Header list of 1ymo.pdb file
Complete list - r 2 2 Bytes
HEADER RNA 21-JAN-05 1YMO
TITLE SOLUTION STRUCTURE OF THE P2B-P3 PSEUDOKNOT FROM HUMAN TELOMERASE RNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TELOMERASE RNA P2B-P3 PSEUDOKNOT;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: P2B-P3 PSEUDOKNOT;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: A UNIMOLECULAR PSEUDOKNOT CONSTRUCT COMPOSED OF
COMPND 8 NUCLEOTIDES 95-119 AND 166-183 WITH A U177 DELETION (MATURE HTR RNA
COMPND 9 NUMBERING SYSTEM)
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA IS SYNTHESIZED USING IN VITRO TRANSCRIPTION WITH
SOURCE 4 T7 RNA POLYMERASE AND A PARTIALLY DOUBLE-STRANDED DNA TEMPLATE. THE
SOURCE 5 SEQUENCE OF THIS RNA CAN BE FOUND NATURALLY IN HOMO SAPIENS (HUMAN).
KEYWDS PSEUDOKNOT, NON-CANONICAL, TERTIARY STRUCTURE, HOOGSTEEN, TRIPLEX,
KEYWDS 2 RNA
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR C.A.THEIMER,C.A.BLOIS,J.FEIGON
REVDAT 3 02-MAR-22 1YMO 1 REMARK
REVDAT 2 24-FEB-09 1YMO 1 VERSN
REVDAT 1 15-MAR-05 1YMO 0
JRNL AUTH C.A.THEIMER,C.A.BLOIS,J.FEIGON
JRNL TITL STRUCTURE OF THE HUMAN TELOMERASE RNA PSEUDOKNOT REVEALS
JRNL TITL 2 CONSERVED TERTIARY INTERACTIONS ESSENTIAL FOR FUNCTION
JRNL REF MOL.CELL V. 17 671 2005
JRNL REFN ISSN 1097-2765
JRNL PMID 15749017
JRNL DOI 10.1016/J.MOLCEL.2005.01.017
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.A.THEIMER,L.D.FINGER,L.TRANTIREK,J.FEIGON
REMARK 1 TITL MUTATIONS LINKED TO DYSKERATOSIS CONGENITA CAUSE CHANGES IN
REMARK 1 TITL 2 THE STRUCTURAL EQUILIBRIUM IN TELOMERASE RNA
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 449 2003
REMARK 1 REFN ISSN 0027-8424
REMARK 1 REFERENCE 2
REMARK 1 AUTH C.A.THEIMER,L.D.FINGER,J.FEIGON
REMARK 1 TITL YNMG TETRALOOP FORMATION BY A DYSKERATOSIS CONGENITA
REMARK 1 TITL 2 MUTATION IN HUMAN TELOMERASE RNA
REMARK 1 REF RNA V. 9 1446 2003
REMARK 1 REFN ISSN 1355-8382
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, XPLOR-NIH 1.0.6
REMARK 3 AUTHORS : BRUKER (XWINNMR), NIH (XPLOR-NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 790 NOE-DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 210 DIHEDRAL ANGLE RESTRAINTS, 50 DISTANCE
REMARK 3 RESTRAINTS FROM HYDROGEN BONDS, AND 20 H-C RESIDUAL DIPOLAR
REMARK 3 COUPLINGS. PDB ENTRY PDB ENTRY 2K96 IS A BETTER REFINED
REMARK 3 STRUCTURE OF ENTRY 1YMO.
REMARK 4
REMARK 4 1YMO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000031691.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 283; 293
REMARK 210 PH : 6.3; 6.3
REMARK 210 IONIC STRENGTH : 200 MM KCL; 200 MM KCL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : ~0.8 MM UNLABELED RNA, 10 MM
REMARK 210 SODIUM PHOSPHATE BUFFER, PH 6.3,
REMARK 210 200 MM KCL, 50 UM EDTA, 0.2%
REMARK 210 SODIUM AZIDE, 95% H2O,5% D2O OR
REMARK 210 100% D2O; ~0.8 MM 13C,15N-FULLY
REMARK 210 LABELED RNA, 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER, PH 6.3, 200 MM
REMARK 210 KCL, 50 UM EDTA, 0.2% SODIUM
REMARK 210 AZIDE, 95% H2O,5% D2O OR 100%
REMARK 210 D2O; ~0.8 MM 13C,15N-A LABELED
REMARK 210 RNA, 10 MM SODIUM PHOSPHATE
REMARK 210 BUFFER, PH 6.3, 200 MM KCL, 50
REMARK 210 UM EDTA, 0.2% SODIUM AZIDE , 95%
REMARK 210 H2O,5% D2O OR 100% D2O; ~0.8 MM
REMARK 210 13C,15N-C LABELED RNA, 10 MM
REMARK 210 SODIUM PHOSPHATE BUFFER, PH 6.3,
REMARK 210 200 MM KCL, 50 UM EDTA, 0.2%
REMARK 210 SODIUM AZIDE, 95% H2O,5% D2O OR
REMARK 210 100% D2O; ~0.8 MM 13C,15N-G
REMARK 210 LABELED RNA, 10 MM SODIUM
REMARK 210 PHOSPHATE BUFFER, PH 6.3, 200 MM
REMARK 210 KCL, 50 UM EDTA, 0.2% SODIUM
REMARK 210 AZIDE, 95% H2O,5% D2O OR 100%
REMARK 210 D2O; ~0.8 MM 13C,15N-U LABELED
REMARK 210 RNA, 10 MM SODIUM PHOSPHATE
REMARK 210 BUFFER, PH 6.3, 200 MM KCL, 50
REMARK 210 UM EDTA, 0.2% SODIUM AZIDE, 95%
REMARK 210 H2O,5% D2O OR 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY (11ECHO AND WATERGATE);
REMARK 210 2D NOESY, 2D TOCSY (PRESAT); 2D
REMARK 210 15N-HMQC,2D 15N-CPMG-NOESY, 2D
REMARK 210 JNN-HNN-COSY; 2D 13C-HSQC; 2D
REMARK 210 13C-HSQC, 2D HCCH COSY, 3D HCCH-
REMARK 210 TOCSY, 2D 13C FILTERED/EDITED
REMARK 210 NOESYS
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.6, AURELIA 3.108,
REMARK 210 XPLOR-NIH 1.0.6
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY, NO RESTRAINT VIOLATIONS,
REMARK 210 CONSISTENT WITH RESIDUAL DIPOLAR
REMARK 210 COUPLINGS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE SAME EXPERIMENTS WERE PERFORMED ON ALL OF THE SINGLY
REMARK 210 -LABELED SAMPLES EXCEPT FOR RESIDUAL DIPOLAR COUPLINGS WHICH
REMARK 210 WERE ONLY COLLECTED FOR THE A- AND G-ONLY LABELED SAMPLES.
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 O4 U A 13 H42 C A 46 1.42
REMARK 500 O2 U A 5 H62 A A 35 1.43
REMARK 500 O2' A A 35 H8 A A 36 1.47
REMARK 500 HO2' A A 31 O4' A A 32 1.48
REMARK 500 H5'' G A 6 OP1 U A 7 1.57
REMARK 500 O2' C A 27 H6 C A 28 1.58
REMARK 500 O2' G A 2 H8 G A 3 1.58
REMARK 500 O2' A A 39 H8 A A 40 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 33 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 36 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 A A 37 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 38 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 39 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 A A 40 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 G A 41 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 41 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 A A 44 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 G A 45 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 G A 45 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 A A 47 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 A A 33 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 623 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1NA2 RELATED DB: NDB
REMARK 900 SOLUTION STRUCTURE OF THE WILDTYPE P2B HAIRPIN FROM HUMAN
REMARK 900 TELOMERASE RNA
REMARK 900 RELATED ID: 1Q75 RELATED DB: NDB
REMARK 900 SOLUTION STRUCTURE OF THE DYSKERATOSIS CONGENITA MUTANT P2B HAIRPIN
REMARK 900 FROM HUMAN TELOMERASE RNA
REMARK 900 RELATED ID: 2K96 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF P2B-P3 PSEUDOKNOT MUTANT OF HUMAN TELOMERASE
REMARK 900 RNA
DBREF 1YMO A 1 47 PDB 1YMO 1YMO 1 47
SEQRES 1 A 47 G G G C U G U U U U U C U
SEQRES 2 A 47 C G C U G A C U U U C A G
SEQRES 3 A 47 C C C C A A A C A A A A A
SEQRES 4 A 47 A G U C A G C A
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