HEADER TOXIN 07-SEP-16 5T8A TITLE RECOMBINANT CYTOTOXIN-I FROM THE VENOM OF COBRA N. OXIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOTOXIN I,CTI; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THIS TOXIN FEATURES THE PRESENCE OF AN ADDITIONAL MET- COMPND 7 RESIDUE AT THE N-TERMINUS, COMPARED TO THE NATIVE TOXIN, ISOLATED COMPND 8 FROM COBRA VENOM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: CENTRAL ASIAN COBRA; SOURCE 4 ORGANISM_TAXID: 8657; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET-22B(+) KEYWDS TOXIN, CYTOLYTIC PEPTIDE, ALL-BETA SHEET PROTEIN, RECOMBINANT KEYWDS 2 PRODUCTION, STRUCTURE FROM MOLMOL EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.V.DUBOVSKII,M.A.DUBINNYI,M.A.SHULEPKO,E.N.LYUKMANOVA,D.A.DOLGIKH, AUTHOR 2 M.P.KIRPICHNIKOV,R.G.EFREMOV REVDAT 4 20-NOV-24 5T8A 1 REMARK REVDAT 3 08-MAY-19 5T8A 1 REMARK REVDAT 2 08-NOV-17 5T8A 1 JRNL REVDAT 1 20-SEP-17 5T8A 0 JRNL AUTH P.V.DUBOVSKII,M.A.DUBINNYI,A.G.KONSHINA,E.D.KAZAKOVA, JRNL AUTH 2 G.M.SOROKOUMOVA,T.M.ILYASOVA,M.A.SHULEPKO,R.V.CHERTKOVA, JRNL AUTH 3 E.N.LYUKMANOVA,D.A.DOLGIKH,A.S.ARSENIEV,R.G.EFREMOV JRNL TITL STRUCTURAL AND DYNAMIC "PORTRAITS" OF RECOMBINANT AND NATIVE JRNL TITL 2 CYTOTOXIN I FROM NAJA OXIANA: HOW CLOSE ARE THEY? JRNL REF BIOCHEMISTRY V. 56 4468 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28749688 JRNL DOI 10.1021/ACS.BIOCHEM.7B00453 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.0.6, ROSETTA 3.3 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), DAVID REMARK 3 BAKER, UNIVERSITY OF WASHINGTON (ROSETTA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AS IN: J AM CHEM SOC. 2014 FEB REMARK 3 5;136(5):1893-90. PROTEIN NMR STRUCTURES REFINED WITH ROSETTA REMARK 3 HAVE HIGHER ACCURACY RELATIVE TO CORRESPONDING X-RAY CRYSTAL REMARK 3 STRUCTURES. MAO B, TEJERO R, BAKER D, MONTELIONE GT. REMARK 4 REMARK 4 5T8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223758. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 101325 PA REMARK 210 SAMPLE CONTENTS : 1 MM U-99% 13C; U-99% 15N REMARK 210 RECOMBINANT CYTOTOXIN-I, 95 V/V REMARK 210 NON-LABELED H2O, 5 V/V 99.9% 2H REMARK 210 D2O, 3 UM NON-LABELED NAOH, 1 UM REMARK 210 NON-LABELED HCL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D HNCO; 3D REMARK 210 HN(COCA)CB; 3D HCCH-TOCSY; 2D 1H- REMARK 210 15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 1D- REMARK 210 WATERGATE REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.0.A, CARA 1.8.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 ASN A 19 -49.40 -135.60 REMARK 500 1 SER A 28 -76.64 -62.35 REMARK 500 2 ASN A 19 -46.96 -135.73 REMARK 500 3 ASN A 19 -29.05 -153.67 REMARK 500 3 SER A 28 -75.85 -61.91 REMARK 500 4 ASN A 19 -28.42 -152.02 REMARK 500 4 SER A 28 -76.09 -60.39 REMARK 500 5 ASN A 19 -28.12 -153.94 REMARK 500 6 ASN A 19 -30.05 -151.19 REMARK 500 6 SER A 28 -75.99 -60.07 REMARK 500 7 ASN A 19 -46.98 -135.91 REMARK 500 7 SER A 28 -76.18 -61.09 REMARK 500 8 ASN A 19 -27.80 -153.52 REMARK 500 9 ASN A 19 -31.12 -152.34 REMARK 500 10 ASN A 19 -50.49 -136.16 REMARK 500 11 ASN A 19 -47.64 -136.79 REMARK 500 11 SER A 28 -75.99 -60.93 REMARK 500 12 ASN A 19 -45.88 -136.33 REMARK 500 13 LEU A 1 -179.20 -67.08 REMARK 500 13 ASN A 19 -28.52 -154.05 REMARK 500 14 ASN A 19 -46.66 -137.09 REMARK 500 14 SER A 28 -76.56 -61.35 REMARK 500 15 ASN A 19 -27.30 -154.05 REMARK 500 15 SER A 28 -76.69 -61.76 REMARK 500 16 ASN A 19 -27.81 -153.30 REMARK 500 17 ASN A 19 -29.17 -151.52 REMARK 500 17 SER A 28 -76.13 -62.25 REMARK 500 18 ASN A 19 -29.89 -150.98 REMARK 500 18 SER A 28 -75.99 -61.13 REMARK 500 19 ASN A 19 -47.73 -136.48 REMARK 500 19 SER A 28 -77.30 -62.39 REMARK 500 20 ASN A 19 -47.53 -135.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RL5 RELATED DB: PDB REMARK 900 1RL5 HAS THE SAME AMINO ACID SEQUENCE, LACKING ONLY THE N-TERMINAL REMARK 900 MET-RESIDUE REMARK 900 RELATED ID: 1ZAD RELATED DB: PDB REMARK 900 SAME AS 1RL5, BUT EMBEDDED INTO A DETERGENT MICELLE REMARK 900 RELATED ID: 30172 RELATED DB: BMRB REMARK 900 RECOMBINANT CYTOTOXIN-I FROM THE VENOM OF COBRA N. OXIANA DBREF 5T8A A 1 60 UNP P01451 3SA1_NAJOX 1 60 SEQADV 5T8A MET A 0 UNP P01451 INITIATING METHIONINE SEQRES 1 A 61 MET LEU LYS CYS ASN LYS LEU VAL PRO ILE ALA TYR LYS SEQRES 2 A 61 THR CYS PRO GLU GLY LYS ASN LEU CYS TYR LYS MET PHE SEQRES 3 A 61 MET MET SER ASP LEU THR ILE PRO VAL LYS ARG GLY CYS SEQRES 4 A 61 ILE ASP VAL CYS PRO LYS ASN SER LEU LEU VAL LYS TYR SEQRES 5 A 61 VAL CYS CYS ASN THR ASP ARG CYS ASN SHEET 1 AA1 2 LYS A 2 ASN A 4 0 SHEET 2 AA1 2 TYR A 11 THR A 13 -1 O LYS A 12 N CYS A 3 SHEET 1 AA2 3 LYS A 35 ILE A 39 0 SHEET 2 AA2 3 LEU A 20 MET A 26 -1 N MET A 24 O LYS A 35 SHEET 3 AA2 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 2.02 SSBOND 2 CYS A 14 CYS A 38 1555 1555 2.03 SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.02 SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.03 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