HEADER AMINO-ACID TRANSPORT 11-JUN-85 9TNA OBSLTE 19-APR-89 9TNA 3TRA TITLE THREE-*DIMENSIONAL STRUCTURE OF YEAST $T/RNA$==ASP==. I. TITLE 2 STRUCTURE DETERMINATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-RNA (75-MER); COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS T-RNA EXPDTA X-RAY DIFFRACTION AUTHOR E.WESTHOF,P.DUMAS,D.MORAS REVDAT 6 19-APR-89 9TNA 3 OBSLTE REVDAT 5 16-APR-87 9TNA 1 REMARK REVDAT 4 22-OCT-86 9TNA 1 REMARK REVDAT 3 14-JUL-86 9TNA 1 JRNL REVDAT 2 15-JAN-86 9TNA 1 REMARK REVDAT 1 08-NOV-85 9TNA 0 JRNL AUTH M.B.COMARMOND,R.GIEGE,J.C.THIERRY,D.MORAS,J.FISCHER JRNL TITL THREE-DIMENSIONAL STRUCTURE OF YEAST T/RNA==ASP==. JRNL TITL 2 I. STRUCTURE DETERMINATION JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 42 272 1986 JRNL REFN ASTM ASBSDK DK ISSN 0108-7681 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.MORAS,A.-C.DOCK,P.DUMAS,E.WESTHOF,P.ROMBY, REMARK 1 AUTH 2 J.-P.EBEL,R.GIEGE REMARK 1 TITL ANTICODON-ANTICODON INTERACTION INDUCES REMARK 1 TITL 2 CONFORMATIONAL CHANGES IN T/RNA. YEAST REMARK 1 TITL 3 T/RNA==ASP==, A MODEL FOR T/RNA-M/RNA RECOGNITION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 83 932 1986 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.WESTHOF,P.DUMAS,D.MORAS REMARK 1 TITL CRYSTALLOGRAPHIC REFINEMENT OF YEAST ASPARTIC ACID REMARK 1 TITL 2 TRANSFER /RNA REMARK 1 REF J.MOL.BIOL. V. 184 119 1985 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.DUMAS,J.P.EBEL,R.GIEGE,D.MORAS,J.C.THIERRY, REMARK 1 AUTH 2 E.WESTHOF REMARK 1 TITL CRYSTAL STRUCTURE OF YEAST T/RNA==ASP==. ATOMIC REMARK 1 TITL 2 COORDINATES REMARK 1 REF BIOCHIMIE V. 67 597 1985 REMARK 1 REFN ASTM BICMBE FR ISSN 0300-9084 REMARK 1 REFERENCE 4 REMARK 1 AUTH E.WESTHOF,P.DUMAS,D.MORAS REMARK 1 TITL LOOP STEREOCHEMISTRY AND DYNAMICS IN TRANSFER /RNA REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 1 337 1983 REMARK 1 REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REFERENCE 5 REMARK 1 AUTH D.MORAS,M.B.COMARMOND,J.FISCHER,R.WEISS, REMARK 1 AUTH 2 J.C.THIERRY,J.P.EBEL,R.GIEGE REMARK 1 TITL CRYSTAL STRUCTURE OF YEAST T/RNA==ASP== REMARK 1 REF NATURE V. 288 669 1980 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 6 REMARK 1 AUTH R.GIEGE,D.MORAS,J.C.THIERRY REMARK 1 TITL YEAST TRANSFER /RNA==ASP==. A NEW HIGH-RESOLUTION REMARK 1 TITL 2 X-RAY DIFFRACTING CRYSTAL FORM OF A TRANSFER /RNA REMARK 1 REF J.MOL.BIOL. V. 115 91 1977 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 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 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 : 0 REMARK 3 NUCLEIC ACID ATOMS : 1602 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) : NULL 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : 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 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 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9TNA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 9TNA THIS FORM OF TRNA CONTAINS 75 RESIDUES WHILE TRNA PHE REMARK 5 9TNA CONTAINS 76 RESIDUES. IN ORDER TO FOLLOW THE RESIDUE REMARK 5 9TNA NUMBERING SCHEME OF TRNA PHE, IT WAS NECESSARY TO SKIP REMARK 5 47. 9TNA THUS THE RESIDUES IN THIS ENTRY ARE NUMBERED 1 - REMARK 5 46, 48 - 9TNA 76. 9TNA REMARK 6 REMARK 6 9TNA CORRECTION. CORRECT COUNTRY CODE FOR REFERENCE 2. 9TNA REMARK 6 15-JAN-86. 9TNA REMARK 7 REMARK 7 9TNA CORRECTION. UPDATE JRNL REFERENCE TO REFLECT REMARK 7 PUBLICATION. 9TNA 14-JUL-86. 9TNA REMARK 8 REMARK 8 9TNA CORRECTION. INSERT NEW PUBLICATION AS REFERENCE 1 AND REMARK 8 9TNA RENUMBER THE OTHERS. 22-OCT-86. 9TNA REMARK 9 REMARK 9 9TNA CORRECTION. CORRECT TYPOGRAPHICAL ERROR IN REFERENCE REMARK 9 9TNA 1. 16-APR-87. 9TNA REMARK 10 REMARK 10 9TNA CORRECTION. THIS ENTRY IS OBSOLETE. 19-APR-89. 9TNA REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: 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 (%): 61.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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,1/2+Z REMARK 290 3555 -X,Y,1/2-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 1/2+X,1/2+Y,Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-X,1/2+Y,1/2-Z REMARK 290 8555 1/2+X,1/2-Y,-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 0.020930 0.000000 1.000000 74.74959 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 74.74959 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 -0.020930 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.14954 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.99973 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 -0.31551 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.14954 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.99973 REMARK 290 SMTRY3 6 0.020930 0.000000 1.000000 74.43408 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.14954 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.99973 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.43408 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.14954 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.99973 REMARK 290 SMTRY3 8 -0.020930 0.000000 -1.000000 -0.31551 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N7 G 17 O4* C 75 5455 0.94 REMARK 500 O5* G 17 O2 C 75 5455 1.00 REMARK 500 O1P G 17 O4* A 76 5455 1.06 REMARK 500 C8 G 17 C1* C 75 5455 1.22 REMARK 500 O4* C 61 O2P A 76 5455 1.34 REMARK 500 C4* C 61 O2P A 76 5455 1.53 REMARK 500 P G 17 O2 C 75 5455 1.54 REMARK 500 N7 G 17 C1* C 75 5455 1.66 REMARK 500 C8 G 17 O4* C 75 5455 1.70 REMARK 500 O1P G 17 C1* A 76 5455 1.75 REMARK 500 O2P G 17 C2* C 75 5455 1.78 REMARK 500 N7 G 17 C4* C 75 5455 1.81 REMARK 500 C4* H2U 16 N3 A 76 5455 1.89 REMARK 500 P G 17 O4* A 76 5455 2.00 REMARK 500 O3* H2U 16 N9 A 76 5455 2.07 REMARK 500 O2P G 17 C2 C 75 5455 2.07 REMARK 500 O2P G 17 O2 C 75 5455 2.12 REMARK 500 O4* H2U 16 N3 A 76 5455 2.13 REMARK 500 O2P G 17 N1 C 75 5455 2.13 REMARK 500 C5* C 61 O2P A 76 5455 2.18 REMARK 500 O5* G 17 C2 C 75 5455 2.19 SEQRES 1 75 U C C G U G A U A G U U PSU SEQRES 2 75 A A H2U G G H2U C A G A A U G SEQRES 3 75 G G C G C PSU U G U C 1MG C G SEQRES 4 75 U G C C A G A U 5MC G G G G SEQRES 5 75 5MU PSU C A A U U C C C C G U SEQRES 6 75 C G C G G A G C C A MODRES 9TNA PSU 13 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 9TNA H2U 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 9TNA H2U 19 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 9TNA PSU 32 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 9TNA 1MG 37 G 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 9TNA 5MC 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 9TNA 5MU 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 9TNA PSU 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET PSU 13 20 HET H2U 16 20 HET H2U 19 20 HET PSU 32 20 HET 1MG 37 24 HET 5MC 49 21 HET 5MU 54 21 HET PSU 55 20 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM 1MG 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE FORMUL 1 PSU 3(C9 H13 N2 O9 P) FORMUL 1 H2U 2(C9 H15 N2 O9 P) FORMUL 1 1MG C11 H16 N5 O8 P FORMUL 1 5MC C10 H16 N3 O8 P FORMUL 1 5MU C10 H15 N2 O9 P CRYST1 60.300 68.000 149.500 90.00 90.00 90.00 C 2 2 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 0.016584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014706 0.000000 0.00000 SCALE3 0.000070 0.000000 0.006689 0.00000