HEADER RIBOSOMAL PROTEIN 19-AUG-10 3OIN TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NEP1/EMG1 BOUND TO S- TITLE 2 ADENOSYLHOMOCYSTEINE AND 1 MOLECULE OF COGNATE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE NEP1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 18S RRNA (PSEUDOURIDINE(1189)-N1)-METHYLTRANSFERASE,18S RRNA COMPND 5 PSI1189 METHYLTRANSFERASE,ESSENTIAL FOR MITOTIC GROWTH PROTEIN 1, COMPND 6 NUCLEOLAR ESSENTIAL PROTEIN 1; COMPND 7 EC: 2.1.1.260; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: EMG1, NEP1, YLR186W, L9470.5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST527; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_TAXID: 4932; SOURCE 14 OTHER_DETAILS: COGNATE RNA SYNTHESIZED TO MIMIC NATURAL RNA SOURCE 15 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 3OIN 1 REMARK LINK REVDAT 3 22-APR-20 3OIN 1 TITLE COMPND SOURCE REMARK REVDAT 3 2 1 DBREF SEQADV SEQRES LINK REVDAT 3 3 1 SITE ATOM REVDAT 2 13-APR-11 3OIN 1 JRNL REVDAT 1 01-DEC-10 3OIN 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 36186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1803 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 27.6825 - 4.0792 0.99 3748 181 0.1758 0.2057 REMARK 3 2 4.0792 - 3.2394 1.00 3606 201 0.1684 0.1843 REMARK 3 3 3.2394 - 2.8304 1.00 3527 226 0.2016 0.2588 REMARK 3 4 2.8304 - 2.5718 1.00 3560 178 0.2079 0.2310 REMARK 3 5 2.5718 - 2.3876 1.00 3552 167 0.2052 0.2742 REMARK 3 6 2.3876 - 2.2469 1.00 3500 188 0.2101 0.2536 REMARK 3 7 2.2469 - 2.1344 1.00 3515 188 0.2111 0.2728 REMARK 3 8 2.1344 - 2.0415 0.98 3416 183 0.2296 0.2839 REMARK 3 9 2.0415 - 1.9630 0.91 3195 159 0.2307 0.2746 REMARK 3 10 1.9630 - 1.9000 0.78 2764 132 0.2518 0.3139 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 : 0.34 REMARK 3 B_SOL : 59.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 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) : 48.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.62530 REMARK 3 B22 (A**2) : 2.95250 REMARK 3 B33 (A**2) : -8.57770 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 3855 REMARK 3 ANGLE : 1.069 5277 REMARK 3 CHIRALITY : 0.074 637 REMARK 3 PLANARITY : 0.004 611 REMARK 3 DIHEDRAL : 17.813 1470 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 8.5678 6.7735 5.5123 REMARK 3 T TENSOR REMARK 3 T11: 0.2171 T22: 0.1684 REMARK 3 T33: 0.2086 T12: 0.0253 REMARK 3 T13: 0.0588 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.4904 L22: 1.6450 REMARK 3 L33: 1.6707 L12: 0.7639 REMARK 3 L13: 0.7519 L23: 0.3228 REMARK 3 S TENSOR REMARK 3 S11: -0.0087 S12: -0.0107 S13: -0.0675 REMARK 3 S21: -0.1082 S22: -0.0031 S23: -0.1277 REMARK 3 S31: -0.1359 S32: 0.0178 S33: 0.0054 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 12.7665 -3.2063 29.7459 REMARK 3 T TENSOR REMARK 3 T11: 0.2546 T22: 0.3038 REMARK 3 T33: 0.2696 T12: 0.0158 REMARK 3 T13: 0.0365 T23: 0.0520 REMARK 3 L TENSOR REMARK 3 L11: 1.8512 L22: 1.3568 REMARK 3 L33: 1.7392 L12: 0.0088 REMARK 3 L13: 0.7998 L23: -0.4308 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.1418 S13: -0.1825 REMARK 3 S21: 0.0907 S22: -0.0072 S23: -0.0783 REMARK 3 S31: -0.0426 S32: -0.0597 S33: -0.0198 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): -10.5465 -10.5009 12.5782 REMARK 3 T TENSOR REMARK 3 T11: 0.3529 T22: 0.3278 REMARK 3 T33: 0.3441 T12: 0.0137 REMARK 3 T13: 0.0067 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 3.6943 L22: 3.4594 REMARK 3 L33: 1.8574 L12: 3.1694 REMARK 3 L13: 0.3858 L23: 1.2391 REMARK 3 S TENSOR REMARK 3 S11: -0.0305 S12: -0.0864 S13: -0.4827 REMARK 3 S21: -0.2619 S22: -0.1493 S23: -0.2330 REMARK 3 S31: 0.2133 S32: -0.2864 S33: 0.1641 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 3OIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061163. 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 : 7.0 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39200 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 (%): 35.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10% PEG 6000, 20% REMARK 280 GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 22.38700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.87550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.37450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.87550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.38700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.37450 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 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 465 ASP B 63 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 64 CG CD CE NZ REMARK 470 SCY A 70 CD OCD CE REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 MET B 80 CG SD CE 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 ASN B 69 C SCY B 70 N 0.301 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 ASN B 69 CA - C - N ANGL. DEV. = -21.6 DEGREES REMARK 500 ASN B 69 O - C - N ANGL. DEV. = -23.9 DEGREES REMARK 500 U C 6 O4' - C1' - N1 ANGL. DEV. = 8.8 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 LEU A 148 -10.41 83.19 REMARK 500 ARG B 88 51.46 -116.00 REMARK 500 LEU B 148 -4.52 78.26 REMARK 500 ASP B 214 44.43 -87.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN B 69 -30.27 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 B 253 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 MG C 15 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 3 O6 REMARK 620 2 HOH C 17 O 92.9 REMARK 620 3 HOH C 186 O 92.6 90.5 REMARK 620 4 HOH C 188 O 173.0 80.5 89.9 REMARK 620 5 HOH C 209 O 80.1 99.7 167.7 98.5 REMARK 620 6 HOH C 253 O 98.6 156.6 68.9 88.4 102.3 REMARK 620 N 1 2 3 4 5 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 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 253 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCY B 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 16 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 SAME PROTEIN COMPLEXED WITH RNA REMARK 900 RELATED ID: 3OIJ RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH ONLY ONE STRAND OF RNA INSTEAD OF TWO DBREF 3OIN A 1 252 UNP Q06287 NEP1_YEAST 1 252 DBREF 3OIN B 1 252 UNP Q06287 NEP1_YEAST 1 252 DBREF 3OIN C 1 14 PDB 3OIN 3OIN 1 14 SEQADV 3OIN GLY A 0 UNP Q06287 EXPRESSION TAG SEQADV 3OIN 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 SCY 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 SCY 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 MODRES 3OIN SCY A 70 CYS MODIFIED RESIDUE MODRES 3OIN SCY B 70 CYS MODIFIED RESIDUE HET SCY A 70 6 HET SCY B 70 9 HET GOL A 253 6 HET GOL A 254 6 HET SAH B 253 25 HET MG C 15 1 HET CL C 16 1 HETNAM SCY S-ACETYL-CYSTEINE HETNAM GOL GLYCEROL HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SCY 2(C5 H9 N O3 S) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 SAH C14 H20 N6 O5 S FORMUL 7 MG MG 2+ FORMUL 8 CL CL 1- FORMUL 9 HOH *241(H2 O) HELIX 1 1 HIS A 73 MET A 80 1 8 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 SER A 233 TRP A 249 1 17 HELIX 9 9 ASP B 83 ALA B 87 5 5 HELIX 10 10 ARG B 88 ASP B 101 1 14 HELIX 11 11 SER B 102 ALA B 107 1 6 HELIX 12 12 THR B 133 LEU B 148 1 16 HELIX 13 13 PRO B 166 HIS B 170 5 5 HELIX 14 14 ARG B 188 LYS B 195 1 8 HELIX 15 15 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 159 N ILE A 150 SHEET 3 A 8 LEU A 121 VAL A 124 -1 N LEU A 121 O ILE A 163 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 VAL A 43 O GLN A 111 SHEET 6 A 8 SER A 201 GLY A 207 1 O VAL A 204 N ILE A 42 SHEET 7 A 8 CYS A 175 LEU A 180 1 N VAL A 178 O PHE A 205 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 160 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 LEU B 45 O TYR B 113 SHEET 6 C 8 SER B 201 GLY B 207 1 O ILE B 202 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 LINK C ASN A 69 N SCY A 70 1555 1555 1.33 LINK C SCY A 70 N ASP A 71 1555 1555 1.33 LINK C SCY B 70 N ASP B 71 1555 1555 1.34 LINK O6 G C 3 MG MG C 15 1555 1555 2.48 LINK MG MG C 15 O HOH C 17 1555 1555 2.56 LINK MG MG C 15 O HOH C 186 1555 1555 2.90 LINK MG MG C 15 O HOH C 188 1555 1555 2.49 LINK MG MG C 15 O HOH C 209 1555 1555 2.62 LINK MG MG C 15 O HOH C 253 1555 1555 2.79 CISPEP 1 ASN A 165 PRO A 166 0 -1.95 CISPEP 2 ASN B 165 PRO B 166 0 -0.51 SITE 1 AC1 2 LYS A 39 HOH A 265 SITE 1 AC2 7 VAL A 162 LYS A 164 HOH A 284 HOH A 313 SITE 2 AC2 7 ASP B 169 HOH B 275 HOH B 296 SITE 1 AC3 15 LEU B 180 SER B 181 PHE B 182 GLY B 207 SITE 2 AC3 15 MET B 209 ALA B 210 ARG B 211 GLY B 212 SITE 3 AC3 15 ASP B 214 GLY B 226 LEU B 227 SER B 228 SITE 4 AC3 15 TYR B 230 LEU B 232 ALA B 234 SITE 1 AC4 10 ASN B 69 ASP B 71 ASP B 72 HIS B 73 SITE 2 AC4 10 GLN B 74 LEU B 77 ILE B 84 ALA B 87 SITE 3 AC4 10 HOH B 300 C C 7 SITE 1 AC5 6 G C 3 HOH C 17 HOH C 186 HOH C 188 SITE 2 AC5 6 HOH C 209 HOH C 253 SITE 1 AC6 1 G C 3 CRYST1 44.774 88.749 115.751 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 0.022334 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008639 0.00000