PDB Short entry for 1RL5 HEADER TOXIN 25-NOV-03 1RL5 TITLE NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULE OF CYTOTOXIN I FROM TITLE 2 NAJA OXIANA IN AQUEOUS SOLUTION (MAJOR FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIN 1; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: CENTRAL ASIAN COBRA; SOURCE 4 ORGANISM_TAXID: 8657; SOURCE 5 SECRETION: VENOME KEYWDS S-TYPE CYTOTOXIN, MEMBRANE PERTURBATION, CIS/TRANS ISOMERIZATION, KEYWDS 2 BOUND WATER, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.A.DUBINNYI,Y.E.PUSTOVALOVA,P.V.DUBOVSKII,Y.N.UTKIN,A.S.ARSENIEV REVDAT 4 02-MAR-22 1RL5 1 REMARK REVDAT 3 24-FEB-09 1RL5 1 VERSN REVDAT 2 17-MAY-05 1RL5 1 JRNL REVDAT 1 15-FEB-05 1RL5 0 JRNL AUTH P.V.DUBOVSKII,D.M.LESOVOY,M.A.DUBINNYI,A.G.KONSHINA, JRNL AUTH 2 Y.N.UTKIN,R.G.EFREMOV,A.S.ARSENIEV JRNL TITL INTERACTION OF THREE-FINGER TOXINS WITH PHOSPHOLIPID JRNL TITL 2 MEMBRANES: COMPARISON OF S- AND P-TYPE CYTOTOXINS. JRNL REF BIOCHEM.J. V. 387 807 2005 JRNL REFN ISSN 0264-6021 JRNL PMID 15584897 JRNL DOI 10.1042/BJ20041814 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1.A, CYANA 1.0.6 REMARK 3 AUTHORS : GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 478 NOE-DERIVED CONSTRAINTS, 202 REMARK 3 ANGULAR CONSTRAINTS, 186 CONSTRAINTS FOR 31 HYDROGEN BONDS, 24 REMARK 3 CONSTRAINTS FOR 4 SS-BONDS REMARK 4 REMARK 4 1RL5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020856. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 MM REMARK 210 PRESSURE : NORMAL REMARK 210 SAMPLE CONTENTS : 20MM CYTOTOXIN I, 50MM KCL, H2O; REMARK 210 20MM CYTOTOXIN I, 50MM KCL, D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY 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 3.1.A, XEASY 1.2.11, REMARK 210 CYANA 1.0.6, NMRPIPE APRIL 12, REMARK 210 2001, ACME 2001.085.20.47 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CYTOTOXIN I MAJOR AND MINOR CONFORMATIONAL STATES (IN REMARK 210 RATIO OF 6:1) IN AQUEOUS SOLUTION, CORRESPONDING TO TRANS AND REMARK 210 CIS VAL7-PRO8 PEPTIDE BOND CONFORMATIONS, WERE ESTABLISHED VIA REMARK 210 NMR SPECTRA ANALYSIS. HERE IS THE OBTAINED MAJOR STRUCTURE OF REMARK 210 CYTOTOXIN I. THE PRESENTED AT HETATM SECTION HOH IN EACH MODEL REMARK 210 ARE TIGHTLY BOUND WATER MOLECULES (WITH LONGER THAN FOR BULK REMARK 210 WATER LIFETIMES NEARBY PROTEIN), REAVELED BY NMR APPROACH. THE REMARK 210 PRINCIPLE OF APPORTIONMENT OF THESE WATER MOLECULES DIFFERS FROM REMARK 210 THAT IN CRYSTAL STRUCTURES, FOR WHICH THE WATER MOLECULES BEING REMARK 210 AT THE PROXIMITY TO PROTEIN ARE INDICATED. 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 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 PRO A 8 10.99 -60.16 REMARK 500 1 PRO A 15 165.22 -47.66 REMARK 500 1 SER A 28 -96.30 -64.22 REMARK 500 1 PRO A 33 167.74 -45.91 REMARK 500 1 ARG A 58 40.09 39.22 REMARK 500 2 PRO A 8 9.79 -61.42 REMARK 500 2 PRO A 15 165.01 -48.03 REMARK 500 2 SER A 28 -99.64 -68.98 REMARK 500 2 PRO A 33 152.62 -48.61 REMARK 500 2 ARG A 58 41.16 38.09 REMARK 500 3 PRO A 8 10.85 -60.11 REMARK 500 3 PRO A 15 170.40 -48.25 REMARK 500 3 ASN A 19 -44.59 -145.50 REMARK 500 3 SER A 28 -102.01 -72.70 REMARK 500 3 ARG A 58 39.97 38.39 REMARK 500 4 PRO A 8 10.11 -59.84 REMARK 500 4 PRO A 15 172.42 -47.72 REMARK 500 4 SER A 28 -94.94 -64.25 REMARK 500 4 ARG A 58 42.51 37.69 REMARK 500 5 PRO A 8 13.15 -59.89 REMARK 500 5 PRO A 15 169.66 -48.28 REMARK 500 5 ASN A 19 -40.90 -145.72 REMARK 500 5 SER A 28 -96.76 -67.63 REMARK 500 5 PRO A 33 170.93 -47.38 REMARK 500 5 ARG A 58 37.93 38.20 REMARK 500 6 LYS A 5 -156.21 -95.03 REMARK 500 6 PRO A 8 14.67 -60.54 REMARK 500 6 PRO A 15 173.86 -48.15 REMARK 500 6 SER A 28 -97.64 -71.23 REMARK 500 6 ARG A 58 41.62 37.53 REMARK 500 7 PRO A 8 9.27 -61.87 REMARK 500 7 PRO A 15 167.33 -48.11 REMARK 500 7 ASN A 19 -44.05 -145.62 REMARK 500 7 SER A 28 -89.18 -64.60 REMARK 500 7 ARG A 58 39.68 38.03 REMARK 500 8 PRO A 8 12.30 -60.03 REMARK 500 8 PRO A 15 166.76 -48.62 REMARK 500 8 ASN A 19 -42.65 -145.63 REMARK 500 8 SER A 28 -101.60 -66.09 REMARK 500 8 ARG A 58 37.94 36.37 REMARK 500 9 PRO A 8 10.25 -60.06 REMARK 500 9 LYS A 12 -159.94 -135.60 REMARK 500 9 PRO A 15 176.21 -48.45 REMARK 500 9 ASN A 19 -44.77 -145.49 REMARK 500 9 SER A 28 -95.41 -65.34 REMARK 500 9 ARG A 58 43.38 37.68 REMARK 500 10 PRO A 8 9.16 -59.82 REMARK 500 10 PRO A 15 174.60 -47.95 REMARK 500 10 ASN A 19 -44.04 -145.69 REMARK 500 10 SER A 28 -100.18 -65.91 REMARK 500 REMARK 500 THIS ENTRY HAS 103 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5989 RELATED DB: BMRB REMARK 900 1H CHEMICAL SHIFTS AND COUPLING CONSTANTS DBREF 1RL5 A 1 60 UNP P01451 CX1_NAJOX 1 60 SEQRES 1 A 60 LEU LYS CYS ASN LYS LEU VAL PRO ILE ALA TYR LYS THR SEQRES 2 A 60 CYS PRO GLU GLY LYS ASN LEU CYS TYR LYS MET PHE MET SEQRES 3 A 60 MET SER ASP LEU THR ILE PRO VAL LYS ARG GLY CYS ILE SEQRES 4 A 60 ASP VAL CYS PRO LYS ASN SER LEU LEU VAL LYS TYR VAL SEQRES 5 A 60 CYS CYS ASN THR ASP ARG CYS ASN FORMUL 2 HOH *(H2 O) SHEET 1 A 2 LYS A 2 ASN A 4 0 SHEET 2 A 2 TYR A 11 THR A 13 -1 O LYS A 12 N CYS A 3 SHEET 1 B 3 LYS A 35 ILE A 39 0 SHEET 2 B 3 LEU A 20 MET A 26 -1 N LEU A 20 O ILE A 39 SHEET 3 B 3 VAL A 49 CYS A 54 -1 O CYS A 54 N CYS A 21 SSBOND 1 CYS A 3 CYS A 21 1555 1555 1.99 SSBOND 2 CYS A 14 CYS A 38 1555 1555 1.99 SSBOND 3 CYS A 42 CYS A 53 1555 1555 1.99 SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.00 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