Header list of 1yne.pdb file
Complete list - r 2 2 Bytes
HEADER RNA 24-JAN-05 1YNE
TITLE NMR STRUCTURE OF THE APOB MRNA STEM-LOOP AND ITS INTERACTION WITH THE
TITLE 2 C TO U EDITING APOBEC1 COMPLEMENTARY FACTOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: APOLIPOPROTEIN B MRNA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: EDITING SITE OF APOB ENZYME;
COMPND 5 SYNONYM: APOB MRNA;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: IN VITRO T7 POLYMERASE TRANSCRIPTION. THE SEQUENCE OF
SOURCE 4 THIS RNA NATURALLY EXISTS IN HOMO SAPIENS (HUMAN).
KEYWDS RNA EDITING; APOB MRNA; APOBEC1; ACF; NMR STRUCTURE, RNA
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.MARIS,J.MASSE,F.H.ALLAIN,A.CHESTER,N.NAVARATNAM
REVDAT 4 02-MAR-22 1YNE 1 REMARK
REVDAT 3 24-FEB-09 1YNE 1 VERSN
REVDAT 2 24-MAY-05 1YNE 1 DBREF
REVDAT 1 08-FEB-05 1YNE 0
JRNL AUTH C.MARIS,J.MASSE,A.CHESTER,N.NAVARATNAM,F.H.ALLAIN
JRNL TITL NMR STRUCTURE OF THE APOB MRNA STEM-LOOP AND ITS INTERACTION
JRNL TITL 2 WITH THE C TO U EDITING APOBEC1 COMPLEMENTARY FACTOR.
JRNL REF RNA V. 11 173 2005
JRNL REFN ISSN 1355-8382
JRNL PMID 15659357
JRNL DOI 10.1261/RNA.7190705
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.0, AMBER 7
REMARK 3 AUTHORS : GUENTERT, P. (CYANA), PONDER, J.W. AND CASE, D.A.
REMARK 3 (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: CALCULATION IN VACUUM CONDITION
REMARK 4
REMARK 4 1YNE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000031714.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 313; 278
REMARK 210 PH : 5.8; 5.8
REMARK 210 IONIC STRENGTH : 10 MM NA2HPO4; 10 MM NA2HPO4
REMARK 210 PRESSURE : 1 ATM; 1 ATM
REMARK 210 SAMPLE CONTENTS : 2 MM EDITED APOB RNA SL31;10 MM
REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8;
REMARK 210 NATURAL ABUNDANCE LABELING; 90%
REMARK 210 H2O, 10% D2O AND ONLY 99.98% D2O;
REMARK 210 1.5 MM EDITED APOB RNA SL31; 10
REMARK 210 MM NAH2HPO4 ADJUSTED AT PH 5.8;
REMARK 210 FULL 15N&C13 LABELING; 90% H2O,
REMARK 210 10% D2O AND ONLY 99.98% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C
REMARK 210 -SEPARATED_NOESY; DQF-COSY; HNN-
REMARK 210 COSY; HCCH-TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 900 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2004, SPARKY 2002, X
REMARK 210 -EASY 2001
REMARK 210 METHOD USED : CYANA & AMBER7
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM,
REMARK 210 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 : 18
REMARK 210
REMARK 210 REMARK: NULL
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' G A 19 O5' A A 20 1.54
REMARK 500 HO2' U A 13 O5' A A 14 1.58
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 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 U A 18 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES
REMARK 500 1 U A 18 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 A A 10 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES
REMARK 500 2 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 3 U A 11 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES
REMARK 500 3 A A 12 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES
REMARK 500 3 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 3 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 4 A A 10 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES
REMARK 500 4 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 4 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 4 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 4 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 4 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 G A 24 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES
REMARK 500 4 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 4 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 4 U A 29 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 6 A A 26 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES
REMARK 500 7 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 7 G A 2 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 7 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 7 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 7 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 7 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 7 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 7 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 7 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 7 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 7 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 7 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES
REMARK 500 7 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 7 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 7 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 7 A A 14 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES
REMARK 500 7 A A 14 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 7 A A 14 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES
REMARK 500 7 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES
REMARK 500 7 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 281 ANGLE DEVIATIONS.
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 U A 18 0.07 SIDE CHAIN
REMARK 500 1 A A 23 0.07 SIDE CHAIN
REMARK 500 2 A A 23 0.06 SIDE CHAIN
REMARK 500 7 U A 25 0.08 SIDE CHAIN
REMARK 500 18 G A 19 0.08 SIDE CHAIN
REMARK 500 18 A A 26 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YLG RELATED DB: PDB
REMARK 900 UNEDITED APOB MRNA STRUCTURE (G19 ANTI CONFORMATION)
REMARK 900 RELATED ID: 1YNC RELATED DB: PDB
REMARK 900 UNEDITED APOB MRNA STRUCTURE (G19 SYN CONFORMATION)
REMARK 900 RELATED ID: 1YNG RELATED DB: PDB
REMARK 900 EDITED APOB MRNA STRUCTURE (G19 SYN CONFORMATION)
REMARK 999
REMARK 999 SEQUENCE THIS ENTRY 1YNE HAS EDITED RNA WITH U6666 IN ANTI
REMARK 999 CONFORMATION. THE EDITED APOB MRNA SEQUENCE LEADING TO THE
REMARK 999 TRUNCATED PROTEIN HAS THE SAME ACCESSION NUMBER SINCE IT COMES
REMARK 999 FROM THE SAME GENE. THE NUMBERING STARTS AT 6656 ON THE APOB
REMARK 999 MRNA SEQUENCE BUT FOR EXPERIMENTAL REASON THE FIRST AND LAST TWO
REMARK 999 NUCLEOTIDES GG AND CC WERE ADDED, WHICH DO NOT BELONG TO THE
REMARK 999 NATIVE SEQUENCE, THE NUMBER STARTS AT 6654.
DBREF 1YNE A 3 29 GB 4502152 NM_000384 6656 6682
SEQADV 1YNE G A 1 GB 4502152 SEE REMARK 999
SEQADV 1YNE G A 2 GB 4502152 SEE REMARK 999
SEQADV 1YNE U A 13 GB 4502152 C 6666 SEE REMARK 999
SEQADV 1YNE C A 30 GB 4502152 SEE REMARK 999
SEQADV 1YNE C A 31 GB 4502152 SEE REMARK 999
SEQRES 1 A 31 G G A U A U A U G A U A U
SEQRES 2 A 31 A A U U U G A U C A G U A
SEQRES 3 A 31 U A U C C
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 - r 2 2 Bytes