PDB Short entry for 1CT6 HEADER DNA BINDING PROTEIN 19-AUG-99 1CT6 TITLE SOLUTION STRUCTURE OF CGGIRGERG IN CONTACT WITH THE MONOCLONAL TITLE 2 ANTIBODY MAB 4X11, NMR, 11 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE H3 PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL REGION 130-135; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE PEPTIDE SOURCE 4 CORRESPONDS TO THE IRGERA SEQUENCE PRESENT IN THEC-TERMINAL REGION SOURCE 5 130-135 OF HISTONE H3 BOUND TO THE MAB4X11 MONOCLONAL ANTIBODY SOURCE 6 (IGG1). THE SEQUENCE CGG WAS ADDED TO THE N- TERMINUS OF THE IRGERA SOURCE 7 SEQUENCE AS A LINKER TO THE DEXTRAN MATRIX IN BIACORE EXPERIMENTS SOURCE 8 VIA THE CYS THIOL GROUP. ALA WAS REPLACED BY GLY. KEYWDS SYNTHETIC PEPTIDE, ANALOGUE, TR-NOE, ANTIGEN-ANTIBODY COMPLEX, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.PHAN CHAN DU,M.C.PETIT,G.GUICHARD,J.P.BRIAND,S.MULLER,M.T.CUNG REVDAT 5 16-FEB-22 1CT6 1 REMARK REVDAT 4 24-FEB-09 1CT6 1 VERSN REVDAT 3 01-APR-03 1CT6 1 JRNL REVDAT 2 13-JUN-01 1CT6 1 JRNL REVDAT 1 02-SEP-99 1CT6 0 JRNL AUTH A.PHAN-CHAN-DU,M.C.PETIT,G.GUICHARD,J.P.BRIAND,S.MULLER, JRNL AUTH 2 M.T.CUNG JRNL TITL STRUCTURE OF ANTIBODY-BOUND PEPTIDES AND RETRO-INVERSO JRNL TITL 2 ANALOGUES. A TRANSFERRED NUCLEAR OVERHAUSER EFFECT JRNL TITL 3 SPECTROSCOPY AND MOLECULAR DYNAMICS APPROACH. JRNL REF BIOCHEMISTRY V. 40 5720 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11341837 JRNL DOI 10.1021/BI001151H REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.4, DISCOVER 3 REMARK 3 AUTHORS : GUNTERT, WUTHRICH (DYANA), MOLECULAR SIMULATIONS REMARK 3 INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ENERGY MINIMISATION. A DISTANT REMARK 3 DEPENDENT DIELECTRIC CONSTANT EQUAL TO 4R WAS APPLIED. THE NET REMARK 3 ELECTRIC CHARGES WERE DECREASED, WHILE THOSE OF THE N AND C REMARK 3 TERMINAL CHARGED GROUPS WERE NEGLECTED. IN THE PDB, NH3+ IS REMARK 3 INCLUDED IN THE RESIDUE CYS, AND COO- IS INCLUDED IN THE RESIDUE REMARK 3 GLY. THE RESIDUE GLU HAS MISSING ATOMS HE2 IN ALL STRUCTURES REMARK 3 BECAUSE IN DISCOVER, THIS RESIDUE IS MODELLED AS A CHARGED REMARK 3 GROUP(WE HAVE COO- AND NOT COOH). REMARK 4 REMARK 4 1CT6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.1M PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5 MM PEPTIDE, 0.1 MM MAB; 100 MM REMARK 210 PHOSPHTE BUFFER CONTAINING 0.02% REMARK 210 SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TOCSY, NOESY, COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISCOVER 3 REMARK 210 METHOD USED : ENERGY MINIMISATION MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 REMARK 210 REMARK 210 REMARK: THE PEPTIDE/MAB MOLAR RATIO WAS ADJUSTED TO 50/1 (I.E. 5MM REMARK 210 OF PEPTIDE AND 0.1 MM MAB) 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: 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 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 7 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES 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 ARG A 5 89.49 -155.36 REMARK 500 1 GLU A 7 -59.33 -158.91 REMARK 500 1 ARG A 8 -65.66 -159.48 REMARK 500 3 ARG A 5 116.22 -162.86 REMARK 500 4 ILE A 4 -9.79 -55.99 REMARK 500 5 ARG A 5 82.91 -156.05 REMARK 500 6 ARG A 5 86.43 -151.10 REMARK 500 8 ARG A 5 -66.61 -153.84 REMARK 500 9 GLU A 7 -40.67 -154.71 REMARK 500 10 GLU A 7 -75.50 -155.64 REMARK 500 11 ARG A 5 86.22 -152.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CS9 RELATED DB: PDB DBREF 1CT6 A 4 9 UNP P16106 H31_HUMAN 130 135 SEQADV 1CT6 GLY A 9 UNP P16106 ALA 130 SEE REMARK 999 SEQRES 1 A 9 CYS GLY GLY ILE ARG GLY GLU ARG GLY 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