HEADER TOXIN 26-DEC-13 2MJ4 TITLE NEUROTOXIN II FROM SNAKE VENOM NAJA OXIANA IN SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHORT NEUROTOXIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEUROTOXIN II, NTX II, NEUROTOXIN ALPHA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: OXUS COBRA; SOURCE 4 ORGANISM_TAXID: 8657; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: NTII KEYWDS 13C RELAXATION, SIDE CHAIN DYNAMICS, MOLECULAR DYNAMICS, MOLECULAR KEYWDS 2 MECHANICS FORCE FIELDS, OPTIMIZATION, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.M.LESOVOY,S.B.NOLDE,E.V.BOCHAROV,E.N.LYUKMANOVA,A.S.ARSENIEV REVDAT 1 28-JAN-15 2MJ4 0 JRNL AUTH D.M.LESOVOY,S.B.NOLDE,E.V.BOCHAROV,E.N.LYUKMANOVA, JRNL AUTH 2 A.S.ARSENIEV JRNL TITL AN NMR-BASED APPROACH FOR VALIDATION OF PROTEIN SIDE-CHAINS JRNL TITL 2 DYNAMICS IN SILICO JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE 1H-1H NOE AMPLITUDES SHOULD BE REMARK 3 TREATED ONLY ACCORDING TO THE FLEXIBILITY OF THE CORRESPONDING REMARK 3 BACKBONE OR SIDE CHAIN GROUPS: DERIVED FROM THE HETERONUCLEAR REMARK 3 NOE, R1, R2, 1CHCH(DIPOLAR CROSS-CORRELATION CONTRIBUTION TO R1), REMARK 3 2CHCH(DIPOLAR CROSS-CORRELATION CONTRIBUTION TO R2), AND 3J REMARK 3 SCALAR COUPLING CONSTANT VALUES. REMARK 4 REMARK 4 2MJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB103674. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 NEUROTOXIN II-1, 0.3 MM SODIUM REMARK 210 AZIDE-2, 10 MM CITRIC ACID-3, 20 REMARK 210 MM NA2HPO4-4, 95% H2O/5% D2O; 1 REMARK 210 MM [U-99% 15N] NEUROTOXIN II-5, REMARK 210 0.3 MM SODIUM AZIDE-6, 10 MM REMARK 210 CITRIC ACID-7, 20 MM NA2HPO4-8, REMARK 210 100% D2O; 1 MM [U-99% 15N] REMARK 210 NEUROTOXIN II-9, 0.3 MM SODIUM REMARK 210 AZIDE-10, 10 MM CITRIC ACID-11, REMARK 210 20 MM NA2HPO4-12, 50% H2O/50% REMARK 210 D2O; 2 MM NEUROTOXIN II-13, 0.3 REMARK 210 MM SODIUM AZIDE-14, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 13C-15N HSQC CARBON; REMARK 210 2D 13C->13C CARBON; 2D 1H->(13C)- REMARK 210 >13C CARBON; 3D HNCO; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HN(CA)CO; 3D HCCH- REMARK 210 TOCSY; 3D HNHA; 3D HNHB; 2D DQF- REMARK 210 COSY; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-15N CLEANEX; 2D REMARK 210 1H-15N HSQC H/D; 2D 1H-15N 15N REMARK 210 R1; 2D 1H-15N NH-NH/15N R1; 2D 1H REMARK 210 -15N 15N R2; 2D 1H-15N 15N-1H REMARK 210 NOE; 2D 1H-13C 13C R1; 2D 1H-13C REMARK 210 13C-1H NOE; 2D 1H-13C CH-CH/13C REMARK 210 R1; 2D 1H-13C CH-CH/13C R2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, CARA 1.8.4, REMARK 210 MATHEMATICA, NMRPIPE(ACME) 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 : 1 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: 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 SER A 8 -135.37 35.49 REMARK 500 1 GLN A 10 168.83 -44.24 REMARK 500 1 PRO A 43 -179.49 -69.81 REMARK 500 1 ASN A 60 46.79 -95.10 REMARK 500 2 SER A 8 -132.40 35.04 REMARK 500 2 GLN A 10 168.86 -44.70 REMARK 500 2 THR A 21 15.34 -140.53 REMARK 500 2 PRO A 43 -179.14 -69.81 REMARK 500 2 ASN A 60 47.26 -95.18 REMARK 500 3 SER A 8 -133.41 36.04 REMARK 500 3 GLN A 10 168.71 -44.47 REMARK 500 3 PRO A 43 -179.28 -69.79 REMARK 500 3 ASN A 60 48.81 -95.47 REMARK 500 4 SER A 8 -133.73 34.81 REMARK 500 4 GLN A 10 169.15 -44.42 REMARK 500 4 PRO A 43 -179.44 -69.75 REMARK 500 4 ASN A 60 49.11 -95.49 REMARK 500 5 SER A 8 -133.06 34.66 REMARK 500 5 GLN A 10 169.14 -44.44 REMARK 500 5 ASN A 60 48.70 -95.44 REMARK 500 6 SER A 8 -135.21 35.11 REMARK 500 6 GLN A 10 169.13 -44.28 REMARK 500 6 PRO A 43 -179.21 -69.78 REMARK 500 6 ASN A 60 48.62 -95.44 REMARK 500 7 SER A 8 -135.27 34.97 REMARK 500 7 GLN A 10 169.10 -44.26 REMARK 500 7 PRO A 43 -179.09 -69.84 REMARK 500 7 ASN A 60 49.48 -95.55 REMARK 500 8 SER A 8 -133.71 34.57 REMARK 500 8 GLN A 10 169.23 -44.15 REMARK 500 8 ASN A 60 48.65 -95.41 REMARK 500 9 SER A 8 -135.18 47.77 REMARK 500 9 GLN A 10 170.14 -58.98 REMARK 500 9 PRO A 43 -179.35 -69.82 REMARK 500 9 ASN A 60 44.80 -94.71 REMARK 500 10 SER A 8 -133.26 54.54 REMARK 500 10 GLN A 10 169.60 -44.61 REMARK 500 10 PRO A 43 -179.48 -69.88 REMARK 500 10 ASN A 60 48.55 -95.45 REMARK 500 11 SER A 8 -136.62 38.53 REMARK 500 11 PRO A 43 -178.93 -69.82 REMARK 500 11 ASN A 60 47.78 -95.29 REMARK 500 12 SER A 8 -128.67 36.62 REMARK 500 12 GLN A 10 168.26 -44.42 REMARK 500 12 PRO A 43 -179.52 -69.80 REMARK 500 12 ASN A 60 42.97 -94.31 REMARK 500 13 SER A 8 -135.48 47.35 REMARK 500 13 ASN A 60 43.23 -94.37 REMARK 500 14 SER A 8 -135.19 34.58 REMARK 500 14 GLN A 10 169.20 -44.26 REMARK 500 REMARK 500 THIS ENTRY HAS 74 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NOR RELATED DB: PDB REMARK 900 OLD STRUCTURE AT PH=3.0 REMARK 900 RELATED ID: 5052 RELATED DB: BMRB REMARK 900 OLD 1H CHEMICAL SHIFTS AT PH=3.0 REMARK 900 RELATED ID: 5690 RELATED DB: BMRB REMARK 900 CURRENT DATA IS THE REFINEMENT OF THE OLD ONE REMARK 900 RELATED ID: 19704 RELATED DB: BMRB DBREF 2MJ4 A 1 61 UNP P01427 NXS1_NAJOX 1 61 SEQRES 1 A 61 LEU GLU CYS HIS ASN GLN GLN SER SER GLN PRO PRO THR SEQRES 2 A 61 THR LYS THR CYS SER GLY GLU THR ASN CYS TYR LYS LYS SEQRES 3 A 61 TRP TRP SER ASP HIS ARG GLY THR ILE ILE GLU ARG GLY SEQRES 4 A 61 CYS GLY CYS PRO LYS VAL LYS PRO GLY VAL ASN LEU ASN SEQRES 5 A 61 CYS CYS ARG THR ASP ARG CYS ASN ASN SHEET 1 A 2 GLU A 2 CYS A 3 0 SHEET 2 A 2 LYS A 15 THR A 16 -1 O LYS A 15 N CYS A 3 SHEET 1 B 3 ILE A 35 CYS A 40 0 SHEET 2 B 3 CYS A 23 TRP A 28 -1 N TRP A 28 O ILE A 35 SHEET 3 B 3 ASN A 50 CYS A 54 -1 O CYS A 54 N CYS A 23 SSBOND 1 CYS A 3 CYS A 23 1555 1555 2.10 SSBOND 2 CYS A 3 CYS A 17 1555 1555 2.46 SSBOND 3 CYS A 17 CYS A 40 1555 1555 2.11 SSBOND 4 CYS A 42 CYS A 53 1555 1555 2.10 SSBOND 5 CYS A 54 CYS A 59 1555 1555 1.98 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