HEADER PLANT SEED PROTEIN 14-APR-93 1CCM TITLE DIRECT NOE REFINEMENT OF CRAMBIN FROM 2D NMR DATA USING A SLOW-COOLING TITLE 2 ANNEALING PROTOCOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRAMBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA; SOURCE 3 ORGANISM_TAXID: 3721; SOURCE 4 STRAIN: SUBSP. ABYSSINICA KEYWDS PLANT SEED PROTEIN EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR A.M.J.J.BONVIN,J.A.C.RULLMANN,R.M.J.N.LAMERICHS,R.BOELENS,R.KAPTEIN REVDAT 4 20-NOV-24 1CCM 1 REMARK REVDAT 3 29-NOV-17 1CCM 1 REMARK HELIX REVDAT 2 24-FEB-09 1CCM 1 VERSN REVDAT 1 31-OCT-93 1CCM 0 JRNL AUTH A.M.BONVIN,J.A.RULLMANN,R.M.LAMERICHS,R.BOELENS,R.KAPTEIN JRNL TITL "ENSEMBLE" ITERATIVE RELAXATION MATRIX APPROACH: A NEW NMR JRNL TITL 2 REFINEMENT PROTOCOL APPLIED TO THE SOLUTION STRUCTURE OF JRNL TITL 3 CRAMBIN. JRNL REF PROTEINS V. 15 385 1993 JRNL REFN ISSN 0887-3585 JRNL PMID 8460109 JRNL DOI 10.1002/PROT.340150406 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.M.J.J.BONVIN,J.A.C.RULLMANN,R.M.J.N.LAMERICHS,R.BOELENS, REMARK 1 AUTH 2 R.KAPTEIN REMARK 1 TITL "ENSEMBLE" ITERATIVE RELAXATION MATRIX APPROACH: A NEW NMR REMARK 1 TITL 2 REFINEMENT PROTOCOL APPLIED TO THE SOLUTION STRUCTURE OF REMARK 1 TITL 3 CRAMBIN REMARK 1 REF PROTEINS V. 15 385 1993 REMARK 1 REFN ISSN 0887-3585 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.A.C.RULLMANN,A.M.J.J.BONVIN,R.BOELENS,R.KAPTEIN REMARK 1 TITL STRUCTURE DETERMINATION BY NMR-APPLICATION TO CRAMBIN REMARK 1 EDIT D.M.SOUMPASIS, T.M.JOVIN REMARK 1 REF COMPUTATION OF BIOMOLECULAR 1 1992 REMARK 1 REF 2 STRUCTURES; ACHIEVEMENTS REMARK 1 REF 3 PROBLEMS, AND PERSPECTIVES REMARK 1 PUBL SPRINGER-VERLAG, BERLIN REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 AUTH R.M.J.M.LAMERICHS REMARK 1 TITL 2D NMR STUDIES OF BIOMOLECULES: PROTEIN STRUCTURE AND REMARK 1 TITL 2 PROTEIN-DNA INTERACTIONS REMARK 1 REF THESIS 1989 REMARK 1 REFN REMARK 1 REFERENCE 4 REMARK 1 AUTH R.M.J.N.LAMERICHS,L.J.BERLINER,R.BOELENS,A.DEMARCO,M.LLINAS, REMARK 1 AUTH 2 R.KAPTEIN REMARK 1 TITL SECONDARY STRUCTURE AND HYDROGEN BONDING OF CRAMBIN IN REMARK 1 TITL 2 SOLUTION REMARK 1 REF EUR.J.BIOCHEM. V. 171 307 1988 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 5 REMARK 1 AUTH J.A.W.H.VERMEULEN,R.M.J.M.LAMERICHS,L.J.BERLINER,A.DEMARCO, REMARK 1 AUTH 2 M.LLINAS,R.BOELENS,J.ALLEMAN,R.KAPTEIN REMARK 1 TITL 1H NMR CHARACTERIZATION OF TWO CRAMBIN SPECIES REMARK 1 REF FEBS LETT. V. 219 426 1987 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMOS REMARK 3 AUTHORS : VAN GUNSTEREN,BERENDSEN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CCM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172234. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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: 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 THR A 1 CA - CB - CG2 ANGL. DEV. = 8.9 DEGREES REMARK 500 1 ILE A 7 CA - CB - CG1 ANGL. DEV. = 18.1 DEGREES REMARK 500 1 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 ARG A 17 CB - CA - C ANGL. DEV. = 20.3 DEGREES REMARK 500 1 TYR A 29 CB - CG - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 THR A 1 CA - CB - CG2 ANGL. DEV. = 9.3 DEGREES REMARK 500 2 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 ARG A 17 CB - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 2 ARG A 17 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 2 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 ARG A 17 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 TYR A 29 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 ILE A 33 CG1 - CB - CG2 ANGL. DEV. = -13.8 DEGREES REMARK 500 2 TYR A 44 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 3 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 TYR A 29 CB - CG - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 3 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 4 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 4 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 TYR A 29 CB - CG - CD2 ANGL. DEV. = -5.3 DEGREES REMARK 500 4 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 5 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 5 TYR A 29 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 6 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 TYR A 29 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 7 PHE A 13 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 7 TYR A 29 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 7 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 8 PHE A 13 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 8 TYR A 29 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 8 TYR A 44 CB - CG - CD1 ANGL. DEV. = -5.3 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 THR A 21 -71.71 -8.51 REMARK 500 1 PRO A 36 -38.51 -38.71 REMARK 500 2 SER A 6 41.34 -108.67 REMARK 500 2 ILE A 7 -41.24 47.84 REMARK 500 2 THR A 21 -68.39 -148.78 REMARK 500 2 ALA A 38 -0.64 73.50 REMARK 500 3 THR A 30 50.10 -143.50 REMARK 500 3 ALA A 38 -16.49 111.41 REMARK 500 3 ALA A 45 43.70 -103.75 REMARK 500 4 THR A 2 60.09 -101.55 REMARK 500 4 THR A 21 -71.30 -147.14 REMARK 500 4 ALA A 45 78.43 -108.56 REMARK 500 5 THR A 2 73.66 -110.85 REMARK 500 5 THR A 21 -70.39 -61.14 REMARK 500 5 ALA A 45 50.40 -95.21 REMARK 500 6 THR A 2 60.19 -101.87 REMARK 500 6 THR A 21 -67.52 -149.47 REMARK 500 7 ARG A 17 40.71 -97.07 REMARK 500 7 PRO A 19 -65.88 0.24 REMARK 500 8 THR A 2 68.66 -102.51 REMARK 500 8 THR A 21 -69.28 -154.55 REMARK 500 8 THR A 30 49.12 -145.19 REMARK 500 8 ALA A 38 -29.13 48.21 REMARK 500 8 ALA A 45 35.75 -91.07 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 ARG A 17 LEU A 18 7 147.58 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 ARG A 10 0.15 SIDE CHAIN REMARK 500 1 TYR A 29 0.07 SIDE CHAIN REMARK 500 2 ARG A 17 0.11 SIDE CHAIN REMARK 500 3 TYR A 29 0.08 SIDE CHAIN REMARK 500 4 TYR A 29 0.10 SIDE CHAIN REMARK 500 6 TYR A 44 0.07 SIDE CHAIN REMARK 500 7 TYR A 29 0.08 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 2 ARG A 17 -12.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CCN RELATED DB: PDB DBREF 1CCM A 1 46 UNP P01542 CRAM_CRAAB 1 46 SEQRES 1 A 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE SEQRES 2 A 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA LEU CYS SEQRES 3 A 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR SEQRES 4 A 46 CYS PRO GLY ASP TYR ALA ASN HELIX 1 H1 ILE A 7 LEU A 18 13/10 CONFORMATION RES 17,18 12 HELIX 2 H2 GLU A 23 THR A 30 1 8 SHEET 1 S1 2 THR A 1 CYS A 4 0 SHEET 2 S1 2 CYS A 32 ILE A 35 -1 SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.03 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.04 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.05 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