HEADER TRANSFERASE/RNA 29-SEP-08 3EPL TITLE CRYSTALLOGRAPHIC SNAPSHOTS OF EUKARYOTIC DIMETHYLALLYLTRANSFERASE TITLE 2 ACTING ON TRNA: INSIGHT INTO TRNA RECOGNITION AND REACTION MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA ISOPENTENYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 13-421; COMPND 5 SYNONYM: ISOPENTENYL-DIPHOSPHATE: TRNA ISOPENTENYLTRANSFERASE, IPP COMPND 6 TRANSFERASE, IPTASE, IPPT, DIMETHYLALLYLTRANSFERASE; COMPND 7 EC: 2.5.1.8; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRNA; COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: TRNA; COMPND 15 CHAIN: F; COMPND 16 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: MOD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLM-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 14 RNA POLYMERASE; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES KEYWDS TRANSFERASE, ALTERNATIVE INITIATION, ATP-BINDING, CYTOPLASM, KEYWDS 2 MITOCHONDRION, NUCLEOTIDE-BINDING, NUCLEUS, TRNA PROCESSING, KEYWDS 3 TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.H.HUANG,C.ZHOU REVDAT 3 21-FEB-24 3EPL 1 REMARK DBREF LINK REVDAT 2 24-FEB-09 3EPL 1 REMARK VERSN REVDAT 1 04-NOV-08 3EPL 0 JRNL AUTH C.ZHOU,R.H.HUANG JRNL TITL CRYSTALLOGRAPHIC SNAPSHOTS OF EUKARYOTIC JRNL TITL 2 DIMETHYLALLYLTRANSFERASE ACTING ON TRNA: INSIGHT INTO TRNA JRNL TITL 3 RECOGNITION AND REACTION MECHANISM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 16142 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18852462 JRNL DOI 10.1073/PNAS.0805680105 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1495.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 77.5 REMARK 3 NUMBER OF REFLECTIONS : 20022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1562 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6678 REMARK 3 NUCLEIC ACID ATOMS : 2951 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 135.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -38.00300 REMARK 3 B22 (A**2) : 49.48600 REMARK 3 B33 (A**2) : -11.48200 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.209 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.397 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.525 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.432 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.429 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 60.13 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 GROUP 2 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 2 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : PP.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : PP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3EPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-07; 12-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 21-ID-F; 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785; 0.9785 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21517 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PENTAERYTHRITOL PROPOXYLATE 426, PH REMARK 280 6.5, VAPOR DIFFUSION, TEMPERATURE 278K,, VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.65900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.65900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 82.03700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 104.92500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 82.03700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 104.92500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.65900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 82.03700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 104.92500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.65900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 82.03700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 104.92500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, B, F 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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 269 REMARK 465 LYS A 270 REMARK 465 THR A 271 REMARK 465 ASP A 272 REMARK 465 ASP A 273 REMARK 465 ASN A 274 REMARK 465 THR A 275 REMARK 465 GLY B 269 REMARK 465 LYS B 270 REMARK 465 THR B 271 REMARK 465 ASP B 272 REMARK 465 ASP B 273 REMARK 465 ASN B 274 REMARK 465 THR B 275 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 C E 2 P C E 2 OP3 -0.087 REMARK 500 C F 2 P C F 2 OP3 -0.088 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 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 342 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 U E 32 C2' - C3' - O3' ANGL. DEV. = 15.7 DEGREES REMARK 500 U E 33 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES REMARK 500 G E 34 C2' - C3' - O3' ANGL. DEV. = 10.7 DEGREES REMARK 500 A F 7 N9 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 G F 18 C2' - C3' - O3' ANGL. DEV. = 13.6 DEGREES REMARK 500 U F 32 C2' - C3' - O3' ANGL. DEV. = 15.7 DEGREES REMARK 500 U F 33 C2' - C3' - O3' ANGL. DEV. = 12.5 DEGREES REMARK 500 G F 34 C2' - C3' - O3' ANGL. DEV. = 12.0 DEGREES REMARK 500 A F 37 C2' - C3' - O3' ANGL. DEV. = 12.8 DEGREES REMARK 500 G F 46 N9 - C1' - C2' ANGL. DEV. = 10.5 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 22 -165.90 -66.24 REMARK 500 THR A 23 66.18 -115.43 REMARK 500 VAL A 25 -60.69 -124.16 REMARK 500 GLN A 36 -66.48 -90.03 REMARK 500 ASN A 39 106.32 57.93 REMARK 500 ASP A 53 -131.40 38.22 REMARK 500 ILE A 56 -18.56 -39.33 REMARK 500 ASN A 59 123.65 51.66 REMARK 500 LYS A 60 110.51 171.39 REMARK 500 HIS A 61 127.01 -27.19 REMARK 500 VAL A 73 72.79 34.57 REMARK 500 MET A 74 147.22 -175.78 REMARK 500 TRP A 79 -38.27 -37.43 REMARK 500 GLU A 81 142.94 -174.76 REMARK 500 LYS A 104 -164.72 -116.06 REMARK 500 ILE A 107 58.51 -114.69 REMARK 500 VAL A 109 -132.81 -129.74 REMARK 500 HIS A 113 -17.46 -47.39 REMARK 500 LEU A 119 15.63 -68.14 REMARK 500 LYS A 122 -76.53 -143.43 REMARK 500 ARG A 123 166.12 -44.92 REMARK 500 THR A 126 38.44 -79.04 REMARK 500 GLU A 130 24.28 -74.64 REMARK 500 ARG A 131 138.10 -37.67 REMARK 500 GLU A 142 43.34 -86.40 REMARK 500 LYS A 155 -76.21 -65.46 REMARK 500 ASP A 157 69.94 78.98 REMARK 500 ASP A 159 -70.58 -59.81 REMARK 500 PRO A 166 -1.10 -55.68 REMARK 500 TYR A 169 -76.38 -48.12 REMARK 500 ILE A 195 -15.20 72.04 REMARK 500 PHE A 199 123.86 61.90 REMARK 500 ASP A 223 0.33 -62.45 REMARK 500 ARG A 227 -6.77 -59.74 REMARK 500 ASN A 243 -5.95 69.83 REMARK 500 LYS A 244 73.53 30.94 REMARK 500 PHE A 245 98.08 -52.96 REMARK 500 THR A 246 176.48 -57.13 REMARK 500 PRO A 247 20.77 -63.53 REMARK 500 GLN A 249 60.22 -108.87 REMARK 500 PHE A 260 -88.48 -53.67 REMARK 500 LEU A 267 6.43 -158.44 REMARK 500 MET A 303 -81.43 -106.07 REMARK 500 LEU A 304 -78.54 -37.74 REMARK 500 ALA A 327 -44.76 -131.22 REMARK 500 SER A 328 -75.84 -67.03 REMARK 500 ASN A 336 -70.85 -56.27 REMARK 500 SER A 340 10.19 -69.03 REMARK 500 GLU A 347 -2.76 -54.62 REMARK 500 ARG A 348 -17.14 76.65 REMARK 500 REMARK 500 THIS ENTRY HAS 124 RAMACHANDRAN OUTLIERS. 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 DMA A 422 REMARK 610 DMA B 422 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 375 SG REMARK 620 2 CYS A 378 SG 114.7 REMARK 620 3 HIS A 397 NE2 92.7 107.4 REMARK 620 4 HIS A 403 ND1 110.5 126.8 96.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 375 SG REMARK 620 2 CYS B 378 SG 106.0 REMARK 620 3 HIS B 397 NE2 84.0 127.9 REMARK 620 4 HIS B 403 ND1 90.5 127.5 102.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6IA E 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMA A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 72 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMA B 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 72 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 73 DBREF 3EPL A 13 421 UNP P07884 MOD5_YEAST 13 421 DBREF 3EPL E 2 71 PDB 3EPL 3EPL 2 71 DBREF 3EPL B 13 421 UNP P07884 MOD5_YEAST 13 421 DBREF 3EPL F 2 71 PDB 3EPL 3EPL 2 71 SEQRES 1 A 409 SER LYS LYS VAL ILE VAL ILE ALA GLY THR THR GLY VAL SEQRES 2 A 409 GLY LYS SER GLN LEU SER ILE GLN LEU ALA GLN LYS PHE SEQRES 3 A 409 ASN GLY GLU VAL ILE ASN SER ASP SER MET GLN VAL TYR SEQRES 4 A 409 LYS ASP ILE PRO ILE ILE THR ASN LYS HIS PRO LEU GLN SEQRES 5 A 409 GLU ARG GLU GLY ILE PRO HIS HIS VAL MET ASN HIS VAL SEQRES 6 A 409 ASP TRP SER GLU GLU TYR TYR SER HIS ARG PHE GLU THR SEQRES 7 A 409 GLU CYS MET ASN ALA ILE GLU ASP ILE HIS ARG ARG GLY SEQRES 8 A 409 LYS ILE PRO ILE VAL VAL GLY GLY THR HIS TYR TYR LEU SEQRES 9 A 409 GLN THR LEU PHE ASN LYS ARG VAL ASP THR LYS SER SER SEQRES 10 A 409 GLU ARG LYS LEU THR ARG LYS GLN LEU ASP ILE LEU GLU SEQRES 11 A 409 SER THR ASP PRO ASP VAL ILE TYR ASN THR LEU VAL LYS SEQRES 12 A 409 CYS ASP PRO ASP ILE ALA THR LYS TYR HIS PRO ASN ASP SEQRES 13 A 409 TYR ARG ARG VAL GLN ARG MET LEU GLU ILE TYR TYR LYS SEQRES 14 A 409 THR GLY LYS LYS PRO SER GLU THR PHE ASN GLU GLN LYS SEQRES 15 A 409 ILE THR LEU LYS PHE ASP THR LEU PHE LEU TRP LEU TYR SEQRES 16 A 409 SER LYS PRO GLU PRO LEU PHE GLN ARG LEU ASP ASP ARG SEQRES 17 A 409 VAL ASP ASP MET LEU GLU ARG GLY ALA LEU GLN GLU ILE SEQRES 18 A 409 LYS GLN LEU TYR GLU TYR TYR SER GLN ASN LYS PHE THR SEQRES 19 A 409 PRO GLU GLN CYS GLU ASN GLY VAL TRP GLN VAL ILE GLY SEQRES 20 A 409 PHE LYS GLU PHE LEU PRO TRP LEU THR GLY LYS THR ASP SEQRES 21 A 409 ASP ASN THR VAL LYS LEU GLU ASP CYS ILE GLU ARG MET SEQRES 22 A 409 LYS THR ARG THR ARG GLN TYR ALA LYS ARG GLN VAL LYS SEQRES 23 A 409 TRP ILE LYS LYS MET LEU ILE PRO ASP ILE LYS GLY ASP SEQRES 24 A 409 ILE TYR LEU LEU ASP ALA THR ASP LEU SER GLN TRP ASP SEQRES 25 A 409 THR ASN ALA SER GLN ARG ALA ILE ALA ILE SER ASN ASP SEQRES 26 A 409 PHE ILE SER ASN ARG PRO ILE LYS GLN GLU ARG ALA PRO SEQRES 27 A 409 LYS ALA LEU GLU GLU LEU LEU SER LYS GLY GLU THR THR SEQRES 28 A 409 MET LYS LYS LEU ASP ASP TRP THR HIS TYR THR CYS ASN SEQRES 29 A 409 VAL CYS ARG ASN ALA ASP GLY LYS ASN VAL VAL ALA ILE SEQRES 30 A 409 GLY GLU LYS TYR TRP LYS ILE HIS LEU GLY SER ARG ARG SEQRES 31 A 409 HIS LYS SER ASN LEU LYS ARG ASN THR ARG GLN ALA ASP SEQRES 32 A 409 PHE GLU LYS TRP LYS ILE SEQRES 1 E 69 C U C G U A U G G C G C A SEQRES 2 E 69 G U G G U A G C G C A G C SEQRES 3 E 69 A G A U U G C A 6IA A U C U SEQRES 4 E 69 G U U G G U C C U U A G U SEQRES 5 E 69 U C G A U C C U G A G U G SEQRES 6 E 69 C G A G SEQRES 1 B 409 SER LYS LYS VAL ILE VAL ILE ALA GLY THR THR GLY VAL SEQRES 2 B 409 GLY LYS SER GLN LEU SER ILE GLN LEU ALA GLN LYS PHE SEQRES 3 B 409 ASN GLY GLU VAL ILE ASN SER ASP SER MET GLN VAL TYR SEQRES 4 B 409 LYS ASP ILE PRO ILE ILE THR ASN LYS HIS PRO LEU GLN SEQRES 5 B 409 GLU ARG GLU GLY ILE PRO HIS HIS VAL MET ASN HIS VAL SEQRES 6 B 409 ASP TRP SER GLU GLU TYR TYR SER HIS ARG PHE GLU THR SEQRES 7 B 409 GLU CYS MET ASN ALA ILE GLU ASP ILE HIS ARG ARG GLY SEQRES 8 B 409 LYS ILE PRO ILE VAL VAL GLY GLY THR HIS TYR TYR LEU SEQRES 9 B 409 GLN THR LEU PHE ASN LYS ARG VAL ASP THR LYS SER SER SEQRES 10 B 409 GLU ARG LYS LEU THR ARG LYS GLN LEU ASP ILE LEU GLU SEQRES 11 B 409 SER THR ASP PRO ASP VAL ILE TYR ASN THR LEU VAL LYS SEQRES 12 B 409 CYS ASP PRO ASP ILE ALA THR LYS TYR HIS PRO ASN ASP SEQRES 13 B 409 TYR ARG ARG VAL GLN ARG MET LEU GLU ILE TYR TYR LYS SEQRES 14 B 409 THR GLY LYS LYS PRO SER GLU THR PHE ASN GLU GLN LYS SEQRES 15 B 409 ILE THR LEU LYS PHE ASP THR LEU PHE LEU TRP LEU TYR SEQRES 16 B 409 SER LYS PRO GLU PRO LEU PHE GLN ARG LEU ASP ASP ARG SEQRES 17 B 409 VAL ASP ASP MET LEU GLU ARG GLY ALA LEU GLN GLU ILE SEQRES 18 B 409 LYS GLN LEU TYR GLU TYR TYR SER GLN ASN LYS PHE THR SEQRES 19 B 409 PRO GLU GLN CYS GLU ASN GLY VAL TRP GLN VAL ILE GLY SEQRES 20 B 409 PHE LYS GLU PHE LEU PRO TRP LEU THR GLY LYS THR ASP SEQRES 21 B 409 ASP ASN THR VAL LYS LEU GLU ASP CYS ILE GLU ARG MET SEQRES 22 B 409 LYS THR ARG THR ARG GLN TYR ALA LYS ARG GLN VAL LYS SEQRES 23 B 409 TRP ILE LYS LYS MET LEU ILE PRO ASP ILE LYS GLY ASP SEQRES 24 B 409 ILE TYR LEU LEU ASP ALA THR ASP LEU SER GLN TRP ASP SEQRES 25 B 409 THR ASN ALA SER GLN ARG ALA ILE ALA ILE SER ASN ASP SEQRES 26 B 409 PHE ILE SER ASN ARG PRO ILE LYS GLN GLU ARG ALA PRO SEQRES 27 B 409 LYS ALA LEU GLU GLU LEU LEU SER LYS GLY GLU THR THR SEQRES 28 B 409 MET LYS LYS LEU ASP ASP TRP THR HIS TYR THR CYS ASN SEQRES 29 B 409 VAL CYS ARG ASN ALA ASP GLY LYS ASN VAL VAL ALA ILE SEQRES 30 B 409 GLY GLU LYS TYR TRP LYS ILE HIS LEU GLY SER ARG ARG SEQRES 31 B 409 HIS LYS SER ASN LEU LYS ARG ASN THR ARG GLN ALA ASP SEQRES 32 B 409 PHE GLU LYS TRP LYS ILE SEQRES 1 F 69 C U C G U A U G G C G C A SEQRES 2 F 69 G U G G U A G C G C A G C SEQRES 3 F 69 A G A U U G C A A A U C U SEQRES 4 F 69 G U U G G U C C U U A G U SEQRES 5 F 69 U C G A U C C U G A G U G SEQRES 6 F 69 C G A G MODRES 3EPL 6IA E 37 A HET 6IA E 37 27 HET ZN A 1 1 HET DMA A 422 9 HET MG E 72 1 HET ZN B 1 1 HET MG B 2 1 HET DMA B 422 9 HET MG F 72 1 HET MG F 73 1 HETNAM 6IA N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM DMA DIMETHYLALLYL DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 6IA C15 H24 N5 O7 P FORMUL 5 ZN 2(ZN 2+) FORMUL 6 DMA 2(C5 H12 O7 P2) FORMUL 7 MG 4(MG 2+) FORMUL 13 HOH *122(H2 O) HELIX 1 1 GLY A 26 PHE A 38 1 13 HELIX 2 2 ILE A 54 ASN A 59 1 6 HELIX 3 3 PRO A 62 GLU A 67 5 6 HELIX 4 4 TYR A 84 ARG A 101 1 18 HELIX 5 5 TYR A 114 PHE A 120 5 7 HELIX 6 6 THR A 134 GLU A 142 1 9 HELIX 7 7 ASP A 145 CYS A 156 1 12 HELIX 8 8 ASP A 157 LYS A 163 1 7 HELIX 9 9 ASP A 168 GLY A 183 1 16 HELIX 10 10 LYS A 185 GLU A 192 1 8 HELIX 11 11 LYS A 209 ARG A 227 1 19 HELIX 12 12 GLY A 228 GLN A 242 1 15 HELIX 13 13 ASN A 243 PHE A 245 5 3 HELIX 14 14 GLY A 253 VAL A 257 5 5 HELIX 15 15 PHE A 260 LEU A 267 5 8 HELIX 16 16 LEU A 278 MET A 303 1 26 HELIX 17 17 MET A 303 ILE A 308 1 6 HELIX 18 18 GLN A 322 ALA A 327 1 6 HELIX 19 19 ALA A 327 SER A 340 1 14 HELIX 20 20 GLU A 354 LYS A 366 5 13 HELIX 21 21 GLY A 390 LEU A 398 1 9 HELIX 22 22 SER A 400 GLN A 413 1 14 HELIX 23 23 PHE A 416 ILE A 421 1 6 HELIX 24 24 GLY B 26 LYS B 37 1 12 HELIX 25 25 PRO B 55 ASN B 59 5 5 HELIX 26 26 PRO B 62 ARG B 66 5 5 HELIX 27 27 TYR B 84 ARG B 101 1 18 HELIX 28 28 THR B 112 PHE B 120 5 9 HELIX 29 29 THR B 134 GLU B 142 1 9 HELIX 30 30 ASP B 145 CYS B 156 1 12 HELIX 31 31 ASP B 157 LYS B 163 1 7 HELIX 32 32 ASP B 168 GLY B 183 1 16 HELIX 33 33 LYS B 185 GLU B 192 1 8 HELIX 34 34 LYS B 209 ARG B 227 1 19 HELIX 35 35 GLY B 228 SER B 241 1 14 HELIX 36 36 GLY B 253 VAL B 257 5 5 HELIX 37 37 GLY B 259 LEU B 264 1 6 HELIX 38 38 PRO B 265 THR B 268 5 4 HELIX 39 39 LEU B 278 MET B 303 1 26 HELIX 40 40 MET B 303 ILE B 308 1 6 HELIX 41 41 ASP B 319 SER B 321 5 3 HELIX 42 42 GLN B 322 ALA B 327 1 6 HELIX 43 43 ALA B 327 SER B 340 1 14 HELIX 44 44 GLU B 354 LYS B 366 5 13 HELIX 45 45 GLY B 390 LEU B 398 1 9 HELIX 46 46 SER B 400 ALA B 414 1 15 HELIX 47 47 ASP B 415 GLU B 417 5 3 SHEET 1 A 3 LYS A 15 ALA A 20 0 SHEET 2 A 3 ASP A 200 TRP A 205 1 O LEU A 204 N ALA A 20 SHEET 3 A 3 TYR A 313 LEU A 314 1 O TYR A 313 N PHE A 203 SHEET 1 B 2 VAL A 42 ILE A 43 0 SHEET 2 B 2 HIS A 71 HIS A 72 1 O HIS A 72 N VAL A 42 SHEET 1 C 2 HIS A 372 ARG A 379 0 SHEET 2 C 2 ASN A 385 ILE A 389 -1 O VAL A 386 N CYS A 375 SHEET 1 D 5 GLY B 40 SER B 45 0 SHEET 2 D 5 ILE B 105 GLY B 110 1 O ILE B 107 N GLU B 41 SHEET 3 D 5 LYS B 15 ALA B 20 1 N ILE B 19 O VAL B 108 SHEET 4 D 5 ASP B 200 TRP B 205 1 O LEU B 204 N VAL B 18 SHEET 5 D 5 TYR B 313 LEU B 314 1 O TYR B 313 N PHE B 203 SHEET 1 E 2 HIS B 372 ARG B 379 0 SHEET 2 E 2 ASN B 385 ILE B 389 -1 O ALA B 388 N TYR B 373 LINK O3' A E 36 P 6IA E 37 1555 1555 1.59 LINK O3' 6IA E 37 P A E 38 1555 1555 1.62 LINK ZN ZN A 1 SG CYS A 375 1555 1555 2.10 LINK ZN ZN A 1 SG CYS A 378 1555 1555 2.03 LINK ZN ZN A 1 NE2 HIS A 397 1555 1555 2.36 LINK ZN ZN A 1 ND1 HIS A 403 1555 1555 1.83 LINK ZN ZN B 1 SG CYS B 375 1555 1555 2.57 LINK ZN ZN B 1 SG CYS B 378 1555 1555 2.12 LINK ZN ZN B 1 NE2 HIS B 397 1555 1555 2.09 LINK ZN ZN B 1 ND1 HIS B 403 1555 1555 1.96 SITE 1 AC1 11 THR A 23 ASP A 46 MET A 48 THR A 112 SITE 2 AC1 11 ARG A 220 GLN A 256 ARG A 288 TYR A 292 SITE 3 AC1 11 ARG A 295 A E 36 A E 38 SITE 1 AC2 4 CYS A 375 CYS A 378 HIS A 397 HIS A 403 SITE 1 AC3 10 THR A 22 THR A 23 GLY A 24 VAL A 25 SITE 2 AC3 10 GLY A 26 LYS A 27 SER A 28 ASN A 59 SITE 3 AC3 10 ARG A 220 HOH A 437 SITE 1 AC4 3 U E 55 C E 56 G E 57 SITE 1 AC5 4 CYS B 375 CYS B 378 HIS B 397 HIS B 403 SITE 1 AC6 3 SER B 28 ASN B 59 DMA B 422 SITE 1 AC7 10 MG B 2 THR B 23 GLY B 24 VAL B 25 SITE 2 AC7 10 GLY B 26 LYS B 27 SER B 28 ASN B 59 SITE 3 AC7 10 ARG B 220 HOH B 456 SITE 1 AC8 2 C F 2 HOH F 100 SITE 1 AC9 1 A F 26 CRYST1 164.074 209.850 127.318 90.00 90.00 90.00 C 2 2 21 16 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 0.006095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007854 0.00000