Header list of 1t28.pdb file
Complete list - 2 20 Bytes
HEADER RNA 20-APR-04 1T28
TITLE HIGH RESOLUTION STRUCTURE OF A PICORNAVIRAL INTERNAL CIS-ACTING
TITLE 2 REPLICATION ELEMENT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 34-MER;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CRE OF THE HUMAN RHINOVIRUS TYPE 14;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: MINIMAL FUNCTIONAL SEQUENCE OF HRV-14 CRE
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THE RNA SEQUENCE WAS SYNTHESIZED USING T7 SYSTEM. THE
SOURCE 4 SEQUENCE OCCURS IN HUMAN RHINOVIRUS TYPE 14.
KEYWDS CRE, PICORNAVIRUS, RHINO VIRUS, STEM LOOP, RNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR V.THIVIYANATHAN,Y.YANG,K.KALUARACHCHI,R.REYNBRAND,D.G.GORENSTEIN,
AUTHOR 2 S.M.LEMON
REVDAT 4 02-MAR-22 1T28 1 REMARK
REVDAT 3 24-FEB-09 1T28 1 VERSN
REVDAT 2 07-SEP-04 1T28 1 JRNL
REVDAT 1 10-AUG-04 1T28 0
JRNL AUTH V.THIVIYANATHAN,Y.YANG,K.KALUARACHCHI,R.REYNBRAND,
JRNL AUTH 2 D.G.GORENSTEIN,S.M.LEMON
JRNL TITL HIGH RESOLUTION STRUCTURE OF A PICORNAVIRAL INTERNAL
JRNL TITL 2 CIS-ACTING REPLICATION ELEMENT(CRE).
JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 12688 2004
JRNL REFN ISSN 0027-8424
JRNL PMID 15314212
JRNL DOI 10.1073/PNAS.0403079101
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 2000, X-PLOR 3.1
REMARK 3 AUTHORS : MSI (FELIX), BRUNGER, A.T., ET AL., (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1T28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-04.
REMARK 100 THE DEPOSITION ID IS D_1000022219.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298
REMARK 210 PH : 6.8; 6.8; 6.8; 6.8
REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT;
REMARK 210 AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.4 MM RNA U-15N,13C, 10 MM
REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 MM
REMARK 210 KCL, 0.02 MM EDTA, 90% H2O, 10%
REMARK 210 D2O; 1.8 MM RNA, 8-10 MM
REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 MM
REMARK 210 KCL, 0.02 MM EDTA, 90% H2O, 10%
REMARK 210 D2O; 1.8 MM RNA, 8-10 MM
REMARK 210 PHOSPHATE BUFFER (PH 6.8), 10 MM
REMARK 210 KCL, 0.4-4 MM MG2+, 90% H2O, 10%
REMARK 210 D2O; 0.8 MM RNA, 15N,13C (ONLY
REMARK 210 THE A RESIDUES), 10 MM PHOSPHATE
REMARK 210 BUFFER (PH 6.8), 10 MM KCL, 0.02
REMARK 210 MM EDTA, 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; 15N, AND 13C
REMARK 210 HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR
REMARK 210 DYNAMICS, SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 18
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 8 HO2' U A 9 0.64
REMARK 500 HO2' G A 1 H5' G A 2 0.78
REMARK 500 HO2' G A 8 O2' U A 9 1.08
REMARK 500 HO2' C A 7 H5' G A 8 1.14
REMARK 500 HO2' A A 26 H5' C A 27 1.16
REMARK 500 HO2' G A 29 O5' U A 30 1.30
REMARK 500 O2' A A 26 H5' C A 27 1.30
REMARK 500 HO2' U A 30 H5' G A 31 1.32
REMARK 500 HO2' C A 4 O5' A A 5 1.33
REMARK 500 HO2' G A 25 H5' A A 26 1.33
REMARK 500 HO2' G A 32 O2' C A 33 1.34
REMARK 500 HO2' U A 30 O5' G A 31 1.34
REMARK 500 HO2' A A 26 C5' C A 27 1.41
REMARK 500 HO2' A A 5 O5' U A 6 1.41
REMARK 500 HO2' A A 26 O5' C A 27 1.42
REMARK 500 HO2' G A 32 O4' C A 33 1.47
REMARK 500 HO2' G A 8 O4' U A 9 1.49
REMARK 500 O2' G A 8 HO2' U A 9 1.50
REMARK 500 O2' G A 1 H5' G A 2 1.52
REMARK 500 HO2' U A 30 C5' G A 31 1.56
REMARK 500 O2' G A 1 O4' G A 2 1.58
REMARK 500 HO2' C A 4 C5' A A 5 1.60
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 G A 1 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 U A 9 C4' - C3' - O3' ANGL. DEV. = -18.3 DEGREES
REMARK 500 U A 9 C4' - C3' - C2' ANGL. DEV. = -68.5 DEGREES
REMARK 500 U A 9 C3' - C2' - C1' ANGL. DEV. = 9.0 DEGREES
REMARK 500 U A 9 O4' - C1' - C2' ANGL. DEV. = -66.9 DEGREES
REMARK 500 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 A A 12 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 A A 14 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 A A 15 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 A A 17 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 A A 20 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 A A 21 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 A A 22 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 C A 23 C2' - C3' - O3' ANGL. DEV. = -17.3 DEGREES
REMARK 500 A A 24 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 G A 25 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 G A 25 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 A A 26 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 G A 28 C4' - C3' - C2' ANGL. DEV. = -13.3 DEGREES
REMARK 500 G A 28 C3' - C2' - C1' ANGL. DEV. = 7.5 DEGREES
REMARK 500 G A 28 O4' - C1' - C2' ANGL. DEV. = -12.5 DEGREES
REMARK 500 G A 28 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 G A 28 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 G A 31 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 G A 32 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 C A 33 C4' - C3' - O3' ANGL. DEV. = -19.2 DEGREES
REMARK 500 C A 33 C4' - C3' - C2' ANGL. DEV. = -71.5 DEGREES
REMARK 500 C A 33 C3' - C2' - C1' ANGL. DEV. = 10.9 DEGREES
REMARK 500 C A 33 O4' - C1' - C2' ANGL. DEV. = -64.5 DEGREES
REMARK 500 C A 33 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES
REMARK 500 C A 33 O4' - C1' - N1 ANGL. DEV. = -8.1 DEGREES
REMARK 500 C A 34 C3' - C2' - C1' ANGL. DEV. = 6.3 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 G A 25 0.05 SIDE CHAIN
REMARK 500 G A 29 0.05 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6115 RELATED DB: BMRB
REMARK 900 CHEMICAL SHIFTS
DBREF 1T28 A 1 34 PDB 1T28 1T28 1 34
SEQRES 1 A 34 G G U C A U C G U U G A G
SEQRES 2 A 34 A A A A C G A A A C A G A
SEQRES 3 A 34 C G G U G G 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
Complete list - 2 20 Bytes