Header list of 1j9n.pdb file
Complete list - 25 20 Bytes
HEADER DNA BINDING PROTEIN/DNA 28-MAY-01 1J9N TITLE SOLUTION STRUCTURE OF THE NUCLEOPEPTIDE [AC-LYS-TRP-LYS- TITLE 2 HSE(P3*DGCATCG)-ALA]-[P5*DCGTAGC] CAVEAT 1J9N THERE ARE CHIRALITY ERRORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*AP*CP*(PGN))-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*GP*TP*AP*GP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PEPTIDE ACE-LYS-TRP-LYS-HSE-ALA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS COVALENTLY LINKED PEPTIDE-DNA COMPLEX, TRYPTOPHAN STACKING, KEYWDS 2 DNA BINDING PROTEIN/DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR I.GOMEZ-PINTO,V.MARCHAN,F.GAGO,A.GRANDAS,C.GONZALEZ REVDAT 2 24-FEB-09 1J9N 1 VERSN REVDAT 1 21-JAN-03 1J9N 0 JRNL AUTH I.GOMEZ-PINTO,V.MARCHAN,F.GAGO,A.GRANDAS,C.GONZALEZ JRNL TITL SOLUTION STRUCTURE AND STABILITY OF JRNL TITL 2 TRYPTOPHAN-CONTAINING NUCLEOPEPTIDE DUPLEXES JRNL REF CHEMBIOCHEM V. 4 40 2003 JRNL REFN ISSN 1439-4227 JRNL PMID 12512075 JRNL DOI 10.1002/CBIC.200390012 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SANDER 5.0 REMARK 3 AUTHORS : KOLLMAN, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 276 NOE-DERIVED DISTANCE CONSTRAINTS, AND 33 DIHEDRAL ANGLE REMARK 3 RESTRAINTS REMARK 4 REMARK 4 1J9N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-01. REMARK 100 THE RCSB ID CODE IS RCSB013533. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 278 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM NUCLEOPEPTIDE, 25 MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL, REMARK 210 90% H2O, 10% D2O; 2MM REMARK 210 NUCLEOPEPTIDE, 25 MM PHOSPHATE REMARK 210 BUFFER, 100 MM NACL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1.3, MARDIGRAS 5.2, REMARK 210 DYANA 1.5 REMARK 210 METHOD USED : MOLECULAR DYNAMICS MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 PGN A 6 O6P REMARK 470 HSE C 16 O2 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 DC A 2 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DT A 3 C4 - C5 - C7 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT B 9 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 9 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DT B 9 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DT B 9 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 9 O4' - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 DT B 9 C4 - C5 - C7 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT B 9 C6 - C5 - C7 ANGL. DEV. = -9.7 DEGREES REMARK 500 1 DA B 10 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG B 11 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC B 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 3 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DA A 4 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC B 7 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DG B 8 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG B 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DT B 9 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT B 9 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DT B 9 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 2 DT B 9 C4' - C3' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DT B 9 O4' - C1' - C2' ANGL. DEV. = -9.2 DEGREES REMARK 500 2 DT B 9 C4 - C5 - C7 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -8.7 DEGREES REMARK 500 2 DA B 10 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG B 11 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC B 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DC A 2 N3 - C4 - N4 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 DT A 3 C4 - C5 - C7 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 DA A 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 3 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DT B 9 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES REMARK 500 3 DT B 9 C5' - C4' - O4' ANGL. DEV. = 11.6 DEGREES REMARK 500 3 DT B 9 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 3 DT B 9 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 3 DT B 9 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 3 DT B 9 C4 - C5 - C7 ANGL. DEV. = 7.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 176 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 TRP C 14 -116.07 29.86 REMARK 500 2 TRP C 14 -81.96 -146.18 REMARK 500 3 TRP C 14 87.83 -163.00 REMARK 500 4 TRP C 14 75.15 -162.11 REMARK 500 6 TRP C 14 176.93 -59.19 REMARK 500 7 TRP C 14 85.09 -46.42 REMARK 500 8 TRP C 14 70.33 5.79 REMARK 500 9 TRP C 14 64.46 15.93 REMARK 500 10 TRP C 14 -100.99 60.55 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 DG A 1 0.10 SIDE_CHAIN REMARK 500 1 DA B 10 0.08 SIDE_CHAIN REMARK 500 1 DG B 11 0.06 SIDE_CHAIN REMARK 500 1 DC B 12 0.10 SIDE_CHAIN REMARK 500 2 DG B 11 0.06 SIDE_CHAIN REMARK 500 3 DA B 10 0.08 SIDE_CHAIN REMARK 500 3 DG B 11 0.07 SIDE_CHAIN REMARK 500 4 DC B 7 0.06 SIDE_CHAIN REMARK 500 4 DA B 10 0.09 SIDE_CHAIN REMARK 500 4 DG B 11 0.10 SIDE_CHAIN REMARK 500 5 DA B 10 0.07 SIDE_CHAIN REMARK 500 5 DG B 11 0.06 SIDE_CHAIN REMARK 500 5 DC B 12 0.08 SIDE_CHAIN REMARK 500 6 DG A 1 0.07 SIDE_CHAIN REMARK 500 6 DA B 10 0.07 SIDE_CHAIN REMARK 500 6 DG B 11 0.07 SIDE_CHAIN REMARK 500 6 DC B 12 0.09 SIDE_CHAIN REMARK 500 7 DG A 1 0.07 SIDE_CHAIN REMARK 500 7 DG B 11 0.06 SIDE_CHAIN REMARK 500 7 DC B 12 0.10 SIDE_CHAIN REMARK 500 8 DT B 9 0.07 SIDE_CHAIN REMARK 500 8 DA B 10 0.08 SIDE_CHAIN REMARK 500 8 DG B 11 0.08 SIDE_CHAIN REMARK 500 9 DG A 1 0.07 SIDE_CHAIN REMARK 500 9 DT B 9 0.06 SIDE_CHAIN REMARK 500 9 DA B 10 0.11 SIDE_CHAIN REMARK 500 9 DG B 11 0.08 SIDE_CHAIN REMARK 500 10 DG A 1 0.09 SIDE_CHAIN REMARK 500 10 DA B 10 0.08 SIDE_CHAIN REMARK 500 10 DG B 11 0.06 SIDE_CHAIN REMARK 500 10 DC B 12 0.13 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 4 LYS C 13 123.0 ALPHA-CARBON REMARK 500 4 LYS C 15 129.4 ALPHA-CARBON REMARK 500 6 ALA C 17 122.5 ALPHA-CARBON REMARK 500 9 ALA C 17 124.1 ALPHA-CARBON REMARK 500 10 TRP C 14 131.1 ALPHA-CARBON REMARK 500 REMARK 500 REMARK: NULL SEQRES 1 A 6 DG DC DT DA DC PGN SEQRES 1 B 6 DC DG DT DA DG DC SEQRES 1 C 6 ACE LYS TRP LYS HSE ALA MODRES 1J9N PGN A 6 DG 2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE MODRES 1J9N HSE C 16 SER L-HOMOSERINE HET PGN A 6 36 HET ACE C 12 6 HET HSE C 16 13 HETNAM PGN 2'-DEOXYGUANOSINE-3',5'-DIPHOSPHATE HETNAM ACE ACETYL GROUP HETNAM HSE L-HOMOSERINE FORMUL 1 PGN C10 H15 N5 O10 P2 FORMUL 3 ACE C2 H4 O FORMUL 3 HSE C4 H9 N O3 LINK O3 HSE C 16 P1 PGN A 6 1555 1555 1.62 LINK C ACE C 12 N LYS C 13 1555 1555 1.34 LINK O3' DC A 5 P PGN A 6 1555 1555 1.62 LINK C LYS C 15 NA HSE C 16 1555 1555 1.34 LINK C2 HSE C 16 N ALA C 17 1555 1555 1.34 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 - 25 20 Bytes