HEADER RNA 03-MAY-99 1KOS TITLE SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP TITLE 2 CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH) COMPND 3 P*CP*AP*CP*AP*G)- 3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: TPSIC DOMAIN OF TRNA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: C60 IS PROTONATED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE FROM YEAST (SACCHAROMYCES CEREVISIAE) TRNA SOURCE 4 PHE KEYWDS TRNA, T STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, RNA FOLDING, RNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR K.M.KOSHLAP,R.GUENTHER,E.SOCHACKA,A.MALKIEWICZ,P.F.AGRIS REVDAT 5 27-DEC-23 1KOS 1 REMARK REVDAT 4 23-FEB-22 1KOS 1 REMARK LINK REVDAT 3 24-FEB-09 1KOS 1 VERSN REVDAT 2 26-SEP-01 1KOS 3 ATOM REVDAT 1 22-OCT-99 1KOS 0 JRNL AUTH K.M.KOSHLAP,R.GUENTHER,E.SOCHACKA,A.MALKIEWICZ,P.F.AGRIS JRNL TITL A DISTINCTIVE RNA FOLD: THE SOLUTION STRUCTURE OF AN JRNL TITL 2 ANALOGUE OF THE YEAST TRNAPHE T PSI C DOMAIN. JRNL REF BIOCHEMISTRY V. 38 8647 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10393540 JRNL DOI 10.1021/BI990118W REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH U.SCHMITZ,A.DONATI,T.L.JAMES,N.B.ULYANOV,L.YAO REMARK 1 TITL SMALL STRUCTURAL ENSEMBLES FOR A 17-NUCLEOTIDE MIMIC OF THE REMARK 1 TITL 2 TRNA TPSIC-LOOP VIA FITTING DIPOLAR RELAXATION RATES WITH REMARK 1 TITL 3 THE QUADRATIC PROGRAMMING ALGORITHM REMARK 1 REF BIOPOLYMERS V. 46 329 1998 REMARK 1 REFN ISSN 0006-3525 REMARK 1 DOI 10.1002/(SICI)1097-0282(19981015)46:5<329::AID-BIP4>3.3.CO;2 REMARK 1 DOI 2 -K REMARK 1 REFERENCE 2 REMARK 1 AUTH L.J.YAO,T.L.JAMES,J.T.KEALEY,D.V.SANTI,U.SCHMITZ REMARK 1 TITL THE DYNAMIC NMR STRUCTURE OF THE T PSI C-LOOP: IMPLICATIONS REMARK 1 TITL 2 FOR THE SPECIFICITY OF TRNA METHYLATION REMARK 1 REF J.BIOMOL.NMR V. 3 229 1997 REMARK 1 REFN ISSN 0925-2738 REMARK 1 DOI 10.1023/A:1018618606857 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.WESTHOF,M.SUNDARALINGAM REMARK 1 TITL RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST REMARK 1 TITL 2 PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND REMARK 1 TITL 3 DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST REMARK 1 TITL 4 ANGLES REMARK 1 REF BIOCHEMISTRY V. 25 4868 1986 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1KOS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000990. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 100% D2O, 94% WATER/6% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY; HSQC; REMARK 210 HETCOR; HETEROTOCSY; HETEROTOCSY- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: EXPERIMENTS IN 100% D2O CONDUCTED AT 283, 288,293, AND 298 REMARK 210 KELVIN; EXPERIMENTS IN 6% D2O/ 94% H2O CONDUCTED AT 274 AND 283 REMARK 210 KELVIN. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO2' C A 15 O4' A A 16 1.57 REMARK 500 O4 U A 2 H61 A A 16 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 1 C A 1 C2' C A 1 C1' -0.059 REMARK 500 1 G A 3 C2' G A 3 C1' -0.051 REMARK 500 1 G A 3 C8 G A 3 N9 -0.056 REMARK 500 1 G A 5 C2' G A 5 C1' -0.065 REMARK 500 1 G A 5 C8 G A 5 N9 -0.071 REMARK 500 1 C A 13 N1 C A 13 C6 -0.040 REMARK 500 1 G A 17 C8 G A 17 N9 -0.046 REMARK 500 2 C A 1 C2' C A 1 C1' -0.050 REMARK 500 2 G A 3 C2' G A 3 C1' -0.051 REMARK 500 2 G A 3 C8 G A 3 N9 -0.055 REMARK 500 2 G A 5 C2' G A 5 C1' -0.066 REMARK 500 2 G A 5 C8 G A 5 N9 -0.080 REMARK 500 2 C A 8 C3' C A 8 C2' -0.068 REMARK 500 2 C A 15 N1 C A 15 C6 -0.041 REMARK 500 2 G A 17 C8 G A 17 N9 -0.056 REMARK 500 2 G A 17 N9 G A 17 C4 -0.057 REMARK 500 3 C A 1 C2' C A 1 C1' -0.056 REMARK 500 3 G A 3 C2' G A 3 C1' -0.050 REMARK 500 3 G A 3 C8 G A 3 N9 -0.058 REMARK 500 3 G A 5 C2' G A 5 C1' -0.056 REMARK 500 3 G A 5 C8 G A 5 N9 -0.069 REMARK 500 3 G A 17 C8 G A 17 N9 -0.049 REMARK 500 4 C A 1 C2' C A 1 C1' -0.056 REMARK 500 4 G A 3 C2' G A 3 C1' -0.054 REMARK 500 4 G A 3 C8 G A 3 N9 -0.058 REMARK 500 4 G A 5 C2' G A 5 C1' -0.052 REMARK 500 4 G A 5 C8 G A 5 N9 -0.074 REMARK 500 4 G A 17 C8 G A 17 N9 -0.058 REMARK 500 5 C A 1 C2' C A 1 C1' -0.064 REMARK 500 5 G A 3 C2' G A 3 C1' -0.064 REMARK 500 5 G A 3 C8 G A 3 N9 -0.054 REMARK 500 5 G A 5 C2' G A 5 C1' -0.058 REMARK 500 5 G A 5 C8 G A 5 N9 -0.077 REMARK 500 5 C A 15 N1 C A 15 C6 -0.039 REMARK 500 5 G A 17 C8 G A 17 N9 -0.049 REMARK 500 6 C A 1 C2' C A 1 C1' -0.067 REMARK 500 6 G A 3 C8 G A 3 N9 -0.061 REMARK 500 6 G A 5 C2' G A 5 C1' -0.059 REMARK 500 6 G A 5 C8 G A 5 N9 -0.078 REMARK 500 6 G A 17 C8 G A 17 N9 -0.043 REMARK 500 7 C A 1 C2' C A 1 C1' -0.069 REMARK 500 7 G A 3 C2' G A 3 C1' -0.050 REMARK 500 7 G A 3 C8 G A 3 N9 -0.054 REMARK 500 7 G A 5 C8 G A 5 N9 -0.078 REMARK 500 7 C A 8 C3' C A 8 C2' -0.068 REMARK 500 7 C A 13 N1 C A 13 C6 -0.041 REMARK 500 7 C A 15 N1 C A 15 C6 -0.036 REMARK 500 7 G A 17 C8 G A 17 N9 -0.048 REMARK 500 8 C A 1 C2' C A 1 C1' -0.061 REMARK 500 8 G A 3 C8 G A 3 N9 -0.059 REMARK 500 REMARK 500 THIS ENTRY HAS 53 BOND DEVIATIONS. 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 1 C A 1 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 C A 1 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 C A 1 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 C A 1 N1 - C1' - C2' ANGL. DEV. = -10.4 DEGREES REMARK 500 1 C A 1 O4' - C1' - N1 ANGL. DEV. = 14.9 DEGREES REMARK 500 1 C A 1 N3 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C A 1 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 1 G A 3 C3' - C2' - C1' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 G A 3 N9 - C1' - C2' ANGL. DEV. = -12.6 DEGREES REMARK 500 1 G A 3 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 3 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 5 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 G A 5 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 5 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 U A 7 C5' - C4' - O4' ANGL. DEV. = 13.7 DEGREES REMARK 500 1 U A 7 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 C A 8 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 U A 11 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 C A 13 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 C A 13 O4' - C1' - C2' ANGL. DEV. = -11.0 DEGREES REMARK 500 1 A A 14 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 A A 14 C2' - C3' - O3' ANGL. DEV. = 11.9 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 C A 15 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 C A 15 N1 - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 C A 15 N3 - C4 - N4 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 15 C5 - C4 - N4 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 15 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 1 A A 16 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 16 C3' - C2' - C1' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 A A 16 N9 - C1' - C2' ANGL. DEV. = -9.7 DEGREES REMARK 500 1 A A 16 O4' - C1' - N9 ANGL. DEV. = 13.0 DEGREES REMARK 500 1 G A 17 C1' - O4' - C4' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 G A 17 N9 - C1' - C2' ANGL. DEV. = -18.4 DEGREES REMARK 500 1 G A 17 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 C A 1 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C A 1 C2' - C3' - O3' ANGL. DEV. = 10.2 DEGREES REMARK 500 2 C A 1 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 2 C A 1 O4' - C1' - C2' ANGL. DEV. = -9.3 DEGREES REMARK 500 2 C A 1 O4' - C1' - N1 ANGL. DEV. = 11.9 DEGREES REMARK 500 2 U A 2 P - O5' - C5' ANGL. DEV. = 11.3 DEGREES REMARK 500 2 U A 2 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 364 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1KOS A 1 17 PDB 1KOS 1KOS 1 17 SEQRES 1 A 17 C U G U G 5MU U C G A U CH C SEQRES 2 A 17 A C A G MODRES 1KOS 5MU A 6 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1KOS CH A 12 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HET 5MU A 6 33 HET CH A 12 32 HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 1 CH C9 H15 N3 O8 P 1+ LINK O3' G A 5 P 5MU A 6 1555 1555 1.61 LINK O3' 5MU A 6 P U A 7 1555 1555 1.63 LINK O3' U A 11 P CH A 12 1555 1555 1.61 LINK O3' CH A 12 P C A 13 1555 1555 1.62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1