 0.2898 REMARK 3 T13: 0.1211 T23: -0.1888 REMARK 3 L TENSOR REMARK 3 L11: 1.9634 L22: 2.0557 REMARK 3 L33: 0.6260 L12: 0.4051 REMARK 3 L13: -0.4804 L23: 0.4993 REMARK 3 S TENSOR REMARK 3 S11: 0.2651 S12: 0.6805 S13: -0.3863 REMARK 3 S21: -0.2381 S22: -0.2082 S23: -0.3159 REMARK 3 S31: 0.6086 S32: 0.0170 S33: -0.0931 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 3OIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000061159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.00931 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16553 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2V3J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MES, 15MM MGS04, 7% PEG 4000, REMARK 280 20% GLYCEROL, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 41.68850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.46550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.93000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.46550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.68850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.93000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 REMARK 465 ASP A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 VAL A 7 REMARK 465 ARG A 8 REMARK 465 ASP A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LYS A 12 REMARK 465 GLY A 13 REMARK 465 GLY A 14 REMARK 465 ASP A 15 REMARK 465 GLN A 16 REMARK 465 LYS A 17 REMARK 465 ALA A 18 REMARK 465 LEU A 19 REMARK 465 PRO A 20 REMARK 465 ALA A 21 REMARK 465 SER A 22 REMARK 465 LEU A 23 REMARK 465 VAL A 24 REMARK 465 PRO A 25 REMARK 465 GLN A 26 REMARK 465 ALA A 27 REMARK 465 SER A 56 REMARK 465 SER A 57 REMARK 465 ASN A 58 REMARK 465 GLY A 59 REMARK 465 PRO A 60 REMARK 465 GLY A 61 REMARK 465 GLY A 62 REMARK 465 ASP A 63 REMARK 465 LYS A 64 REMARK 465 LYS A 78 REMARK 465 LYS A 79 REMARK 465 MET A 80 REMARK 465 GLY A 81 REMARK 465 ARG A 82 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 GLU B 3 REMARK 465 ASP B 4 REMARK 465 SER B 5 REMARK 465 ARG B 6 REMARK 465 VAL B 7 REMARK 465 ARG B 8 REMARK 465 ASP B 9 REMARK 465 ALA B 10 REMARK 465 LEU B 11 REMARK 465 LYS B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ASP B 15 REMARK 465 GLN B 16 REMARK 465 LYS B 17 REMARK 465 ALA B 18 REMARK 465 LEU B 19 REMARK 465 PRO B 20 REMARK 465 ALA B 21 REMARK 465 SER B 22 REMARK 465 LEU B 23 REMARK 465 VAL B 24 REMARK 465 PRO B 25 REMARK 465 GLN B 26 REMARK 465 ALA B 27 REMARK 465 SER B 56 REMARK 465 SER B 57 REMARK 465 ASN B 58 REMARK 465 GLY B 59 REMARK 465 PRO B 60 REMARK 465 GLY B 61 REMARK 465 GLY B 62 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 B 78 CG CD CE NZ REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN B 190 CG OE1 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 6 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 U D 5 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 U D 6 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 U D 6 C3' - O3' - P ANGL. DEV. = 7.6 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 PRO A 29 133.33 -39.91 REMARK 500 CYS A 70 -62.31 -29.36 REMARK 500 LEU A 76 -35.40 -38.56 REMARK 500 SER A 149 148.15 -173.44 REMARK 500 VAL A 153 -6.72 -56.55 REMARK 500 ASN A 154 -61.68 -136.99 REMARK 500 ASP A 183 43.88 -82.98 REMARK 500 ARG B 82 -142.19 -168.66 REMARK 500 ASP B 83 35.79 23.23 REMARK 500 ILE B 84 96.24 -62.17 REMARK 500 GLN B 115 107.51 -161.03 REMARK 500 LEU B 148 -3.96 76.57 REMARK 500 ASP B 214 52.88 -90.76 REMARK 500 PHE B 216 0.64 -63.55 REMARK 500 ALA B 217 11.58 -153.02 REMARK 500 ASN B 250 63.25 64.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SAH A 253 REMARK 610 SAH B 253 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 15 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O7B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS NEP1 BOUND TO S- REMARK 900 ADENOSYLHOMOCYSTEINE REMARK 900 RELATED ID: 3OII RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO S-ADENOSYLHOMOCYSTEINE REMARK 900 RELATED ID: 3OIN RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO S-ADENOSYLHOMOCYSTEINE AND 1 MOLECULE OF REMARK 900 COGNATE RNA DBREF 3OIJ A 1 252 UNP Q06287 EMG1_YEAST 1 252 DBREF 3OIJ B 1 252 UNP Q06287 EMG1_YEAST 1 252 DBREF 3OIJ C 1 14 PDB 3OIJ 3OIJ 1 14 DBREF 3OIJ D 1 14 PDB 3OIJ 3OIJ 1 14 SEQADV 3OIJ GLY A 0 UNP Q06287 EXPRESSION TAG SEQADV 3OIJ GLY B 0 UNP Q06287 EXPRESSION TAG SEQRES 1 A 253 GLY MET VAL GLU ASP SER ARG VAL ARG ASP ALA LEU LYS SEQRES 2 A 253 GLY GLY ASP GLN LYS ALA LEU PRO ALA SER LEU VAL PRO SEQRES 3 A 253 GLN ALA PRO PRO VAL LEU THR SER LYS ASP LYS ILE THR SEQRES 4 A 253 LYS ARG MET ILE VAL VAL LEU ALA MET ALA SER LEU GLU SEQRES 5 A 253 THR HIS LYS ILE SER SER ASN GLY PRO GLY GLY ASP LYS SEQRES 6 A 253 TYR VAL LEU LEU ASN CYS ASP ASP HIS GLN GLY LEU LEU SEQRES 7 A 253 LYS LYS MET GLY ARG ASP ILE SER GLU ALA ARG PRO ASP SEQRES 8 A 253 ILE THR HIS GLN CYS LEU LEU THR LEU LEU ASP SER PRO SEQRES 9 A 253 ILE ASN LYS ALA GLY LYS LEU GLN VAL TYR ILE GLN THR SEQRES 10 A 253 SER ARG GLY ILE LEU ILE GLU VAL ASN PRO THR VAL ARG SEQRES 11 A 253 ILE PRO ARG THR PHE LYS ARG PHE SER GLY LEU MET VAL SEQRES 12 A 253 GLN LEU LEU HIS LYS LEU SER ILE ARG SER VAL ASN SER SEQRES 13 A 253 GLU GLU LYS LEU LEU LYS VAL ILE LYS ASN PRO ILE THR SEQRES 14 A 253 ASP HIS LEU PRO THR LYS CYS ARG LYS VAL THR LEU SER SEQRES 15 A 253 PHE ASP ALA PRO VAL ILE ARG VAL GLN ASP TYR ILE GLU SEQRES 16 A 253 LYS LEU ASP ASP ASP GLU SER ILE CYS VAL PHE VAL GLY SEQRES 17 A 253 ALA MET ALA ARG GLY LYS ASP ASN PHE ALA ASP GLU TYR SEQRES 18 A 253 VAL ASP GLU LYS VAL GLY LEU SER ASN TYR PRO LEU SER SEQRES 19 A 253 ALA SER VAL ALA CYS SER LYS PHE CYS HIS GLY ALA GLU SEQRES 20 A 253 ASP ALA TRP ASN ILE LEU SEQRES 1 B 253 GLY MET VAL GLU ASP SER ARG VAL ARG ASP ALA LEU LYS SEQRES 2 B 253 GLY GLY ASP GLN LYS ALA LEU PRO ALA SER LEU VAL PRO SEQRES 3 B 253 GLN ALA PRO PRO VAL LEU THR SER LYS ASP LYS ILE THR SEQRES 4 B 253 LYS ARG MET ILE VAL VAL LEU ALA MET ALA SER LEU GLU SEQRES 5 B 253 THR HIS LYS ILE SER SER ASN GLY PRO GLY GLY ASP LYS SEQRES 6 B 253 TYR VAL LEU LEU ASN CYS ASP ASP HIS GLN GLY LEU LEU SEQRES 7 B 253 LYS LYS MET GLY ARG ASP ILE SER GLU ALA ARG PRO ASP SEQRES 8 B 253 ILE THR HIS GLN CYS LEU LEU THR LEU LEU ASP SER PRO SEQRES 9 B 253 ILE ASN LYS ALA GLY LYS LEU GLN VAL TYR ILE GLN THR SEQRES 10 B 253 SER ARG GLY ILE LEU ILE GLU VAL ASN PRO THR VAL ARG SEQRES 11 B 253 ILE PRO ARG THR PHE LYS ARG PHE SER GLY LEU MET VAL SEQRES 12 B 253 GLN LEU LEU HIS LYS LEU SER ILE ARG SER VAL ASN SER SEQRES 13 B 253 GLU GLU LYS LEU LEU LYS VAL ILE LYS ASN PRO ILE THR SEQRES 14 B 253 ASP HIS LEU PRO THR LYS CYS ARG LYS VAL THR LEU SER SEQRES 15 B 253 PHE ASP ALA PRO VAL ILE ARG VAL GLN ASP TYR ILE GLU SEQRES 16 B 253 LYS LEU ASP ASP ASP GLU SER ILE CYS VAL PHE VAL GLY SEQRES 17 B 253 ALA MET ALA ARG GLY LYS ASP ASN PHE ALA ASP GLU TYR SEQRES 18 B 253 VAL ASP GLU LYS VAL GLY LEU SER ASN TYR PRO LEU SER SEQRES 19 B 253 ALA SER VAL ALA CYS SER LYS PHE CYS HIS GLY ALA GLU SEQRES 20 B 253 ASP ALA TRP ASN ILE LEU SEQRES 1 C 14 G G G C U U C A A C G C C SEQRES 2 C 14 C SEQRES 1 D 14 G G G C U U C A A C G C C SEQRES 2 D 14 C HET SAH A 253 25 HET SAH B 253 25 HET MG D 15 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM MG MAGNESIUM ION FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 7 MG MG 2+ FORMUL 8 HOH *61(H2 O) HELIX 1 1 ASN A 69 GLN A 74 1 6 HELIX 2 2 ASP A 83 ALA A 87 5 5 HELIX 3 3 ARG A 88 ASP A 101 1 14 HELIX 4 4 SER A 102 ALA A 107 1 6 HELIX 5 5 THR A 133 LEU A 148 1 16 HELIX 6 6 PRO A 166 HIS A 170 5 5 HELIX 7 7 ARG A 188 LYS A 195 1 8 HELIX 8 8 LYS A 213 ASP A 218 5 6 HELIX 9 9 SER A 233 TRP A 249 1 17 HELIX 10 10 HIS B 73 MET B 80 1 8 HELIX 11 11 ARG B 88 ASP B 101 1 14 HELIX 12 12 SER B 102 ALA B 107 1 6 HELIX 13 13 THR B 133 LEU B 148 1 16 HELIX 14 14 PRO B 166 LEU B 171 1 6 HELIX 15 15 ARG B 188 LYS B 195 1 8 HELIX 16 16 SER B 233 TRP B 249 1 17 SHEET 1 A 8 SER A 149 ARG A 151 0 SHEET 2 A 8 LYS A 158 ILE A 163 -1 O LEU A 160 N ILE A 150 SHEET 3 A 8 LEU A 121 VAL A 124 -1 N GLU A 123 O LYS A 161 SHEET 4 A 8 LEU A 110 THR A 116 -1 N ILE A 114 O ILE A 122 SHEET 5 A 8 MET A 41 ALA A 48 1 N LEU A 45 O GLN A 115 SHEET 6 A 8 SER A 201 GLY A 207 1 O ILE A 202 N ILE A 42 SHEET 7 A 8 CYS A 175 LEU A 180 1 N ARG A 176 O CYS A 203 SHEET 8 A 8 GLU A 223 VAL A 225 1 O VAL A 225 N THR A 179 SHEET 1 B 2 THR A 52 HIS A 53 0 SHEET 2 B 2 VAL A 66 LEU A 67 -1 O VAL A 66 N HIS A 53 SHEET 1 C 8 SER B 149 ARG B 151 0 SHEET 2 C 8 LYS B 158 ILE B 163 -1 O LEU B 159 N ILE B 150 SHEET 3 C 8 LEU B 121 VAL B 124 -1 N GLU B 123 O LYS B 161 SHEET 4 C 8 LEU B 110 THR B 116 -1 N ILE B 114 O ILE B 122 SHEET 5 C 8 MET B 41 ALA B 48 1 N ALA B 48 O GLN B 115 SHEET 6 C 8 SER B 201 GLY B 207 1 O VAL B 204 N ILE B 42 SHEET 7 C 8 CYS B 175 LEU B 180 1 N ARG B 176 O CYS B 203 SHEET 8 C 8 GLU B 223 VAL B 225 1 O VAL B 225 N THR B 179 SHEET 1 D 2 THR B 52 HIS B 53 0 SHEET 2 D 2 VAL B 66 LEU B 67 -1 O VAL B 66 N HIS B 53 CISPEP 1 ASN A 165 PRO A 166 0 1.41 CISPEP 2 ILE A 251 LEU A 252 0 -10.89 CISPEP 3 ASN B 165 PRO B 166 0 -0.69 SITE 1 AC1 12 LEU A 180 PHE A 182 GLY A 207 MET A 209 SITE 2 AC1 12 ARG A 211 GLY A 212 GLY A 226 LEU A 227 SITE 3 AC1 12 SER A 228 TYR A 230 PRO A 231 LEU A 232 SITE 1 AC2 14 LEU B 180 PHE B 182 GLY B 207 MET B 209 SITE 2 AC2 14 ALA B 210 ARG B 211 GLY B 212 ASP B 214 SITE 3 AC2 14 PHE B 216 GLY B 226 LEU B 227 SER B 228 SITE 4 AC2 14 TYR B 230 LEU B 232 SITE 1 AC3 1 G D 3 CRYST1 83.377 91.860 96.931 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 0.011994 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010317 0.00000