HEADER PLANT PROTEIN, ANTIBIOTIC 12-MAY-05 1ZNU TITLE STRUCTURE OF CYCLOTIDE KALATA B1 IN DPC MICELLES SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: KALATA B1; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OLDENLANDIA AFFINIS; SOURCE 3 ORGANISM_TAXID: 60225 KEYWDS CYCLOTIDE, CYCLIC PEPTIDE, KNOTTIN, CYSTINE KNOT, ANTIMICROBIAL KEYWDS 2 PEPTIDE, PLANT PROTEIN, ANTIBIOTIC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.O.SHENKAREV,K.D.NADEZHDIN,V.A.SOBOL,A.G.SOBOL,L.SKJELDAL, AUTHOR 2 A.S.ARSENIEV REVDAT 4 05-FEB-20 1ZNU 1 REMARK LINK ATOM REVDAT 3 24-FEB-09 1ZNU 1 VERSN REVDAT 2 31-OCT-06 1ZNU 1 JRNL REVDAT 1 25-APR-06 1ZNU 0 JRNL AUTH Z.O.SHENKAREV,K.D.NADEZHDIN,V.A.SOBOL,A.G.SOBOL,L.SKJELDAL, JRNL AUTH 2 A.S.ARSENIEV JRNL TITL CONFORMATION AND MODE OF MEMBRANE INTERACTION IN CYCLOTIDES. JRNL TITL 2 SPATIAL STRUCTURE OF KALATA B1 BOUND TO A JRNL TITL 3 DODECYLPHOSPHOCHOLINE MICELLE. JRNL REF FEBS J. V. 273 2658 2006 JRNL REFN ISSN 1742-464X JRNL PMID 16817894 JRNL DOI 10.1111/J.1742-4658.2006.05282.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.01, CYANA 1.01 REMARK 3 AUTHORS : GUNTERT,P. (CYANA), P.GUNTERT (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NO ENERGY MINIMIZATION WAS DONE REMARK 4 REMARK 4 1ZNU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000032934. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 2.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.6MM KALATA B1, 216MM REMARK 210 PERDEUTERATED DPC, 90% H2O, 10% REMARK 210 D2O; 3.6MM KALATA B1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 LONG-RANGE HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, VNMR 6.1C, XEASY X REMARK 210 METHOD USED : SIMULATED ANNEALING IN TORSION REMARK 210 ANGLE SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED FROM 1H HOMONUCLEAR DATA IN REMARK 210 COMBINATION WITH 3JHBC' MEASURED FOR CYS RESIDUES IN D2O REMARK 210 SOLUTION. 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 OE1 GLU A 3 HG1 THR A 12 1.53 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 5 49.06 -105.05 REMARK 500 1 SER A 18 65.90 -100.41 REMARK 500 1 TRP A 19 147.89 -36.93 REMARK 500 2 CYS A 5 51.13 -105.87 REMARK 500 2 SER A 18 66.39 -101.07 REMARK 500 2 TRP A 19 148.19 -36.74 REMARK 500 3 CYS A 5 53.04 -102.65 REMARK 500 3 SER A 18 67.05 -104.13 REMARK 500 3 TRP A 19 147.23 -36.10 REMARK 500 4 CYS A 5 53.78 -102.10 REMARK 500 4 SER A 18 66.67 -102.53 REMARK 500 4 TRP A 19 147.30 -36.00 REMARK 500 5 CYS A 5 51.26 -107.72 REMARK 500 5 SER A 18 65.57 -100.98 REMARK 500 5 TRP A 19 148.04 -36.64 REMARK 500 6 CYS A 5 56.41 -107.35 REMARK 500 6 SER A 18 65.89 -104.78 REMARK 500 6 TRP A 19 147.87 -36.88 REMARK 500 7 CYS A 5 52.39 -103.08 REMARK 500 7 SER A 18 65.51 -102.31 REMARK 500 7 TRP A 19 148.05 -36.71 REMARK 500 8 CYS A 5 52.08 -100.11 REMARK 500 8 SER A 18 65.48 -101.45 REMARK 500 8 TRP A 19 147.01 -36.14 REMARK 500 9 CYS A 5 51.29 -102.18 REMARK 500 9 SER A 18 65.57 -100.54 REMARK 500 9 TRP A 19 147.47 -36.73 REMARK 500 10 CYS A 5 49.96 -102.44 REMARK 500 10 SER A 18 65.51 -100.36 REMARK 500 10 TRP A 19 147.42 -36.30 REMARK 500 11 CYS A 5 55.22 -100.34 REMARK 500 11 SER A 18 66.39 -105.88 REMARK 500 11 TRP A 19 146.70 -35.79 REMARK 500 12 CYS A 5 51.06 -97.16 REMARK 500 12 TRP A 19 147.12 -35.63 REMARK 500 13 CYS A 5 51.64 -98.97 REMARK 500 13 SER A 18 66.02 -102.23 REMARK 500 13 TRP A 19 147.13 -35.92 REMARK 500 14 CYS A 5 52.65 -98.79 REMARK 500 14 SER A 18 66.39 -102.48 REMARK 500 14 TRP A 19 147.15 -35.51 REMARK 500 15 CYS A 5 48.23 -101.70 REMARK 500 15 SER A 18 68.06 -102.68 REMARK 500 15 TRP A 19 147.02 -36.03 REMARK 500 16 CYS A 5 56.98 -104.26 REMARK 500 16 SER A 18 64.92 -105.72 REMARK 500 16 TRP A 19 147.00 -35.42 REMARK 500 17 CYS A 5 52.46 -96.67 REMARK 500 17 SER A 18 65.79 -102.31 REMARK 500 17 TRP A 19 147.23 -36.02 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KAL RELATED DB: PDB REMARK 900 FIRST STRUCTURE OF KB1 (KNOT) REMARK 900 RELATED ID: 1JJZ RELATED DB: PDB REMARK 900 STRUCTURE OF KB1 (LADDER) REMARK 900 RELATED ID: 1NB1 RELATED DB: PDB REMARK 900 REFINED STRUCTURE OF KB1 (KNOT) REMARK 900 RELATED ID: 6627 RELATED DB: BMRB DBREF 1ZNU A 1 25 UNP P56254 KAB1_OLDAF 93 117 DBREF 1ZNU A 26 29 UNP P56254 KAB1_OLDAF 89 92 SEQRES 1 A 29 CYS GLY GLU THR CYS VAL GLY GLY THR CYS ASN THR PRO SEQRES 2 A 29 GLY CYS THR CYS SER TRP PRO VAL CYS THR ARG ASN GLY SEQRES 3 A 29 LEU PRO VAL SHEET 1 A 2 CYS A 15 SER A 18 0 SHEET 2 A 2 VAL A 21 ARG A 24 -1 O THR A 23 N THR A 16 SSBOND 1 CYS A 1 CYS A 15 1555 1555 2.12 SSBOND 2 CYS A 5 CYS A 17 1555 1555 2.13 SSBOND 3 CYS A 10 CYS A 22 1555 1555 2.12 LINK N CYS A 1 C VAL A 29 1555 1555 1.33 CISPEP 1 TRP A 19 PRO A 20 1 -8.50 CISPEP 2 TRP A 19 PRO A 20 2 -8.47 CISPEP 3 TRP A 19 PRO A 20 3 -8.66 CISPEP 4 TRP A 19 PRO A 20 4 -8.51 CISPEP 5 TRP A 19 PRO A 20 5 -8.31 CISPEP 6 TRP A 19 PRO A 20 6 -8.51 CISPEP 7 TRP A 19 PRO A 20 7 -8.51 CISPEP 8 TRP A 19 PRO A 20 8 -8.56 CISPEP 9 TRP A 19 PRO A 20 9 -8.48 CISPEP 10 TRP A 19 PRO A 20 10 -8.37 CISPEP 11 TRP A 19 PRO A 20 11 -8.67 CISPEP 12 TRP A 19 PRO A 20 12 -8.65 CISPEP 13 TRP A 19 PRO A 20 13 -8.69 CISPEP 14 TRP A 19 PRO A 20 14 -8.65 CISPEP 15 TRP A 19 PRO A 20 15 -8.67 CISPEP 16 TRP A 19 PRO A 20 16 -8.61 CISPEP 17 TRP A 19 PRO A 20 17 -8.64 CISPEP 18 TRP A 19 PRO A 20 18 -8.39 CISPEP 19 TRP A 19 PRO A 20 19 -8.46 CISPEP 20 TRP A 19 PRO A 20 20 -8.57 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