Header list of 1yg4.pdb file
Complete list - 2 202 Bytes
HEADER RNA 04-JAN-05 1YG4
TITLE SOLUTION STRUCTURE OF THE SCYLV P1-P2 FRAMESHIFTING PSEUDOKNOT,
TITLE 2 REGULARIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SCYLV RNA PSEUDOKNOT;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION
KEYWDS RNA PSEUDOKNOT; RIBOSOMAL FRAMESHIFTING; PROTONATED CYTIDINE, RNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR P.V.CORNISH,M.HENNIG,D.P.GIEDROC
REVDAT 3 02-MAR-22 1YG4 1 REMARK LINK
REVDAT 2 24-FEB-09 1YG4 1 VERSN
REVDAT 1 13-DEC-05 1YG4 0
JRNL AUTH P.V.CORNISH,M.HENNIG,D.P.GIEDROC
JRNL TITL A LOOP 2 CYTIDINE-STEM 1 MINOR GROOVE INTERACTION AS A
JRNL TITL 2 POSITIVE DETERMINANT FOR PSEUDOKNOT-STIMULATED -1 RIBOSOMAL
JRNL TITL 3 FRAMESHIFTING
JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 12694 2005
JRNL REFN ISSN 0027-8424
JRNL PMID 16123125
JRNL DOI 10.1073/PNAS.0506166102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 97.027.12.56, X-PLOR-NIH 2.9.7
REMARK 3 AUTHORS : F. DELAGLIO, S. GRZESIEK, G.W. VUISTER, G. ZHU, J.
REMARK 3 PFEIFER AND A. BAX (NMRPIPE), G.M. CLORE ,
REMARK 3 J.KUSZEWSKI, C.D. SCHWIETERS, AND N.TJANDRA (X-
REMARK 3 PLOR-NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1YG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-05.
REMARK 100 THE DEPOSITION ID IS D_1000031474.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 283; 298; 298
REMARK 210 PH : 6.0; 6.0; 6.0
REMARK 210 IONIC STRENGTH : 100MM KCL; 5MM MGCL2; 100MM KCL;
REMARK 210 5MM MGCL2; 100MM KCL; 5MM MGCL2
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM SCYLV PSEUDOKNOT, 100MM KCL,
REMARK 210 5MM MGCL2, PH6.0; 2MM SCYLV
REMARK 210 PSEUDOKNOT, 100MM KCL, 5MM MGCL2,
REMARK 210 PH6.0; 2MM SCYLV PSEUDOKNOT,
REMARK 210 100MM KCL, 5MM MGCL2, PH6.0,
REMARK 210 12.5MG/ML PF1 PHAGE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; CT-TROSY AND
REMARK 210 CT-ANTITROSY; J-MODULATED HSQC;
REMARK 210 2D TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 900 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SPARKY 3.110, X-PLOR-NIH 2.9.7
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 25
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGED STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
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 4 H62 A A 20 1.11
REMARK 500 H42 CH A 8 O6 G A 12 1.55
REMARK 500 H2' G A 6 O4' G A 7 1.55
REMARK 500 H4' A A 21 OP1 A A 22 1.58
REMARK 500 N2 G A 12 O4' C A 14 2.18
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 G A 6 C2' G A 6 C1' -0.050
REMARK 500 G A 7 N1 G A 7 C2 0.058
REMARK 500 G A 7 C6 G A 7 N1 -0.045
REMARK 500 C A 11 N3 C A 11 C4 -0.048
REMARK 500 G A 12 C5' G A 12 C4' 0.108
REMARK 500 C A 14 C2' C A 14 C1' -0.070
REMARK 500 C A 15 N1 C A 15 C6 0.040
REMARK 500 A A 16 C2' A A 16 C1' -0.078
REMARK 500 A A 16 C6 A A 16 N1 -0.046
REMARK 500 A A 16 N9 A A 16 C4 0.052
REMARK 500 U A 18 C2' U A 18 C1' -0.108
REMARK 500 A A 22 C6 A A 22 N1 -0.044
REMARK 500 C A 28 N1 C A 28 C6 0.063
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 A A 3 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 A A 3 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 G A 4 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES
REMARK 500 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 G A 4 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES
REMARK 500 G A 6 O4' - C1' - N9 ANGL. DEV. = 14.1 DEGREES
REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 G A 6 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES
REMARK 500 G A 6 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 G A 7 P - O5' - C5' ANGL. DEV. = 9.8 DEGREES
REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = 13.3 DEGREES
REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 C A 11 P - O5' - C5' ANGL. DEV. = 14.3 DEGREES
REMARK 500 G A 12 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 G A 12 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES
REMARK 500 G A 12 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 G A 12 C8 - N9 - C4 ANGL. DEV. = -4.4 DEGREES
REMARK 500 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 A A 16 O4' - C1' - N9 ANGL. DEV. = 10.8 DEGREES
REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 A A 16 N9 - C4 - C5 ANGL. DEV. = -3.6 DEGREES
REMARK 500 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 U A 18 C5' - C4' - O4' ANGL. DEV. = 5.9 DEGREES
REMARK 500 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 U A 19 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 A A 20 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES
REMARK 500 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES
REMARK 500 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 A A 21 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 A A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 A A 24 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES
REMARK 500 A A 24 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 A A 24 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 A A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 A A 26 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES
REMARK 500 C A 27 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -5.1 DEGREES
REMARK 500 G A 29 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES
REMARK 500 G A 30 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 G A 30 C8 - N9 - 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 A A 3 0.09 SIDE CHAIN
REMARK 500 G A 4 0.07 SIDE CHAIN
REMARK 500 U A 5 0.07 SIDE CHAIN
REMARK 500 G A 6 0.08 SIDE CHAIN
REMARK 500 G A 7 0.09 SIDE CHAIN
REMARK 500 C A 10 0.09 SIDE CHAIN
REMARK 500 C A 11 0.08 SIDE CHAIN
REMARK 500 G A 12 0.07 SIDE CHAIN
REMARK 500 C A 14 0.09 SIDE CHAIN
REMARK 500 C A 15 0.10 SIDE CHAIN
REMARK 500 A A 16 0.11 SIDE CHAIN
REMARK 500 C A 17 0.09 SIDE CHAIN
REMARK 500 U A 18 0.09 SIDE CHAIN
REMARK 500 A A 23 0.05 SIDE CHAIN
REMARK 500 G A 29 0.08 SIDE CHAIN
REMARK 500 G A 30 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1YG3 RELATED DB: PDB
REMARK 900 THE SAME SEQUENCE, 20 LOWEST ENERGY STRUCTURES
DBREF 1YG4 A 3 30 PDB 1YG4 1YG4 3 30
SEQRES 1 A 28 A G U G G CH G C C G A C C
SEQRES 2 A 28 A C U U A A A A A C A C C
SEQRES 3 A 28 G G
MODRES 1YG4 CH A 8 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
HET CH A 8 32
HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
FORMUL 1 CH C9 H15 N3 O8 P 1+
LINK O3' G A 7 P CH A 8 1555 1555 1.57
LINK O3' CH A 8 P G A 9 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
Complete list - 2 202 Bytes