Header list of 1luu.pdb file
Complete list - 23 20 Bytes
HEADER RNA 23-MAY-02 1LUU
TITLE NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4
TITLE 2 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*(1MG)
COMPND 3 P*AP*UP*(5MC)P*UP*GP*G)-3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH FOUR
COMPND 7 MODIFIED RESIDUES (OMC AT POSITION 32, OMG AT 34, 1MG AT 37, AND 5MC
COMPND 8 AT POSITION 40)
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS
SOURCE 4 SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY.
KEYWDS TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 1MG, 2'-O-
KEYWDS 2 METHYL, 5MC, RNA
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR J.W.STUART,K.M.KOSHLAP,R.H.GUENTHER,P.F.AGRIS
REVDAT 4 23-FEB-22 1LUU 1 REMARK LINK
REVDAT 3 24-FEB-09 1LUU 1 VERSN
REVDAT 2 16-DEC-03 1LUU 1 JRNL
REVDAT 1 09-SEP-03 1LUU 0
JRNL AUTH J.W.STUART,K.M.KOSHLAP,R.GUENTHER,P.F.AGRIS
JRNL TITL NATURALLY-OCCURRING MODIFICATION RESTRICTS THE ANTICODON
JRNL TITL 2 DOMAIN CONFORMATIONAL SPACE OF TRNA(PHE).
JRNL REF J.MOL.BIOL. V. 334 901 2003
JRNL REFN ISSN 0022-2836
JRNL PMID 14643656
JRNL DOI 10.1016/J.JMB.2003.09.058
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR, DISCOVER 98
REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 269 RESTRAINTS (256 NOE-DERIVED, 13 H
REMARK 3 -BOND) 96 DIHEDRAL ANGLE.
REMARK 4
REMARK 4 1LUU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-02.
REMARK 100 THE DEPOSITION ID IS D_1000016293.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 5.60
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1.2 MM RNA, 10 MM CACODYLATE
REMARK 210 BUFFER, PH 5.6, 0.1 MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 98
REMARK 210 METHOD USED : GLOBAL FOLD BY DISTANCE
REMARK 210 GEOMETRY. REFINEMENT BY
REMARK 210 SIMULATED ANNEALING USING THE
REMARK 210 AMBER FORCEFIELD
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES
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: 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 5 A A 38 C6 A A 38 N1 0.042
REMARK 500 8 A A 38 N1 A A 38 C2 0.055
REMARK 500 8 A A 38 C6 A A 38 N1 0.043
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 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 A A 36 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES
REMARK 500 1 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.6 DEGREES
REMARK 500 1 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 A A 35 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES
REMARK 500 2 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 A A 36 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.4 DEGREES
REMARK 500 2 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES
REMARK 500 3 A A 35 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES
REMARK 500 3 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.5 DEGREES
REMARK 500 3 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES
REMARK 500 4 U A 33 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 4 A A 35 N9 - C1' - C2' ANGL. DEV. = 10.6 DEGREES
REMARK 500 4 A A 35 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 4 A A 35 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 4 A A 38 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES
REMARK 500 4 A A 38 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 4 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.4 DEGREES
REMARK 500 4 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES
REMARK 500 5 A A 36 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 5 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.4 DEGREES
REMARK 500 5 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES
REMARK 500 6 U A 33 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 6 A A 35 N9 - C1' - C2' ANGL. DEV. = 11.0 DEGREES
REMARK 500 6 A A 35 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 6 A A 35 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 6 A A 38 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES
REMARK 500 6 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.7 DEGREES
REMARK 500 6 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES
REMARK 500 6 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 7 A A 36 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 7 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.5 DEGREES
REMARK 500 7 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES
REMARK 500 8 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 8 A A 36 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 8 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.3 DEGREES
REMARK 500 8 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES
REMARK 500 8 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 9 A A 36 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES
REMARK 500 9 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.4 DEGREES
REMARK 500 9 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES
REMARK 500 10 A A 36 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 10 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.4 DEGREES
REMARK 500 10 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES
REMARK 500 11 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 11 A A 36 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES
REMARK 500 11 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.6 DEGREES
REMARK 500 11 A A 38 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES
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 1 C A 27 0.09 SIDE CHAIN
REMARK 500 1 C A 28 0.07 SIDE CHAIN
REMARK 500 1 A A 29 0.08 SIDE CHAIN
REMARK 500 1 G A 42 0.08 SIDE CHAIN
REMARK 500 2 C A 27 0.09 SIDE CHAIN
REMARK 500 2 C A 28 0.06 SIDE CHAIN
REMARK 500 2 A A 29 0.07 SIDE CHAIN
REMARK 500 2 U A 33 0.06 SIDE CHAIN
REMARK 500 2 A A 35 0.07 SIDE CHAIN
REMARK 500 2 U A 41 0.07 SIDE CHAIN
REMARK 500 2 G A 42 0.07 SIDE CHAIN
REMARK 500 3 C A 27 0.07 SIDE CHAIN
REMARK 500 3 C A 28 0.06 SIDE CHAIN
REMARK 500 3 G A 30 0.07 SIDE CHAIN
REMARK 500 3 U A 33 0.10 SIDE CHAIN
REMARK 500 3 A A 35 0.07 SIDE CHAIN
REMARK 500 3 G A 42 0.07 SIDE CHAIN
REMARK 500 4 C A 27 0.10 SIDE CHAIN
REMARK 500 4 G A 30 0.09 SIDE CHAIN
REMARK 500 4 A A 35 0.09 SIDE CHAIN
REMARK 500 4 G A 42 0.08 SIDE CHAIN
REMARK 500 5 C A 27 0.06 SIDE CHAIN
REMARK 500 5 C A 28 0.10 SIDE CHAIN
REMARK 500 5 A A 29 0.10 SIDE CHAIN
REMARK 500 5 G A 30 0.08 SIDE CHAIN
REMARK 500 5 U A 33 0.06 SIDE CHAIN
REMARK 500 5 U A 41 0.08 SIDE CHAIN
REMARK 500 5 G A 42 0.07 SIDE CHAIN
REMARK 500 6 C A 27 0.08 SIDE CHAIN
REMARK 500 6 C A 28 0.09 SIDE CHAIN
REMARK 500 6 G A 30 0.08 SIDE CHAIN
REMARK 500 6 A A 35 0.09 SIDE CHAIN
REMARK 500 6 G A 42 0.07 SIDE CHAIN
REMARK 500 7 C A 27 0.10 SIDE CHAIN
REMARK 500 7 A A 29 0.06 SIDE CHAIN
REMARK 500 7 G A 42 0.08 SIDE CHAIN
REMARK 500 8 C A 27 0.08 SIDE CHAIN
REMARK 500 8 C A 28 0.11 SIDE CHAIN
REMARK 500 8 A A 29 0.09 SIDE CHAIN
REMARK 500 8 G A 30 0.06 SIDE CHAIN
REMARK 500 8 U A 33 0.06 SIDE CHAIN
REMARK 500 8 A A 38 0.06 SIDE CHAIN
REMARK 500 8 U A 41 0.07 SIDE CHAIN
REMARK 500 8 G A 42 0.08 SIDE CHAIN
REMARK 500 9 C A 27 0.07 SIDE CHAIN
REMARK 500 9 C A 28 0.10 SIDE CHAIN
REMARK 500 9 A A 29 0.06 SIDE CHAIN
REMARK 500 9 G A 30 0.08 SIDE CHAIN
REMARK 500 9 G A 42 0.07 SIDE CHAIN
REMARK 500 10 C A 27 0.09 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 59 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1LUX RELATED DB: PDB
REMARK 900 NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3
REMARK 900 MODIFICATIONS (OMC32 OMG34 M5C40)
DBREF 1LUU A 27 43 PDB 1LUU 1LUU 27 43
SEQRES 1 A 17 C C A G A OMC U OMG A A 1MG A U
SEQRES 2 A 17 5MC U G G
MODRES 1LUU OMC A 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
MODRES 1LUU OMG A 34 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
MODRES 1LUU 1MG A 37 G 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
MODRES 1LUU 5MC A 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
HET OMC A 32 34
HET OMG A 34 37
HET 1MG A 37 37
HET 5MC A 40 34
HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
HETNAM 1MG 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
FORMUL 1 OMC C10 H16 N3 O8 P
FORMUL 1 OMG C11 H16 N5 O8 P
FORMUL 1 1MG C11 H16 N5 O8 P
FORMUL 1 5MC C10 H16 N3 O8 P
LINK O3' A A 31 P OMC A 32 1555 1555 1.61
LINK O3' OMC A 32 P U A 33 1555 1555 1.61
LINK O3' U A 33 P OMG A 34 1555 1555 1.62
LINK O3' OMG A 34 P A A 35 1555 1555 1.61
LINK O3' A A 36 P 1MG A 37 1555 1555 1.61
LINK O3' 1MG A 37 P A A 38 1555 1555 1.62
LINK O3' U A 39 P 5MC A 40 1555 1555 1.62
LINK O3' 5MC A 40 P U A 41 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
Complete list - 23 20 Bytes