Header list of 1kos.pdb file
Complete list - 23 20 Bytes
HEADER RNA 03-MAY-99 1KOS
TITLE SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP
TITLE 2 CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH)
COMPND 3 P*CP*AP*CP*AP*G)- 3';
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: TPSIC DOMAIN OF TRNA;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 OTHER_DETAILS: C60 IS PROTONATED
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SEQUENCE FROM YEAST (SACCHAROMYCES CEREVISIAE) TRNA
SOURCE 4 PHE
KEYWDS TRNA, T STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, RNA FOLDING, RNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR K.M.KOSHLAP,R.GUENTHER,E.SOCHACKA,A.MALKIEWICZ,P.F.AGRIS
REVDAT 4 23-FEB-22 1KOS 1 REMARK LINK
REVDAT 3 24-FEB-09 1KOS 1 VERSN
REVDAT 2 26-SEP-01 1KOS 3 ATOM
REVDAT 1 22-OCT-99 1KOS 0
JRNL AUTH K.M.KOSHLAP,R.GUENTHER,E.SOCHACKA,A.MALKIEWICZ,P.F.AGRIS
JRNL TITL A DISTINCTIVE RNA FOLD: THE SOLUTION STRUCTURE OF AN
JRNL TITL 2 ANALOGUE OF THE YEAST TRNAPHE T PSI C DOMAIN.
JRNL REF BIOCHEMISTRY V. 38 8647 1999
JRNL REFN ISSN 0006-2960
JRNL PMID 10393540
JRNL DOI 10.1021/BI990118W
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH U.SCHMITZ,A.DONATI,T.L.JAMES,N.B.ULYANOV,L.YAO
REMARK 1 TITL SMALL STRUCTURAL ENSEMBLES FOR A 17-NUCLEOTIDE MIMIC OF THE
REMARK 1 TITL 2 TRNA TPSIC-LOOP VIA FITTING DIPOLAR RELAXATION RATES WITH
REMARK 1 TITL 3 THE QUADRATIC PROGRAMMING ALGORITHM
REMARK 1 REF BIOPOLYMERS V. 46 329 1998
REMARK 1 REFN ISSN 0006-3525
REMARK 1 DOI 10.1002/(SICI)1097-0282(19981015)46:5<329::AID-BIP4>3.3.CO;2
REMARK 1 DOI 2 -K
REMARK 1 REFERENCE 2
REMARK 1 AUTH L.J.YAO,T.L.JAMES,J.T.KEALEY,D.V.SANTI,U.SCHMITZ
REMARK 1 TITL THE DYNAMIC NMR STRUCTURE OF THE T PSI C-LOOP: IMPLICATIONS
REMARK 1 TITL 2 FOR THE SPECIFICITY OF TRNA METHYLATION
REMARK 1 REF J.BIOMOL.NMR V. 3 229 1997
REMARK 1 REFN ISSN 0925-2738
REMARK 1 DOI 10.1023/A:1018618606857
REMARK 1 REFERENCE 3
REMARK 1 AUTH E.WESTHOF,M.SUNDARALINGAM
REMARK 1 TITL RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST
REMARK 1 TITL 2 PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND
REMARK 1 TITL 3 DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST
REMARK 1 TITL 4 ANGLES
REMARK 1 REF BIOCHEMISTRY V. 25 4868 1986
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE
REMARK 4
REMARK 4 1KOS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB.
REMARK 100 THE DEPOSITION ID IS D_1000000990.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : 100% D2O, 94% WATER/6% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY; HSQC;
REMARK 210 HETCOR; HETEROTOCSY; HETEROTOCSY-
REMARK 210 NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : DRX500
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: EXPERIMENTS IN 100% D2O CONDUCTED AT 283, 288,293, AND 298
REMARK 210 KELVIN; EXPERIMENTS IN 6% D2O/ 94% H2O CONDUCTED AT 274 AND 283
REMARK 210 KELVIN.
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' C A 15 O4' A A 16 1.57
REMARK 500 O4 U A 2 H61 A A 16 1.59
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 C A 1 C2' C A 1 C1' -0.059
REMARK 500 1 G A 3 C2' G A 3 C1' -0.051
REMARK 500 1 G A 3 C8 G A 3 N9 -0.056
REMARK 500 1 G A 5 C2' G A 5 C1' -0.065
REMARK 500 1 G A 5 C8 G A 5 N9 -0.071
REMARK 500 1 C A 13 N1 C A 13 C6 -0.040
REMARK 500 1 G A 17 C8 G A 17 N9 -0.046
REMARK 500 2 C A 1 C2' C A 1 C1' -0.050
REMARK 500 2 G A 3 C2' G A 3 C1' -0.051
REMARK 500 2 G A 3 C8 G A 3 N9 -0.055
REMARK 500 2 G A 5 C2' G A 5 C1' -0.066
REMARK 500 2 G A 5 C8 G A 5 N9 -0.080
REMARK 500 2 C A 8 C3' C A 8 C2' -0.068
REMARK 500 2 C A 15 N1 C A 15 C6 -0.041
REMARK 500 2 G A 17 C8 G A 17 N9 -0.056
REMARK 500 2 G A 17 N9 G A 17 C4 -0.057
REMARK 500 3 C A 1 C2' C A 1 C1' -0.056
REMARK 500 3 G A 3 C2' G A 3 C1' -0.050
REMARK 500 3 G A 3 C8 G A 3 N9 -0.058
REMARK 500 3 G A 5 C2' G A 5 C1' -0.056
REMARK 500 3 G A 5 C8 G A 5 N9 -0.069
REMARK 500 3 G A 17 C8 G A 17 N9 -0.049
REMARK 500 4 C A 1 C2' C A 1 C1' -0.056
REMARK 500 4 G A 3 C2' G A 3 C1' -0.054
REMARK 500 4 G A 3 C8 G A 3 N9 -0.058
REMARK 500 4 G A 5 C2' G A 5 C1' -0.052
REMARK 500 4 G A 5 C8 G A 5 N9 -0.074
REMARK 500 4 G A 17 C8 G A 17 N9 -0.058
REMARK 500 5 C A 1 C2' C A 1 C1' -0.064
REMARK 500 5 G A 3 C2' G A 3 C1' -0.064
REMARK 500 5 G A 3 C8 G A 3 N9 -0.054
REMARK 500 5 G A 5 C2' G A 5 C1' -0.058
REMARK 500 5 G A 5 C8 G A 5 N9 -0.077
REMARK 500 5 C A 15 N1 C A 15 C6 -0.039
REMARK 500 5 G A 17 C8 G A 17 N9 -0.049
REMARK 500 6 C A 1 C2' C A 1 C1' -0.067
REMARK 500 6 G A 3 C8 G A 3 N9 -0.061
REMARK 500 6 G A 5 C2' G A 5 C1' -0.059
REMARK 500 6 G A 5 C8 G A 5 N9 -0.078
REMARK 500 6 G A 17 C8 G A 17 N9 -0.043
REMARK 500 7 C A 1 C2' C A 1 C1' -0.069
REMARK 500 7 G A 3 C2' G A 3 C1' -0.050
REMARK 500 7 G A 3 C8 G A 3 N9 -0.054
REMARK 500 7 G A 5 C8 G A 5 N9 -0.078
REMARK 500 7 C A 8 C3' C A 8 C2' -0.068
REMARK 500 7 C A 13 N1 C A 13 C6 -0.041
REMARK 500 7 C A 15 N1 C A 15 C6 -0.036
REMARK 500 7 G A 17 C8 G A 17 N9 -0.048
REMARK 500 8 C A 1 C2' C A 1 C1' -0.061
REMARK 500 8 G A 3 C8 G A 3 N9 -0.059
REMARK 500
REMARK 500 THIS ENTRY HAS 53 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 C A 1 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 C A 1 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 C A 1 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES
REMARK 500 1 C A 1 N1 - C1' - C2' ANGL. DEV. = -10.4 DEGREES
REMARK 500 1 C A 1 O4' - C1' - N1 ANGL. DEV. = 14.9 DEGREES
REMARK 500 1 C A 1 N3 - C4 - N4 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 C A 1 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES
REMARK 500 1 G A 3 C3' - C2' - C1' ANGL. DEV. = 8.9 DEGREES
REMARK 500 1 G A 3 N9 - C1' - C2' ANGL. DEV. = -12.6 DEGREES
REMARK 500 1 G A 3 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 G A 3 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 G A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 1 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 G A 5 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 1 G A 5 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 G A 5 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 U A 7 C5' - C4' - O4' ANGL. DEV. = 13.7 DEGREES
REMARK 500 1 U A 7 C4' - C3' - C2' ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 C A 8 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 A A 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 U A 11 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES
REMARK 500 1 C A 13 C5' - C4' - O4' ANGL. DEV. = 7.5 DEGREES
REMARK 500 1 C A 13 O4' - C1' - C2' ANGL. DEV. = -11.0 DEGREES
REMARK 500 1 A A 14 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES
REMARK 500 1 A A 14 C2' - C3' - O3' ANGL. DEV. = 11.9 DEGREES
REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 C A 15 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 C A 15 N1 - C1' - C2' ANGL. DEV. = -6.7 DEGREES
REMARK 500 1 C A 15 N3 - C4 - N4 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 C A 15 C5 - C4 - N4 ANGL. DEV. = -4.9 DEGREES
REMARK 500 1 C A 15 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES
REMARK 500 1 A A 16 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 A A 16 C3' - C2' - C1' ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 A A 16 N9 - C1' - C2' ANGL. DEV. = -9.7 DEGREES
REMARK 500 1 A A 16 O4' - C1' - N9 ANGL. DEV. = 13.0 DEGREES
REMARK 500 1 G A 17 C1' - O4' - C4' ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 G A 17 N9 - C1' - C2' ANGL. DEV. = -18.4 DEGREES
REMARK 500 1 G A 17 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 C A 1 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES
REMARK 500 2 C A 1 C2' - C3' - O3' ANGL. DEV. = 10.2 DEGREES
REMARK 500 2 C A 1 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 2 C A 1 O4' - C1' - C2' ANGL. DEV. = -9.3 DEGREES
REMARK 500 2 C A 1 O4' - C1' - N1 ANGL. DEV. = 11.9 DEGREES
REMARK 500 2 U A 2 P - O5' - C5' ANGL. DEV. = 11.3 DEGREES
REMARK 500 2 U A 2 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 364 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1KOS A 1 17 PDB 1KOS 1KOS 1 17
SEQRES 1 A 17 C U G U G 5MU U C G A U CH C
SEQRES 2 A 17 A C A G
MODRES 1KOS 5MU A 6 U 5-METHYLURIDINE 5'-MONOPHOSPHATE
MODRES 1KOS CH A 12 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
HET 5MU A 6 33
HET CH A 12 32
HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE
HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
FORMUL 1 5MU C10 H15 N2 O9 P
FORMUL 1 CH C9 H15 N3 O8 P 1+
LINK O3' G A 5 P 5MU A 6 1555 1555 1.61
LINK O3' 5MU A 6 P U A 7 1555 1555 1.63
LINK O3' U A 11 P CH A 12 1555 1555 1.61
LINK O3' CH A 12 P C A 13 1555 1555 1.62
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