HEADER DE NOVO PROTEIN 10-OCT-01 1J4M TITLE MINIMIZED AVERAGE STRUCTURE OF THE 14-RESIDUE PEPTIDE RG-KWTY-NG-ITYE- TITLE 2 GR (MBH12) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MBH12; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED USING FMOC SOURCE 4 CHEMISTRY. KEYWDS BETA-HAIRPIN, DE NOVO PROTEIN EXPDTA SOLUTION NMR AUTHOR M.T.PASTOR,M.LOPEZ DE LA PAZ,E.LACROIX,L.SERRANO,E.PEREZ-PAYA REVDAT 6 27-DEC-23 1J4M 1 REMARK REVDAT 5 23-FEB-22 1J4M 1 REMARK REVDAT 4 24-FEB-09 1J4M 1 VERSN REVDAT 3 01-APR-03 1J4M 1 JRNL REVDAT 2 13-FEB-02 1J4M 1 JRNL REMARK REVDAT 1 17-OCT-01 1J4M 0 JRNL AUTH M.T.PASTOR,M.LOPEZ DE LA PAZ,E.LACROIX,L.SERRANO, JRNL AUTH 2 E.PEREZ-PAYA JRNL TITL COMBINATORIAL APPROACHES: A NEW TOOL TO SEARCH FOR HIGHLY JRNL TITL 2 STRUCTURED BETA-HAIRPIN PEPTIDES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 614 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 11782528 JRNL DOI 10.1073/PNAS.012583999 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, GROMOS 96 REMARK 3 AUTHORS : BRUKER (XWINNMR), VAN GUNSTEREN (GROMOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ENERGY MINIMISATION OF THE MEAN STRUCTURE WAS DONE WITH THE REMARK 3 GROMOS96 IMPLEMENTATION OF SWISS-PDBVIEWER. REMARK 4 REMARK 4 1J4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000001606. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM PEPTIDE MBH12; 1 MM PEPTIDE REMARK 210 MBH12; 1 MM PEPTIDE MBH12 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D ROESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, DYANA 1.5 REMARK 210 METHOD USED : SIMULATED ANNEALING COMBINED REMARK 210 WITH TORSION ANGLE DYNAMICS REMARK 210 (DYANA) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 HA ARG A 1 H GLY A 2 0.67 REMARK 500 HA ARG A 1 N GLY A 2 1.36 REMARK 500 CA ARG A 1 H GLY A 2 1.48 REMARK 500 CA ARG A 1 N GLY A 2 1.55 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 ARG A 1 N ARG A 1 CA -0.260 REMARK 500 ARG A 1 CA ARG A 1 CB -0.204 REMARK 500 ARG A 1 CG ARG A 1 CD -0.186 REMARK 500 ARG A 1 NE ARG A 1 CZ -0.345 REMARK 500 ARG A 1 CZ ARG A 1 NH1 -0.554 REMARK 500 ARG A 1 CZ ARG A 1 NH2 -0.488 REMARK 500 ARG A 1 CA ARG A 1 C -0.181 REMARK 500 ARG A 1 C GLY A 2 N -0.156 REMARK 500 GLY A 2 N GLY A 2 CA -0.240 REMARK 500 GLY A 2 CA GLY A 2 C -0.273 REMARK 500 TRP A 4 CE2 TRP A 4 CD2 -0.079 REMARK 500 TYR A 6 CB TYR A 6 CG -0.115 REMARK 500 TYR A 6 CG TYR A 6 CD2 -0.252 REMARK 500 TYR A 6 CG TYR A 6 CD1 -0.227 REMARK 500 TYR A 6 CD1 TYR A 6 CE1 -0.143 REMARK 500 TYR A 6 CE1 TYR A 6 CZ -0.306 REMARK 500 TYR A 6 CZ TYR A 6 OH -0.136 REMARK 500 TYR A 6 CZ TYR A 6 CE2 -0.223 REMARK 500 TYR A 6 CE2 TYR A 6 CD2 -0.140 REMARK 500 TYR A 11 CG TYR A 11 CD2 -0.157 REMARK 500 TYR A 11 CG TYR A 11 CD1 -0.141 REMARK 500 TYR A 11 CE1 TYR A 11 CZ -0.153 REMARK 500 TYR A 11 CZ TYR A 11 CE2 -0.140 REMARK 500 GLU A 12 CG GLU A 12 CD -0.107 REMARK 500 GLU A 12 CD GLU A 12 OE1 -0.092 REMARK 500 GLU A 12 CD GLU A 12 OE2 -0.202 REMARK 500 ARG A 14 NE ARG A 14 CZ -0.233 REMARK 500 ARG A 14 CZ ARG A 14 NH1 -0.619 REMARK 500 ARG A 14 CZ ARG A 14 NH2 -0.513 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 ARG A 1 CB - CA - C ANGL. DEV. = 32.8 DEGREES REMARK 500 ARG A 1 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 1 CA - CB - CG ANGL. DEV. = -19.1 DEGREES REMARK 500 ARG A 1 CB - CG - CD ANGL. DEV. = -26.5 DEGREES REMARK 500 ARG A 1 CG - CD - NE ANGL. DEV. = -28.4 DEGREES REMARK 500 ARG A 1 NH1 - CZ - NH2 ANGL. DEV. = -48.5 DEGREES REMARK 500 ARG A 1 NE - CZ - NH1 ANGL. DEV. = 24.2 DEGREES REMARK 500 ARG A 1 NE - CZ - NH2 ANGL. DEV. = 24.2 DEGREES REMARK 500 ARG A 1 CA - C - N ANGL. DEV. = -40.6 DEGREES REMARK 500 ARG A 1 O - C - N ANGL. DEV. = 16.4 DEGREES REMARK 500 GLY A 2 CA - C - O ANGL. DEV. = -26.7 DEGREES REMARK 500 GLY A 2 O - C - N ANGL. DEV. = 16.6 DEGREES REMARK 500 TRP A 4 CB - CG - CD1 ANGL. DEV. = -7.9 DEGREES REMARK 500 TRP A 4 CD1 - NE1 - CE2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 4 CZ3 - CH2 - CZ2 ANGL. DEV. = -10.1 DEGREES REMARK 500 TRP A 4 CH2 - CZ2 - CE2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR A 6 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 TYR A 6 CB - CG - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TYR A 6 CD1 - CG - CD2 ANGL. DEV. = -35.4 DEGREES REMARK 500 TYR A 6 CB - CG - CD1 ANGL. DEV. = 29.5 DEGREES REMARK 500 TYR A 6 CG - CD1 - CE1 ANGL. DEV. = 25.5 DEGREES REMARK 500 TYR A 6 CG - CD2 - CE2 ANGL. DEV. = 10.6 DEGREES REMARK 500 TYR A 6 CD1 - CE1 - CZ ANGL. DEV. = 10.3 DEGREES REMARK 500 TYR A 6 OH - CZ - CE2 ANGL. DEV. = 24.1 DEGREES REMARK 500 TYR A 6 CE1 - CZ - CE2 ANGL. DEV. = -32.6 DEGREES REMARK 500 TYR A 6 CZ - CE2 - CD2 ANGL. DEV. = 21.6 DEGREES REMARK 500 TYR A 11 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 TYR A 11 CD1 - CG - CD2 ANGL. DEV. = -24.5 DEGREES REMARK 500 TYR A 11 CB - CG - CD1 ANGL. DEV. = 14.0 DEGREES REMARK 500 TYR A 11 CG - CD1 - CE1 ANGL. DEV. = 14.1 DEGREES REMARK 500 TYR A 11 CG - CD2 - CE2 ANGL. DEV. = 10.0 DEGREES REMARK 500 TYR A 11 CD1 - CE1 - CZ ANGL. DEV. = 11.0 DEGREES REMARK 500 TYR A 11 CE1 - CZ - CE2 ANGL. DEV. = -25.8 DEGREES REMARK 500 TYR A 11 CZ - CE2 - CD2 ANGL. DEV. = 15.3 DEGREES REMARK 500 GLU A 12 CB - CG - CD ANGL. DEV. = -25.9 DEGREES REMARK 500 GLU A 12 OE1 - CD - OE2 ANGL. DEV. = -16.0 DEGREES REMARK 500 GLU A 12 CG - CD - OE1 ANGL. DEV. = 26.1 DEGREES REMARK 500 GLU A 12 CG - CD - OE2 ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 14 CB - CA - C ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 14 CA - CB - CG ANGL. DEV. = -37.7 DEGREES REMARK 500 ARG A 14 CB - CG - CD ANGL. DEV. = -34.0 DEGREES REMARK 500 ARG A 14 CG - CD - NE ANGL. DEV. = -37.6 DEGREES REMARK 500 ARG A 14 NH1 - CZ - NH2 ANGL. DEV. = -25.9 DEGREES REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = 10.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 2 LYS A 3 149.56 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 ARG A 1 0.22 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 1 -15.32 REMARK 500 GLY A 2 -18.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K43 RELATED DB: PDB REMARK 900 ENSEMBLE OF 10 STRUCTURES DBREF 1J4M A 1 14 PDB 1J4M 1J4M 1 14 SEQRES 1 A 14 ARG GLY LYS TRP THR TYR ASN GLY ILE THR TYR GLU GLY SEQRES 2 A 14 ARG SHEET 1 A 2 TRP A 4 TYR A 6 0 SHEET 2 A 2 ILE A 9 TYR A 11 -1 O TYR A 11 N TRP A 4 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