Header list of 1lpw.pdb file
Complete list - 23 20 Bytes
HEADER RNA 08-MAY-02 1LPW
TITLE SOLUTION STRUCTURE OF THE YEAST SPLICEOSOMAL U2 SNRNA-INTRON BRANCH
TITLE 2 SITE HELIX FEATURING A CONSERVED PSEUDOURIDINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*GP*(PSU)P*AP*GP*UP*A)-3';
COMPND 3 CHAIN: A;
COMPND 4 OTHER_DETAILS: U2 SNRNA;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3';
COMPND 7 CHAIN: B;
COMPND 8 OTHER_DETAILS: PRE-MRNA CONSERVED INTRON BRANCH SITE SEQUENCE SITE
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 MOL_ID: 2;
SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 8 ORGANISM_TAXID: 4932
KEYWDS U2 SNRNA, BRANCH SITE, PSEUDOURIDINE, RNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR M.I.NEWBY,N.L.GREENBAUM
REVDAT 3 23-FEB-22 1LPW 1 REMARK LINK
REVDAT 2 24-FEB-09 1LPW 1 VERSN
REVDAT 1 27-NOV-02 1LPW 0
JRNL AUTH M.I.NEWBY,N.L.GREENBAUM
JRNL TITL SCULPTING OF THE SPLICEOSOMAL BRANCH SITE RECOGNITION MOTIF
JRNL TITL 2 BY A CONSERVED PSEUDOURIDINE
JRNL REF NAT.STRUCT.BIOL. V. 12 958 2002
JRNL REFN ISSN 1072-8368
JRNL PMID 12426583
JRNL DOI 10.1038/NSB873
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 5.3, X-PLOR 3.851
REMARK 3 AUTHORS : VARIAN, INC. (VNMR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 191 DISTANCE RESTRAINTS WERE
REMARK 3 USED, NOT INCLUDING THE 40 HYDROGEN BOND DISTANCES IMPOSED.
REMARK 3 INCLUDING THE 133 DIHEDRAL RESTRAINTS APPLIED IN STRUCTURE
REMARK 3 CALCULATIONS, 353 TOTAL RESTRAINTS WERE APPLIED.
REMARK 4
REMARK 4 1LPW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-02.
REMARK 100 THE DEPOSITION ID IS D_1000016167.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 293
REMARK 210 PH : 6.4; 6.4
REMARK 210 IONIC STRENGTH : 50MM SODIUM CHLORIDE; 50MM
REMARK 210 SODIUM CHLORIDE
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM U2 SNRNA-INTRON DUPLEX; 10MM
REMARK 210 SODIUM PHOSPHATE; 1MM U2 SNRNA-
REMARK 210 INTRON DUPLEX; 10MM SODIUM
REMARK 210 PHOSPHATE
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 720 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SPARKY 3.69, VNMR 3.851
REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS
REMARK 210 FOLLOWED BY CONJUGATE GRADIENT
REMARK 210 MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 800
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES THAT
REMARK 210 DID NOT VIOLATE DATA FROM
REMARK 210 FLUORESCENCE EXPERIMENTS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES. NOESY SPECTRA WERE COLLECTED AT MANY
REMARK 210 DIFFERENT MIXING TIMES, SO THAT THE BUILDUP OF CERTAIN NOES
REMARK 210 COULD BE OBSERVED TO RESOLVE SOME SPECTRAL OVERLAP.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
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 2 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 A A 9 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 A B 8 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 A A 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 2 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 2 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 3 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 3 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 3 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 3 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 3 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 3 A B 6 C4' - C3' - C2' ANGL. DEV. = -6.4 DEGREES
REMARK 500 3 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 3 C B 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 4 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 4 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 4 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 4 A B 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 4 A B 8 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES
REMARK 500 5 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES
REMARK 500 5 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 5 U B 1 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 5 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES
REMARK 500 5 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 5 A B 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES
REMARK 500 5 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 5 A B 8 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 6 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 6 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 6 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 6 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 6 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 6 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 6 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 6 C B 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 7 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 7 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 7 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 7 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 7 A B 5 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES
REMARK 500 7 A B 6 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 65 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1LMV RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE UNMODIFIED U2 SNRNA-INTRON BRANCH SITE
REMARK 900 HELIX
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 POSITION 35 IN U2 SNRNA SEQUENCES FROM S.
REMARK 999 CEREVISIAE IS A PSEUDOURIDINE. THIS CORRESPONDS
REMARK 999 TO POSITION 5 ON STRAND A, WHICH IS A URIDINE IN
REMARK 999 1LMV, AND A PSEUDOURIDINE IN 1LPW.
DBREF 1LPW A 1 9 PDB 1LPW 1LPW 1 9
DBREF 1LPW B 1 10 PDB 1LPW 1LPW 1 10
SEQRES 1 A 9 G G U G PSU A G U A
SEQRES 1 B 10 U A C U A A C A C C
MODRES 1LPW PSU A 5 U PSEUDOURIDINE-5'-MONOPHOSPHATE
HET PSU A 5 30
HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE
FORMUL 1 PSU C9 H13 N2 O9 P
LINK O3' G A 4 P PSU A 5 1555 1555 1.60
LINK O3' PSU A 5 P A A 6 1555 1555 1.61
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 - 23 20 Bytes