Header list of 1esy.pdb file
Complete list - r 25 2 Bytes
HEADER RNA 11-APR-00 1ESY
TITLE NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL
TITLE 2 REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM
CAVEAT 1ESY CHIRALITY ERRORS AT C4' CENTERS OF RESIDUES 12 OF MODEL 4,
CAVEAT 2 1ESY 14 OF MODEL 5, 14 OF MODEL 12, 12 OF MODEL 13, 7 OF MODEL
CAVEAT 3 1ESY 14, 7 OF MODEL 16, 7 OF MODEL 19, AND 14 OF MODEL 19
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA (5'-
COMPND 3 R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3');
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: STEM LOOP 2 OF THE PSI RNA PACKAGING SIGNAL IN HIV-1
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: T7 TRANSCRIPT
KEYWDS HIV-1, RNA, SPLICE-DONOR SITE, PLATFORM MOTIF
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR G.K.AMARASINGHE,R.N.DE GUZMAN,R.B.TURNER,M.F.SUMMERS
REVDAT 3 29-DEC-10 1ESY 1 ATOM
REVDAT 2 24-FEB-09 1ESY 1 VERSN
REVDAT 1 31-MAY-00 1ESY 0
JRNL AUTH G.K.AMARASINGHE,R.N.DE GUZMAN,R.B.TURNER,M.F.SUMMERS
JRNL TITL NMR STRUCTURE OF STEM-LOOP SL2 OF THE HIV-1 PSI RNA
JRNL TITL 2 PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM.
JRNL REF J.MOL.BIOL. V. 299 145 2000
JRNL REFN ISSN 0022-2836
JRNL PMID 10860728
JRNL DOI 10.1006/JMBI.2000.3710
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
REMARK 3 AUTHORS : BRUNGER ET AL.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1ESY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-00.
REMARK 100 THE RCSB ID CODE IS RCSB010866.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 5.5
REMARK 210 IONIC STRENGTH : 25 MM NACL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.6-1.2 MM SL2 RNA, NATURAL
REMARK 210 ABUNDANCE, 25 MM NA-D3-ACETATE
REMARK 210 BUFFER; 0.6-1.2 MM SL2 RNA,
REMARK 210 NATURAL ABUNDANCE, 25 MM NA-D3-
REMARK 210 ACETATE BUFFER; 0.6-1.2 MM SL2
REMARK 210 RNA, U-15N,13C; 25 MM NA-D3-
REMARK 210 ACETATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 3D_13C-
REMARK 210 SEPARATED_NOESY; 3D_13C-
REMARK 210 SEPARATED_ROESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : DMX; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE 1.0,
REMARK 210 NMRVIEW 3.0, DYANA 1.5
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING, ENERGY MIMIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: EXPERIMENTAL TEMPERATURE SET TO EITHER 298 OR 278
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 H1 G A 4 N3 C A 16 1.88
REMARK 500 N3 C A 3 H1 G A 17 1.88
REMARK 500 H1 G A 2 N3 C A 18 1.89
REMARK 500 N3 C A 6 H1 G A 13 1.89
REMARK 500 O4 U A 7 H61 A A 12 1.89
REMARK 500 H41 C A 6 O6 G A 13 1.89
REMARK 500 H1 G A 1 N3 C A 19 1.89
REMARK 500 O2 C A 6 H21 G A 13 1.89
REMARK 500 H21 G A 1 O2 C A 19 1.90
REMARK 500 O6 G A 2 H41 C A 18 1.90
REMARK 500 N1 A A 5 H61 A A 15 1.90
REMARK 500 O2 C A 3 H21 G A 17 1.90
REMARK 500 O6 G A 1 H41 C A 19 1.90
REMARK 500 H41 C A 3 O6 G A 17 1.90
REMARK 500 H21 G A 4 O2 C A 16 1.90
REMARK 500 O6 G A 4 H41 C A 16 1.90
REMARK 500 H21 G A 2 O2 C A 18 1.91
REMARK 500 O2 U A 14 H62 A A 15 1.91
REMARK 500 HO2' U A 7 O4' G A 8 2.00
REMARK 500 H3 U A 7 N1 A A 12 2.00
REMARK 500 O2' U A 14 H42 C A 16 2.00
REMARK 500 HO2' C A 18 O4' C A 19 2.07
REMARK 500 H61 A A 5 O2 U A 14 2.16
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 1 G A 1 O4' G A 1 C4' -0.253
REMARK 500 1 G A 2 O4' G A 2 C4' -0.140
REMARK 500 1 C A 3 O4' C A 3 C4' -0.122
REMARK 500 1 G A 4 O4' G A 4 C4' -0.208
REMARK 500 1 U A 7 O4' U A 7 C4' -0.188
REMARK 500 1 G A 13 O4' G A 13 C4' -0.220
REMARK 500 1 U A 14 O4' U A 14 C4' -0.237
REMARK 500 1 C A 16 O4' C A 16 C4' -0.230
REMARK 500 1 G A 17 O4' G A 17 C4' -0.259
REMARK 500 2 G A 1 O4' G A 1 C4' -0.257
REMARK 500 2 G A 2 O4' G A 2 C4' -0.083
REMARK 500 2 G A 4 O4' G A 4 C4' -0.255
REMARK 500 2 U A 7 O4' U A 7 C4' -0.158
REMARK 500 2 G A 13 O4' G A 13 C4' -0.260
REMARK 500 2 A A 15 O4' A A 15 C4' -0.114
REMARK 500 2 C A 16 O4' C A 16 C4' -0.248
REMARK 500 2 G A 17 O4' G A 17 C4' -0.255
REMARK 500 3 G A 1 O4' G A 1 C4' -0.247
REMARK 500 3 G A 2 O4' G A 2 C4' -0.176
REMARK 500 3 G A 4 O4' G A 4 C4' -0.266
REMARK 500 3 U A 7 O4' U A 7 C4' -0.140
REMARK 500 3 G A 13 O4' G A 13 C4' -0.143
REMARK 500 3 U A 14 O4' U A 14 C4' -0.115
REMARK 500 3 A A 15 O4' A A 15 C4' -0.153
REMARK 500 3 C A 16 O4' C A 16 C4' -0.178
REMARK 500 3 G A 17 O4' G A 17 C4' -0.251
REMARK 500 4 G A 1 O4' G A 1 C4' -0.266
REMARK 500 4 C A 3 O4' C A 3 C4' -0.133
REMARK 500 4 G A 4 O4' G A 4 C4' -0.186
REMARK 500 4 G A 13 O4' G A 13 C4' -0.128
REMARK 500 4 U A 14 O4' U A 14 C4' -0.209
REMARK 500 4 A A 15 O4' A A 15 C4' -0.098
REMARK 500 4 C A 16 O4' C A 16 C4' -0.260
REMARK 500 4 G A 17 O4' G A 17 C4' -0.190
REMARK 500 5 G A 1 O4' G A 1 C4' -0.270
REMARK 500 5 C A 3 O4' C A 3 C4' -0.085
REMARK 500 5 G A 4 O4' G A 4 C4' -0.264
REMARK 500 5 C A 6 O4' C A 6 C4' -0.110
REMARK 500 5 U A 7 O4' U A 7 C4' -0.117
REMARK 500 5 G A 13 O4' G A 13 C4' -0.151
REMARK 500 5 A A 15 O4' A A 15 C4' -0.130
REMARK 500 5 C A 16 O4' C A 16 C4' -0.239
REMARK 500 5 G A 17 O4' G A 17 C4' -0.250
REMARK 500 6 G A 1 O4' G A 1 C4' -0.271
REMARK 500 6 C A 3 O4' C A 3 C4' -0.098
REMARK 500 6 G A 4 O4' G A 4 C4' -0.235
REMARK 500 6 G A 13 O4' G A 13 C4' -0.201
REMARK 500 6 U A 14 O4' U A 14 C4' -0.253
REMARK 500 6 A A 15 O4' A A 15 C4' -0.118
REMARK 500 6 C A 16 O4' C A 16 C4' -0.241
REMARK 500
REMARK 500 THIS ENTRY HAS 178 BOND DEVIATIONS.
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 C5' - C4' - O4' ANGL. DEV. = 22.8 DEGREES
REMARK 500 1 G A 1 C1' - O4' - C4' ANGL. DEV. = 10.4 DEGREES
REMARK 500 1 G A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 G A 2 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES
REMARK 500 1 G A 2 C1' - O4' - C4' ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 G A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 C A 3 O4' - C4' - C3' ANGL. DEV. = -8.4 DEGREES
REMARK 500 1 G A 4 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 1 G A 4 C6 - N1 - C2 ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 G A 4 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 4 C5 - C6 - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 A A 5 O4' - C4' - C3' ANGL. DEV. = -11.4 DEGREES
REMARK 500 1 C A 6 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES
REMARK 500 1 C A 6 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 U A 7 C5' - C4' - O4' ANGL. DEV. = -11.7 DEGREES
REMARK 500 1 U A 7 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 G A 8 O4' - C4' - C3' ANGL. DEV. = -10.4 DEGREES
REMARK 500 1 G A 8 C5' - C4' - O4' ANGL. DEV. = 28.6 DEGREES
REMARK 500 1 G A 8 C1' - O4' - C4' ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 G A 8 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 8 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 8 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 G A 9 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 G A 9 C5' - C4' - O4' ANGL. DEV. = 38.3 DEGREES
REMARK 500 1 G A 9 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 G A 9 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 9 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 9 C5 - C6 - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 U A 10 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 U A 10 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 G A 11 O4' - C4' - C3' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 G A 11 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 G A 11 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 11 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 11 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 A A 12 C5' - C4' - O4' ANGL. DEV. = 30.8 DEGREES
REMARK 500 1 G A 13 C5' - C4' - O4' ANGL. DEV. = 22.8 DEGREES
REMARK 500 1 G A 13 C1' - O4' - C4' ANGL. DEV. = 8.8 DEGREES
REMARK 500 1 G A 13 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES
REMARK 500 1 G A 13 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 13 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 U A 14 C5' - C4' - O4' ANGL. DEV. = 30.4 DEGREES
REMARK 500 1 U A 14 C1' - O4' - C4' ANGL. DEV. = 8.9 DEGREES
REMARK 500 1 C A 16 C5' - C4' - O4' ANGL. DEV. = 35.3 DEGREES
REMARK 500 1 C A 16 C1' - O4' - C4' ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 G A 17 C5' - C4' - O4' ANGL. DEV. = 22.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 1252 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1BN0 RELATED DB: PDB
DBREF 1ESY A 1 19 PDB 1ESY 1ESY 1 19
SEQRES 1 A 19 G G C G A C U G G U G A G
SEQRES 2 A 19 U A C 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
MODEL 1
Complete list - r 25 2 Bytes