HEADER RIBOSOMAL PROTEIN 19-AUG-10 3OII TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NEP1/EMG1 BOUND TO S- TITLE 2 ADENOSYLHOMOCYSTEINE 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: EMG1, NEP1, YLR186W, L9470.5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST527 KEYWDS EMG1, SCNEP1, SPOUT, RIBOSOME BIOGENESIS, METHYLTRANSFERASE, RRNA KEYWDS 2 PROCESSING, RIBOSOMAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.R.THOMAS,A.SZYK,N.LARONDE-LEBLANC REVDAT 4 06-SEP-23 3OII 1 REMARK SEQADV REVDAT 3 24-JAN-18 3OII 1 AUTHOR REVDAT 2 13-APR-11 3OII 1 JRNL REVDAT 1 01-DEC-10 3OII 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. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 37397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1891 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2114 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3332 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.80000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -2.01000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3525 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4775 ; 1.881 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 437 ; 6.173 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;35.918 ;24.130 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 681 ;15.591 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;18.115 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 575 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2509 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2166 ; 1.212 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3548 ; 2.104 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1359 ; 3.212 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1219 ; 5.145 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 251 REMARK 3 ORIGIN FOR THE GROUP (A): -6.8037 4.9300 -3.6461 REMARK 3 T TENSOR REMARK 3 T11: -0.0705 T22: -0.0463 REMARK 3 T33: -0.0306 T12: -0.0118 REMARK 3 T13: 0.0289 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.2866 L22: 1.0256 REMARK 3 L33: 1.5494 L12: -0.0079 REMARK 3 L13: 0.1671 L23: 0.1243 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: -0.0404 S13: -0.1105 REMARK 3 S21: 0.0201 S22: -0.0135 S23: 0.0141 REMARK 3 S31: 0.1353 S32: 0.0115 S33: 0.0489 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 251 REMARK 3 ORIGIN FOR THE GROUP (A): -11.2828 -6.4736 -26.9515 REMARK 3 T TENSOR REMARK 3 T11: -0.0175 T22: -0.0551 REMARK 3 T33: -0.0978 T12: 0.0287 REMARK 3 T13: -0.0218 T23: -0.0519 REMARK 3 L TENSOR REMARK 3 L11: 1.8595 L22: 1.4480 REMARK 3 L33: 2.1347 L12: -0.6837 REMARK 3 L13: 0.8032 L23: 0.1975 REMARK 3 S TENSOR REMARK 3 S11: 0.1912 S12: 0.2278 S13: -0.2119 REMARK 3 S21: -0.1393 S22: -0.1308 S23: 0.0915 REMARK 3 S31: 0.3377 S32: 0.0966 S33: -0.0604 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3OII 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_1000061158. 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 : 6.5 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 : 39930 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 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 (%): 37.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M AMMONIUM SULFATE, 0.05M BIS REMARK 280 -TRIS, 30% PENTAERYTHRITOL ETHOXYLATE, 20% GLYCEROL, PH 6.5, REMARK 280 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 22.99400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.27250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.33100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.27250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.99400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.33100 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: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 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 LYS B 54 REMARK 465 ILE B 55 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 465 LYS B 64 REMARK 465 TYR B 65 REMARK 465 VAL B 153 REMARK 465 ASN B 154 REMARK 465 SER B 155 REMARK 465 GLU B 156 REMARK 465 GLU B 157 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 GLY B 81 N GLY B 81 CA 0.109 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 -4.58 80.21 REMARK 500 ASN A 154 -16.11 84.21 REMARK 500 ASP A 214 45.27 -90.33 REMARK 500 ASP B 214 37.28 -91.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 136 0.24 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 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 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: 3OIJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 2 MOLECULES OF COGNATE RNA REMARK 900 RELATED ID: 3OIN RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH S-ADENOSYLHOMOCYSTEINE AND 1 REMARK 900 MOLECULE OF COGNATE RNA DBREF 3OII A 1 252 UNP Q06287 EMG1_YEAST 1 252 DBREF 3OII B 1 252 UNP Q06287 EMG1_YEAST 1 252 SEQADV 3OII GLY A 0 UNP Q06287 EXPRESSION TAG SEQADV 3OII 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 HET SAH A 253 26 HET GOL A 254 6 HET SAH B 253 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SAH 2(C14 H20 N6 O5 S) FORMUL 4 GOL C3 H8 O3 FORMUL 6 HOH *224(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 HIS B 73 MET B 80 1 8 HELIX 10 10 ASP B 83 ALA B 87 5 5 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 HIS B 170 5 5 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 SER A 152 0 SHEET 2 A 8 SER A 155 ILE A 163 -1 O LEU A 159 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 VAL A 204 N ILE A 42 SHEET 7 A 8 CYS A 175 LEU A 180 1 N VAL A 178 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 ILE B 150 0 SHEET 2 C 8 LEU B 160 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 VAL B 112 O VAL B 124 SHEET 5 C 8 MET B 41 ALA B 48 1 N LEU B 45 O GLN B 115 SHEET 6 C 8 SER B 201 GLY B 207 1 O VAL B 204 N VAL B 44 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 CISPEP 1 ASN A 165 PRO A 166 0 4.57 CISPEP 2 ASN B 165 PRO B 166 0 -3.68 SITE 1 AC1 17 ASN A 154 LEU A 180 SER A 181 PHE A 182 SITE 2 AC1 17 VAL A 206 GLY A 207 MET A 209 ALA A 210 SITE 3 AC1 17 GLY A 212 ASP A 214 GLY A 226 LEU A 227 SITE 4 AC1 17 SER A 228 TYR A 230 LEU A 232 ALA A 234 SITE 5 AC1 17 HOH A 351 SITE 1 AC2 5 PRO A 28 VAL A 30 ASN A 105 PRO A 126 SITE 2 AC2 5 HOH A 258 SITE 1 AC3 15 LEU B 180 SER B 181 PHE B 182 VAL B 206 SITE 2 AC3 15 GLY B 207 ARG B 211 GLY B 212 ASP B 214 SITE 3 AC3 15 GLY B 226 LEU B 227 SER B 228 TYR B 230 SITE 4 AC3 15 LEU B 232 ALA B 234 HOH B 331 CRYST1 45.988 84.662 112.545 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 0.021745 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008885 0.00000