Header list of 1d0u.pdb file
Complete list - b 16 2 Bytes
HEADER RNA 14-SEP-99 1D0U TITLE SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE MS2 RNA BINDING SITE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MS2 REPLICASE OPERATOR HAIRPIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRANSCRIPTION BY T7 RNA PLOYMERASE KEYWDS RNA HAIRPIN, BULGED BASE, STEM-LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 23 MDLTYP MINIMIZED AVERAGE AUTHOR J.S.SMITH,E.P.NIKONOWICZ REVDAT 3 16-FEB-22 1D0U 1 REMARK REVDAT 2 24-FEB-09 1D0U 1 VERSN REVDAT 1 24-MAY-00 1D0U 0 JRNL AUTH J.S.SMITH,E.P.NIKONOWICZ JRNL TITL PHOSPHOROTHIOATE SUBSTITUTION CAN SUBSTANTIALLY ALTER RNA JRNL TITL 2 CONFORMATION. JRNL REF BIOCHEMISTRY V. 39 5642 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10801314 JRNL DOI 10.1021/BI992712B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 1994, X-PLOR 3.851 REMARK 3 AUTHORS : SPECTRASPIN (UXNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING 469 REMARK 3 CONFORMATIONALLY RESTRICTIVE NOE DISTANCE CONSTRAINTS (I.E., REMARK 3 INTRA-RESIDUE SUGAR-SUGAR NOES ARE NOT INCLUDED), 20 H-BOND BASE REMARK 3 PAIR CONSTRAINTS, 30 BACKBONE DIHEDRAL RESTRAINTS, AND DIHEDRAL REMARK 3 RESTRAINTS TO RESTRICT SUGAR PUCKER CONFORMATION. REMARK 4 REMARK 4 1D0U COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009693. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : ~50 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.2 MM REPLICASE OPERATOR RNA U REMARK 210 -15N,13C; 10 MM KPI BUFFER; 10 REMARK 210 MM NACL; 0.2 MM EDTA; 2.2 MM REMARK 210 REPLICASE OPERATOR RNA U-15N,13C; REMARK 210 10 MM KPI BUFFER; 10 MM NACL; REMARK 210 0.2 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; 3D_13C-SEPARATED_NOESY; REMARK 210 DQF-COSY; 31P-1H HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 1997, X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 111 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS, STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1/2 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 AND 2D/3D HETERONUCLEAR TECHNIQUES 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 O2' A A 13 H8 G A 14 1.57 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. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 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 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 17 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. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 389 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D0T RELATED DB: PDB REMARK 900 PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 REPLICASE OPERATOR RNA REMARK 900 HAIRPIN. DBREF 1D0U A 1 21 PDB 1D0U 1D0U 1 21 SEQRES 1 A 21 G G G A U C A C C A U U A SEQRES 2 A 21 G G G A U C U 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 - b 16 2 Bytes