HEADER PLANT PROTEIN 10-JUL-01 1JJZ TITLE REFINED STRUCTURE AND DISULFIDE PAIRING OF THE KALATA B1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KALATA-B4; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OLDENLANDIA AFFINIS; SOURCE 3 ORGANISM_TAXID: 60225; SOURCE 4 OTHER_DETAILS: EXTRACTED FROM PLANT KEYWDS CYCLIC PEPTIDE, CYCLOTIDE, DISULFIDE PAIRING, UTEROTONIC, PLANT KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.SKJELDAL,L.GRAN,K.SLETTEN,B.F.VOLKMAN REVDAT 3 12-AUG-20 1JJZ 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV SSBOND ATOM REVDAT 2 24-FEB-09 1JJZ 1 VERSN REVDAT 1 12-JUN-02 1JJZ 0 JRNL AUTH L.SKJELDAL,L.GRAN,K.SLETTEN,B.F.VOLKMAN JRNL TITL REFINED STRUCTURE AND METAL BINDING SITE OF THE KALATA B1 JRNL TITL 2 PEPTIDE. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 399 142 2002 JRNL REFN ISSN 0003-9861 JRNL PMID 11888199 JRNL DOI 10.1006/ABBI.2002.2769 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.SAETHER,D.J.CRAIK,I.D.CAMPBELL,K.SLETTEN,J.JUUL,D.G.NORMAN REMARK 1 TITL ELUCIDATION OF THE PRIMARY AND THREE-DIMENSIONAL STRUCTURE REMARK 1 TITL 2 OF THE UTEROTONIC POLYPEPTIDE KALATA B1 REMARK 1 REF BIOCHEMISTRY V. 34 4147 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : P. GUENTERT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES ARE BASED ON A TOTAL OF 333 DISTANCE CONSTRAINTS. THIS REMARK 3 INCLUDES 6 UPPER AND 6 LOWER LIMITS DEFINING 3 DISULFIDE BONDS, AS REMARK 3 WELL AS 3 UPPER AND 3 LOWER LIMITS DEFINING A PEPTIDE BOND REMARK 3 CYCLIZING THE PEPTIDE BACKBONE. REMARK 3 REMARK 3 REMARK 3 RESIDUE NUMBERING FOLLOWS THE ORIGINAL DESCRIPTION OF CITATION 1, REMARK 3 EXCEPT THAT FOR THE PURPOSES OF STRUCTURE CALCULATIONS, THE N- REMARK 3 TERMINAL RESIDUE WAS TAKEN AS ASN8. THEREFORE, RESIDUES 30-36 IN REMARK 3 THIS DEPOSITION CORRESPOND TO RESIDUES 1-7 IN CITATION 1 AND REMARK 3 RELATED PDB ENTRY 1KAL. REMARK 3 REMARK 3 REMARK 3 STRUCTURES WERE REFINED IN THE ABSENCE OF ANY ARTIFICIAL REMARK 3 CONSTRAINTS DEFINING DISULFIDE BONDS UNTIL ALL NOES HAD BEEN REMARK 3 ASSIGNED AND LOW TARGET FUNCTIONS WERE ACHIEVED (TF=0.6). 15 REMARK 3 ADDITIONAL CALCULATIONS WERE PERFORMED WITH THESE INPUT DATA AND REMARK 3 THE INCLUSION OF CONSTRAINTS DEFINING ALL POSSIBLE DISULFIDE REMARK 3 PAIRING COMBINATIONS. THE STRUCTURES CONTAINING DISULFIDES BETWEEN REMARK 3 [5(34)-13], [17-29] AND [22-27] DISPLAYED THE LOWEST TARGET REMARK 3 FUNCTION (0.74, SECOND LOWEST WAS 1.54). ON THE BASIS OF THIS REMARK 3 RESULT AND ANALYSIS OF NOES OBSERVED BETWEEN CYS SIDECHAIN PROTONS, REMARK 3 THIS DISULFIDE BONDING ARRANGEMENT WAS ASSUMED TO BE CORRECT AND REMARK 3 SERVED AS THE BASIS FOR THIS DEPOSITION. REMARK 4 REMARK 4 1JJZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013862. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM KALATA B1; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, XEASY 1.3.11 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING NOES FROM A SINGLE 100 MS REMARK 210 MIXING TIME NOESY EXPERIMENT 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE KALATA B1 IS CYCLIC PEPTIDE, A MEMBER OF ANTIMICROBIAL, REMARK 400 ANTITUMOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: KALATA B1 REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 N ASN A 1 C ARG A 29 1.37 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 CYS A 10 68.76 -154.46 REMARK 500 1 ASN A 16 16.01 59.86 REMARK 500 1 CYS A 22 114.56 -38.81 REMARK 500 1 TRP A 24 137.26 62.46 REMARK 500 2 CYS A 10 65.90 -153.93 REMARK 500 2 ASN A 16 -1.05 82.43 REMARK 500 2 CYS A 22 109.78 -39.93 REMARK 500 2 TRP A 24 137.62 62.73 REMARK 500 3 VAL A 5 22.82 -142.24 REMARK 500 3 CYS A 10 66.70 -153.36 REMARK 500 3 CYS A 22 113.32 -38.26 REMARK 500 3 TRP A 24 136.22 62.37 REMARK 500 4 LEU A 3 109.41 -52.54 REMARK 500 4 CYS A 10 62.86 -155.54 REMARK 500 4 CYS A 22 112.37 -36.68 REMARK 500 4 TRP A 24 136.72 62.59 REMARK 500 5 VAL A 5 23.52 -142.39 REMARK 500 5 CYS A 10 66.07 -154.28 REMARK 500 5 ASN A 16 -0.93 84.33 REMARK 500 5 CYS A 22 114.43 -38.29 REMARK 500 5 TRP A 24 135.97 62.22 REMARK 500 6 ASN A 16 -0.93 82.53 REMARK 500 6 TRP A 24 138.69 61.87 REMARK 500 7 VAL A 5 20.77 -143.79 REMARK 500 7 CYS A 10 68.91 -153.13 REMARK 500 7 ASN A 16 -0.98 79.26 REMARK 500 7 TRP A 24 135.61 62.16 REMARK 500 8 CYS A 10 71.57 -155.93 REMARK 500 8 CYS A 22 118.94 -39.59 REMARK 500 8 TRP A 24 135.27 62.32 REMARK 500 9 CYS A 10 71.63 -152.28 REMARK 500 9 ASN A 16 -1.20 79.57 REMARK 500 9 CYS A 22 112.53 -37.51 REMARK 500 9 TRP A 24 136.71 62.58 REMARK 500 10 CYS A 10 74.80 -152.50 REMARK 500 10 ASN A 16 -1.80 83.27 REMARK 500 10 CYS A 22 114.85 -38.86 REMARK 500 10 TRP A 24 135.94 62.65 REMARK 500 11 VAL A 5 22.42 -145.10 REMARK 500 11 CYS A 10 68.75 -154.59 REMARK 500 11 CYS A 22 113.98 -39.05 REMARK 500 11 TRP A 24 134.26 62.42 REMARK 500 12 CYS A 10 72.58 -155.18 REMARK 500 12 TRP A 24 135.45 62.33 REMARK 500 13 VAL A 5 24.92 -140.77 REMARK 500 13 CYS A 10 71.86 -154.58 REMARK 500 13 CYS A 22 118.88 -38.55 REMARK 500 13 TRP A 24 134.99 62.43 REMARK 500 14 VAL A 5 23.64 -147.84 REMARK 500 14 CYS A 10 73.46 -151.81 REMARK 500 REMARK 500 THIS ENTRY HAS 75 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KAL RELATED DB: PDB REMARK 900 ELUCIDATION OF THE PRIMARY AND THREE-DIMENSIONAL STRUCTURE OF THE REMARK 900 UTEROTONIC POLYPEPTIDE KALATA B1 DBREF 1JJZ A 2 29 UNP P83938 KAB4_OLDAF 1 28 SEQADV 1JJZ ASN A 1 UNP P83938 EXPRESSION TAG SEQRES 1 A 29 ASN GLY LEU PRO VAL CYS GLY GLU THR CYS VAL GLY GLY SEQRES 2 A 29 THR CYS ASN THR PRO GLY CYS THR CYS SER TRP PRO VAL SEQRES 3 A 29 CYS THR ARG SSBOND 1 CYS A 6 CYS A 27 1555 1555 1.98 SSBOND 2 CYS A 10 CYS A 22 1555 1555 2.11 SSBOND 3 CYS A 15 CYS A 20 1555 1555 2.00 CISPEP 1 TRP A 24 PRO A 25 1 -0.02 CISPEP 2 TRP A 24 PRO A 25 2 0.02 CISPEP 3 TRP A 24 PRO A 25 3 -0.05 CISPEP 4 TRP A 24 PRO A 25 4 -0.04 CISPEP 5 TRP A 24 PRO A 25 5 0.05 CISPEP 6 TRP A 24 PRO A 25 6 -0.01 CISPEP 7 TRP A 24 PRO A 25 7 -0.04 CISPEP 8 TRP A 24 PRO A 25 8 0.01 CISPEP 9 TRP A 24 PRO A 25 9 0.05 CISPEP 10 TRP A 24 PRO A 25 10 0.00 CISPEP 11 TRP A 24 PRO A 25 11 0.07 CISPEP 12 TRP A 24 PRO A 25 12 -0.10 CISPEP 13 TRP A 24 PRO A 25 13 0.02 CISPEP 14 TRP A 24 PRO A 25 14 0.06 CISPEP 15 TRP A 24 PRO A 25 15 0.02 CISPEP 16 TRP A 24 PRO A 25 16 0.01 CISPEP 17 TRP A 24 PRO A 25 17 0.06 CISPEP 18 TRP A 24 PRO A 25 18 -0.01 CISPEP 19 TRP A 24 PRO A 25 19 -0.07 CISPEP 20 TRP A 24 PRO A 25 20 0.03 CRYST1 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