Header list of 1cql.pdb file
Complete list - b 16 2 Bytes
HEADER RNA 06-AUG-99 1CQL
TITLE NMR STRUCTURE OF SRP RNA DOMAIN IV
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SRP DOMAIN IV RNA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: MODIFIED E. COLI SEQUENCE;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562
KEYWDS SRP, RNA STRUCTURE, DOMAIN IV, SIGNAL SEQUENCE RECOGNITION,
KEYWDS 2 RIBONUCLEIC ACID, RNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR U.SCHMITZ,T.L.JAMES
REVDAT 3 16-FEB-22 1CQL 1 REMARK
REVDAT 2 24-FEB-09 1CQL 1 VERSN
REVDAT 1 14-JAN-00 1CQL 0
JRNL AUTH U.SCHMITZ,S.BEHRENS,D.M.FREYMANN,R.J.KEENAN,P.LUKAVSKY,
JRNL AUTH 2 P.WALTER,T.L.JAMES
JRNL TITL STRUCTURE OF THE PHYLOGENETICALLY MOST CONSERVED DOMAIN OF
JRNL TITL 2 SRP RNA.
JRNL REF RNA V. 5 1419 1999
JRNL REFN ISSN 1355-8382
JRNL PMID 10580470
JRNL DOI 10.1017/S1355838299991458
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SPARKY 92, DYANA 1.4
REMARK 3 AUTHORS : D.KNELLER, T.GODDARD (SPARKY), P. GUENTERT (DYANA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: 16.4 DISTANCE RESTRAINTS/RESIDUE
REMARK 4
REMARK 4 1CQL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-99.
REMARK 100 THE DEPOSITION ID IS D_1000009490.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288; 303; 308
REMARK 210 PH : 6.5; 6.5; 6.5
REMARK 210 IONIC STRENGTH : NULL; NULL; NULL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.25 - 1.2 MM RNA 10 MM
REMARK 210 POTASSIUM PHOSHPATE 10 MM
REMARK 210 MAGNESIUM CHLORIDE PH 6.5; 0.25
REMARK 210 MM RNA 10 MM POTASSIUM PHOSHPATE
REMARK 210 10 MM MAGNESIUM CHLORIDE PH 6.5
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; DQF-COSY;
REMARK 210 TOCSY; 3D HCCH-TOCSY; 3D HCCH-
REMARK 210 COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS 92, AMBER 4.1, CURVES
REMARK 210 3.0
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210 RESTRAINED MOLECULAR DYNAMICS
REMARK 210 COMPLETE RELAXATION MATRIX
REMARK 210 ANALYSIS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS IN THE
REMARK 210 CRUCIAL AREAS OT THE MOLECULE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK:
REMARK 210 G- AND A-SINGLE NUCLEOTIDE ISOTOPE LABELED SAMPLES WERE USED
REMARK 210 BESIDES A
REMARK 210 UNIFORMLY LABELED RNA
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' A A 11 OP2 G A 12 1.40
REMARK 500 HO2' G A 23 OP1 A A 24 1.44
REMARK 500 O6 G A 17 HO2' G A 30 1.44
REMARK 500 HO2' A A 37 OP1 G A 38 1.55
REMARK 500 HO2' U A 6 O4' U A 7 1.57
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 U A 7 C2' U A 7 C1' -0.058
REMARK 500 1 G A 22 N1 G A 22 C2 -0.051
REMARK 500 2 G A 22 N1 G A 22 C2 -0.051
REMARK 500 3 U A 7 C2' U A 7 C1' -0.056
REMARK 500 3 G A 22 N1 G A 22 C2 -0.049
REMARK 500 4 U A 7 C2' U A 7 C1' -0.049
REMARK 500 4 G A 22 N1 G A 22 C2 -0.051
REMARK 500 5 G A 22 N1 G A 22 C2 -0.050
REMARK 500 6 G A 22 N1 G A 22 C2 -0.050
REMARK 500 7 G A 22 N1 G A 22 C2 -0.052
REMARK 500 9 U A 7 C2' U A 7 C1' -0.052
REMARK 500 9 G A 22 N1 G A 22 C2 -0.052
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 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 C A 3 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 U A 5 C4 - C5 - C6 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 U A 5 C5 - C6 - N1 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 U A 6 C3' - C2' - C1' ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 U A 7 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES
REMARK 500 1 U A 7 C4' - C3' - C2' ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 U A 7 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 U A 7 C6 - N1 - C1' ANGL. DEV. = -12.3 DEGREES
REMARK 500 1 U A 7 C2 - N1 - C1' ANGL. DEV. = 8.6 DEGREES
REMARK 500 1 A A 8 C5' - C4' - C3' ANGL. DEV. = -10.0 DEGREES
REMARK 500 1 A A 8 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 C A 9 C6 - N1 - C2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 C A 10 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES
REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 G A 12 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 13 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 U A 14 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 A A 16 O5' - C5' - C4' ANGL. DEV. = -5.6 DEGREES
REMARK 500 1 G A 17 N9 - C1' - C2' ANGL. DEV. = -10.0 DEGREES
REMARK 500 1 U A 19 C5' - C4' - C3' ANGL. DEV. = -9.6 DEGREES
REMARK 500 1 G A 22 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 G A 22 N1 - C2 - N2 ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 A A 24 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 A A 25 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES
REMARK 500 1 G A 27 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 A A 28 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 1 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 A A 29 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 G A 30 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 C A 31 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 1 A A 32 C5' - C4' - O4' ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 A A 32 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 A A 32 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 A A 32 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 A A 36 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 A A 37 N7 - C8 - N9 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 A A 37 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 G A 39 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 G A 39 C5 - C6 - O6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 C A 40 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 C A 40 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 544 ANGLE DEVIATIONS.
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 1 G A 1 0.07 SIDE CHAIN
REMARK 500 1 G A 2 0.11 SIDE CHAIN
REMARK 500 1 C A 3 0.10 SIDE CHAIN
REMARK 500 1 G A 4 0.06 SIDE CHAIN
REMARK 500 1 U A 5 0.07 SIDE CHAIN
REMARK 500 1 U A 7 0.09 SIDE CHAIN
REMARK 500 1 C A 9 0.37 SIDE CHAIN
REMARK 500 1 C A 10 0.16 SIDE CHAIN
REMARK 500 1 A A 11 0.11 SIDE CHAIN
REMARK 500 1 G A 12 0.10 SIDE CHAIN
REMARK 500 1 U A 14 0.07 SIDE CHAIN
REMARK 500 1 A A 16 0.09 SIDE CHAIN
REMARK 500 1 G A 17 0.08 SIDE CHAIN
REMARK 500 1 U A 19 0.06 SIDE CHAIN
REMARK 500 1 C A 20 0.09 SIDE CHAIN
REMARK 500 1 G A 22 0.15 SIDE CHAIN
REMARK 500 1 G A 23 0.09 SIDE CHAIN
REMARK 500 1 A A 24 0.10 SIDE CHAIN
REMARK 500 1 A A 25 0.08 SIDE CHAIN
REMARK 500 1 G A 26 0.07 SIDE CHAIN
REMARK 500 1 G A 30 0.10 SIDE CHAIN
REMARK 500 1 C A 31 0.11 SIDE CHAIN
REMARK 500 1 A A 32 0.08 SIDE CHAIN
REMARK 500 1 C A 34 0.07 SIDE CHAIN
REMARK 500 1 C A 35 0.07 SIDE CHAIN
REMARK 500 1 A A 36 0.12 SIDE CHAIN
REMARK 500 1 A A 37 0.39 SIDE CHAIN
REMARK 500 1 G A 38 0.10 SIDE CHAIN
REMARK 500 1 G A 39 0.10 SIDE CHAIN
REMARK 500 1 C A 40 0.08 SIDE CHAIN
REMARK 500 2 G A 2 0.12 SIDE CHAIN
REMARK 500 2 C A 3 0.11 SIDE CHAIN
REMARK 500 2 U A 6 0.07 SIDE CHAIN
REMARK 500 2 U A 7 0.13 SIDE CHAIN
REMARK 500 2 A A 8 0.06 SIDE CHAIN
REMARK 500 2 C A 9 0.43 SIDE CHAIN
REMARK 500 2 C A 10 0.24 SIDE CHAIN
REMARK 500 2 G A 12 0.06 SIDE CHAIN
REMARK 500 2 U A 19 0.10 SIDE CHAIN
REMARK 500 2 C A 20 0.09 SIDE CHAIN
REMARK 500 2 G A 22 0.16 SIDE CHAIN
REMARK 500 2 G A 23 0.10 SIDE CHAIN
REMARK 500 2 A A 24 0.11 SIDE CHAIN
REMARK 500 2 A A 25 0.08 SIDE CHAIN
REMARK 500 2 G A 26 0.07 SIDE CHAIN
REMARK 500 2 G A 30 0.15 SIDE CHAIN
REMARK 500 2 C A 31 0.07 SIDE CHAIN
REMARK 500 2 A A 32 0.08 SIDE CHAIN
REMARK 500 2 C A 34 0.06 SIDE CHAIN
REMARK 500 2 A A 36 0.11 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 230 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CQ5 RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
REMARK 900 RELATED ID: 28SR RELATED DB: PDB
REMARK 900 STRUCTURE OF A TRUNCATED SRP DOMAIN IV RNA
DBREF 1CQL A 1 43 PDB 1CQL 1CQL 1 43
SEQRES 1 A 43 G G C G U U U A C C A G G
SEQRES 2 A 43 U C A G G U C C G G A A G
SEQRES 3 A 43 G A A G C A G C C A A G G
SEQRES 4 A 43 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 - b 16 2 Bytes