HEADER T-RNA 08-MAY-97 1YFG TITLE YEAST INITIATOR TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: YEAST INITIATOR TRNA; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS AMINO ACID TRANSPORT, TRANSFER RIBONUCLEIC ACID, T-RNA EXPDTA X-RAY DIFFRACTION AUTHOR R.BASAVAPPA,P.B.SIGLER REVDAT 5 03-APR-24 1YFG 1 REMARK REVDAT 4 14-FEB-24 1YFG 1 LINK REVDAT 3 13-JUL-11 1YFG 1 VERSN REVDAT 2 24-FEB-09 1YFG 1 VERSN REVDAT 1 03-SEP-97 1YFG 0 JRNL AUTH R.BASAVAPPA,P.B.SIGLER JRNL TITL THE 3 A CRYSTAL STRUCTURE OF YEAST INITIATOR TRNA: JRNL TITL 2 FUNCTIONAL IMPLICATIONS IN INITIATOR/ELONGATOR JRNL TITL 3 DISCRIMINATION. JRNL REF EMBO J. V. 10 3105 1991 JRNL REFN ISSN 0261-4189 JRNL PMID 1915284 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.W.SCHEVITZ,A.D.PODJARNY,N.KRISHNAMACHARI,J.J.HUGHES, REMARK 1 AUTH 2 P.B.SIGLER,J.L.SUSSMAN REMARK 1 TITL CRYSTAL STRUCTURE OF A EUKARYOTIC INITIATOR TRNA REMARK 1 REF NATURE V. 278 188 1979 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT (MODIFIED BY Z.OTWINOWSKI) REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.7 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NONE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1639 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; 0.025 REMARK 3 ANGLE DISTANCE (A) : 0.025 ; 0.035 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.002 ; 0.010 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.247 ; 0.300 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.115 ; 0.200 REMARK 3 MULTIPLE TORSION (A) : 0.168 ; 0.638 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INDIVIDUAL ISOTROPIC TEMP. FACTOR RMS: REMARK 3 0.638. INDIVIDUAL ISOTROPIC TEMP. FACTOR SIGMA: 1.000. THE MODEL REMARK 3 INITIALLY WAS REFINED AGAINST THE SSRL DATA USING NUCLIN/NUCLSQ REMARK 3 AND THEN NUCLIN/PROFFT HYBRID. FACTORY DATA AS THEY BECAME REMARK 3 AVAILABLE. REFINEMENT PERFORMED WITH REFINEMENT CONTINUED REMARK 3 AGAINST CHESS AND CHESS+PHOTON NUCLIN/PROFFT AND THEN X-PLOR. REMARK 3 FINAL MODEL OBTAINED WITH NUCLIN/ PROFFT. REMARK 4 REMARK 4 1YFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000177389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-88; 01-JAN-88; 01-JAN-88 REMARK 200 TEMPERATURE (KELVIN) : 278.00; 278.00; 278.00 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 8 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : SSRL; CHESS; PHOTON FACTORY REMARK 200 BEAMLINE : NULL; NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL; NULL REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : FILM; STORAGE PHOSPHORS; IMAGE REMARK 200 PLATE REMARK 200 DETECTOR MANUFACTURER : NULL; KODAK; Y.AMEMIYA REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10688 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49500 REMARK 200 FOR SHELL : 2.240 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE, DM REMARK 200 STARTING MODEL: 4 A STRUCTURE REPORTED IN REFERENCE 2 REMARK 200 REMARK 200 REMARK: THE DATA QUALITY STATISTICS REPORTED ARE FOR THE COMBINED REMARK 200 DATA SET FROM CHESS AND THE PHOTON FACTORY. THE MODEL SUBMITTED REMARK 200 HERE IS BASED ON THE 4A STRUCTURE REPORTED IN REFERENCE 2 AND REMARK 200 REFINED AGAINST NEWLY COLLECTED DATA TO 3A. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 82.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00, VAPOR DIFFUSION, TEMPERATURE REMARK 280 301.00K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.51367 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.02733 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 45.51367 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.02733 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.51367 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 91.02733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 45.51367 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 91.02733 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 A 13 C2' C A 13 C1' -0.051 REMARK 500 G A 18 O3' G A 19 P 0.086 REMARK 500 A A 21 N9 A A 21 C4 0.038 REMARK 500 C A 41 C5' C A 41 C4' 0.072 REMARK 500 C A 41 O3' U A 42 P -0.103 REMARK 500 A A 54 O3' U A 55 P 0.076 REMARK 500 G A 65 P G A 65 O5' -0.068 REMARK 500 U A 72 C2' U A 72 C1' -0.052 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 A A 1 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 A A 1 O5' - C5' - C4' ANGL. DEV. = -5.7 DEGREES REMARK 500 G A 2 O5' - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 G A 2 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 G A 2 P - O5' - C5' ANGL. DEV. = -12.0 DEGREES REMARK 500 G A 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 C A 3 O5' - C5' - C4' ANGL. DEV. = -7.1 DEGREES REMARK 500 C A 3 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 C A 5 C3' - O3' - P ANGL. DEV. = -10.2 DEGREES REMARK 500 C A 6 P - O5' - C5' ANGL. DEV. = -12.6 DEGREES REMARK 500 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 C A 6 N3 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 G A 7 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 U A 8 C2 - N3 - C4 ANGL. DEV. = -5.0 DEGREES REMARK 500 U A 8 N3 - C4 - C5 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 11 C3' - O3' - P ANGL. DEV. = -11.4 DEGREES REMARK 500 G A 12 O5' - P - OP1 ANGL. DEV. = 9.9 DEGREES REMARK 500 G A 12 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 A A 14 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 A A 14 C5 - C6 - N1 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 14 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 15 O5' - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 G A 15 P - O5' - C5' ANGL. DEV. = -19.2 DEGREES REMARK 500 G A 15 N9 - C1' - C2' ANGL. DEV. = -9.6 DEGREES REMARK 500 H2U A 16 O3' - P - OP1 ANGL. DEV. = 10.6 DEGREES REMARK 500 H2U A 16 C3' - O3' - P ANGL. DEV. = -11.6 DEGREES REMARK 500 G A 18 P - O5' - C5' ANGL. DEV. = -18.1 DEGREES REMARK 500 G A 18 O4' - C1' - N9 ANGL. DEV. = 10.8 DEGREES REMARK 500 G A 18 C3' - O3' - P ANGL. DEV. = -11.8 DEGREES REMARK 500 G A 19 OP1 - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 G A 19 O5' - P - OP2 ANGL. DEV. = 16.7 DEGREES REMARK 500 G A 19 O4' - C1' - N9 ANGL. DEV. = -13.5 DEGREES REMARK 500 A A 21 O4' - C1' - N9 ANGL. DEV. = 9.6 DEGREES REMARK 500 G A 22 O5' - P - OP2 ANGL. DEV. = 8.6 DEGREES REMARK 500 G A 22 P - O5' - C5' ANGL. DEV. = -10.4 DEGREES REMARK 500 G A 22 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 22 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 C A 23 O5' - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 C A 23 P - O5' - C5' ANGL. DEV. = -11.4 DEGREES REMARK 500 G A 24 N9 - C1' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 G A 24 C3' - O3' - P ANGL. DEV. = 12.0 DEGREES REMARK 500 C A 25 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C A 25 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 C A 27 O5' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 A A 28 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 28 N1 - C2 - N3 ANGL. DEV. = -3.0 DEGREES REMARK 500 G A 29 C3' - O3' - P ANGL. DEV. = 21.2 DEGREES REMARK 500 G A 31 N9 - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 C A 32 O3' - P - O5' ANGL. DEV. = 15.5 DEGREES REMARK 500 C A 32 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 163 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 MOST OF THE MODEL IS CLEARLY DEFINED IN THE ELECTRON REMARK 999 DENSITY MAPS. HOWEVER, PLEASE BE AWARE THAT RESIDUES REMARK 999 29-41, COMPRISING MOST OF THE ANTICODON ARM, ARE HIGHLY REMARK 999 DISORDERED.THE POSITIONS OF THESE RESIDUES ARE ONLY A BEST REMARK 999 GUESS. IN PARTICULAR, THE ORIENTATION OF THE T6A REMARK 999 MODIFICATION ON RESIDUE 37 IS VERY TENTATIVE. PLEASE REMARK 999 USE CAUTION WHEN MAKING ANY SUPPOSITIONS BASED REMARK 999 ON THE POSITIONS OF THESE RESIDUES. REMARK 999 REFERENCE: IN ORDER TO ALIGN THE YEAST INITIATOR TRNA TO REMARK 999 THE CANONICAL CLOVERLEAF NUMBERING SYSTEM, THERE IS NO REMARK 999 RESIDUE NUMBERED "17". DBREF 1YFG A 1 76 PDB 1YFG 1YFG 1 76 SEQRES 1 A 75 A G C G C C G U 1MG 2MG C G C SEQRES 2 A 75 A G H2U G G A A G C G C M2G C SEQRES 3 A 75 A G G G C U C A U T6A A C C SEQRES 4 A 75 C U G A U 7MG H2U 5MC 5MC U C G G SEQRES 5 A 75 A U C G 1MA A A C C G RIA G C SEQRES 6 A 75 G G C G C U A C C A MODRES 1YFG 1MG A 9 G 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1YFG 2MG A 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1YFG H2U A 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1YFG M2G A 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1YFG T6A A 37 A MODRES 1YFG 7MG A 46 G MODRES 1YFG H2U A 47 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1YFG 5MC A 48 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1YFG 5MC A 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1YFG 1MA A 58 A MODRES 1YFG RIA A 64 A HET 1MG A 9 24 HET 2MG A 10 24 HET H2U A 16 20 HET M2G A 26 25 HET T6A A 37 32 HET 7MG A 46 24 HET H2U A 47 20 HET 5MC A 48 21 HET 5MC A 49 21 HET 1MA A 58 23 HET RIA A 64 35 HETNAM 1MG 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM T6A N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) HETNAM 2 T6A CARBAMOYL]THREONINE-5'-MONOPHOSPHATE HETNAM 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM RIA 2'-O-[(5'-PHOSPHO)RIBOSYL]ADENOSINE-5'-MONOPHOSPHATE HETSYN T6A N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'- HETSYN 2 T6A MONOPHOSPHATE FORMUL 1 1MG C11 H16 N5 O8 P FORMUL 1 2MG C11 H16 N5 O8 P FORMUL 1 H2U 2(C9 H15 N2 O9 P) FORMUL 1 M2G C12 H18 N5 O8 P FORMUL 1 T6A C15 H21 N6 O11 P FORMUL 1 7MG C11 H18 N5 O8 P FORMUL 1 5MC 2(C10 H16 N3 O8 P) FORMUL 1 1MA C11 H16 N5 O7 P FORMUL 1 RIA C15 H23 N5 O14 P2 LINK O3' U A 8 P 1MG A 9 1555 1555 1.60 LINK O3' 1MG A 9 P 2MG A 10 1555 1555 1.62 LINK O3' 2MG A 10 P C A 11 1555 1555 1.60 LINK O3' G A 15 P H2U A 16 1555 1555 1.60 LINK O3' H2U A 16 P G A 18 1555 1555 1.59 LINK O3' C A 25 P M2G A 26 1555 1555 1.64 LINK O3' M2G A 26 P C A 27 1555 1555 1.62 LINK O3' U A 36 P T6A A 37 1555 1555 1.58 LINK O3' T6A A 37 P A A 38 1555 1555 1.56 LINK O3' U A 45 P 7MG A 46 1555 1555 1.63 LINK O3' 7MG A 46 P H2U A 47 1555 1555 1.62 LINK O3' H2U A 47 P 5MC A 48 1555 1555 1.63 LINK O3' 5MC A 48 P 5MC A 49 1555 1555 1.63 LINK O3' 5MC A 49 P U A 50 1555 1555 1.61 LINK O3' G A 57 P 1MA A 58 1555 1555 1.66 LINK O3' 1MA A 58 P A A 59 1555 1555 1.62 LINK O3' G A 63 P RIA A 64 1555 1555 1.62 LINK O3A RIA A 64 P G A 65 1555 1555 1.59 CRYST1 113.720 113.720 136.541 90.00 90.00 120.00 P 64 2 2 12 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 0.008794 0.005077 0.000000 0.00000 SCALE2 0.000000 0.010154 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007324 0.00000