PDB Short entry for 1NTN HEADER POSTSYNAPTIC NEUROTOXIN 26-SEP-94 1NTN TITLE THE CRYSTAL STRUCTURE OF NEUROTOXIN-I FROM NAJA NAJA OXIANA AT 1.9 TITLE 2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTOXIN I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: CENTRAL ASIAN COBRA; SOURCE 4 ORGANISM_TAXID: 8657 KEYWDS POSTSYNAPTIC NEUROTOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.MIKHAILOV,A.V.NICKITENKO,B.K.VAINSHTEIN,C.BETZEL,K.WILSON REVDAT 3 29-NOV-17 1NTN 1 HELIX REVDAT 2 24-FEB-09 1NTN 1 VERSN REVDAT 1 08-MAY-95 1NTN 0 JRNL AUTH A.V.NICKITENKO,A.M.MICHAILOV,C.BETZEL,K.S.WILSON JRNL TITL THREE-DIMENSIONAL STRUCTURE OF NEUROTOXIN-1 FROM NAJA NAJA JRNL TITL 2 OXIANA VENOM AT 1.9 A RESOLUTION. JRNL REF FEBS LETT. V. 320 111 1993 JRNL REFN ISSN 0014-5793 JRNL PMID 8458425 JRNL DOI 10.1016/0014-5793(93)80073-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.V.NICKITENKO,A.M.MIKHAILOV,C.BETZEL,K.S.WILSON REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF NEUROTOXIN-1 FROM NAJA NAJA REMARK 1 TITL 2 OXIANA VENOM AT 1.9 ANGSTROMS RESOLUTION REMARK 1 REF FEBS LETT. V. 320 111 1993 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.M.MIKHAILOV,A.V.NICKITENKO,E.V.CHETVERINA,S.D.TRAKHANOV, REMARK 1 AUTH 2 B.K.VAINSHTEIN REMARK 1 TITL SPATIAL ORGANIZATION OF BACKBONE OF THE NEUROTOXIN-I REMARK 1 TITL 2 MOLECULE FROM THE NAJA NAJA OXIANA VENOM AND ITS CRYSTAL REMARK 1 TITL 3 PACKING (IN RUSSIAN) REMARK 1 REF BIOORG.KHIM. V. 17 372 1991 REMARK 1 REFN ISSN 0132-3423 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.M.MIKHAILOV,A.V.NICKITENKO,S.D.TRAKHANOV,B.K.VAINSHTEIN, REMARK 1 AUTH 2 E.V.CHETVERINA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDY OF REMARK 1 TITL 2 NEUROTOXIN-I FROM NAJA NAJA OXIANA VENOM REMARK 1 REF FEBS LETT. V. 269 255 1990 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 530 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.020 ; 0.014 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.056 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.040 ; 0.062 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.020 ; 0.018 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.200 ; 0.227 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.300 ; 0.214 REMARK 3 MULTIPLE TORSION (A) : 0.300 ; 0.324 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.300 ; 0.216 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.000 ; 3.300 REMARK 3 STAGGERED (DEGREES) : 20.000; 25.700 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 69 - 71 ARE POORLY DEFINED IN REMARK 3 THE ELECTRON-DENSITY MAP AND IN REFINEMENT REMARK 4 REMARK 4 1NTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 17.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.79000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.79000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 69 CB CG CD OE1 NE2 REMARK 470 LYS A 70 CB CG CD CE NZ REMARK 470 ARG A 71 CB CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB ASP A 28 CG PRO A 72 1455 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 4 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 THR A 6 N - CA - CB ANGL. DEV. = -14.4 DEGREES REMARK 500 PRO A 7 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 ILE A 8 N - CA - CB ANGL. DEV. = 20.5 DEGREES REMARK 500 ILE A 8 O - C - N ANGL. DEV. = 11.3 DEGREES REMARK 500 GLU A 12 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 GLU A 12 CG - CD - OE2 ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 34 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LYS A 36 CB - CG - CD ANGL. DEV. = 21.4 DEGREES REMARK 500 LYS A 36 CG - CD - CE ANGL. DEV. = 23.7 DEGREES REMARK 500 ILE A 38 CA - CB - CG2 ANGL. DEV. = 12.6 DEGREES REMARK 500 THR A 48 N - CA - CB ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU A 50 CG - CD - OE2 ANGL. DEV. = 12.1 DEGREES REMARK 500 TYR A 52 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR A 52 CB - CG - CD1 ANGL. DEV. = -6.8 DEGREES REMARK 500 SER A 59 N - CA - CB ANGL. DEV. = -9.8 DEGREES REMARK 500 THR A 60 O - C - N ANGL. DEV. = 11.0 DEGREES REMARK 500 ASP A 61 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 61 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 GLN A 69 N - CA - C ANGL. DEV. = 28.1 DEGREES 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 ILE A 9 123.07 -20.66 REMARK 500 PRO A 67 21.28 -77.23 REMARK 500 GLN A 69 -108.88 -53.57 REMARK 500 LYS A 70 115.05 -176.88 REMARK 500 ARG A 71 -112.31 -177.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NTN A 1 72 UNP P01382 NXL1_NAJOX 1 73 SEQADV 1NTN A UNP P01382 PRO 9 DELETION SEQADV 1NTN ASN A 62 UNP P01382 ASP 63 CONFLICT SEQRES 1 A 72 ILE THR CYS TYR LYS THR PRO ILE ILE THR SER GLU THR SEQRES 2 A 72 CYS ALA PRO GLY GLN ASN LEU CYS TYR THR LYS THR TRP SEQRES 3 A 72 CYS ASP ALA TRP CYS GLY SER ARG GLY LYS VAL ILE GLU SEQRES 4 A 72 LEU GLY CYS ALA ALA THR CYS PRO THR VAL GLU SER TYR SEQRES 5 A 72 GLN ASP ILE LYS CYS CYS SER THR ASP ASN CYS ASN PRO SEQRES 6 A 72 HIS PRO LYS GLN LYS ARG PRO FORMUL 2 HOH *65(H2 O) HELIX 1 1 TRP A 30 GLY A 35 1 6 SHEET 1 S1 2 THR A 2 LYS A 5 0 SHEET 2 S1 2 THR A 10 THR A 13 -1 O THR A 10 N LYS A 5 SHEET 1 S2 3 VAL A 37 ALA A 43 0 SHEET 2 S2 3 LEU A 20 TRP A 26 -1 N TRP A 26 O VAL A 37 SHEET 3 S2 3 GLN A 53 CYS A 58 -1 N ASP A 54 O THR A 25 SSBOND 1 CYS A 3 CYS A 21 1555 1555 2.07 SSBOND 2 CYS A 14 CYS A 42 1555 1555 1.99 SSBOND 3 CYS A 27 CYS A 31 1555 1555 2.07 SSBOND 4 CYS A 46 CYS A 57 1555 1555 2.05 SSBOND 5 CYS A 58 CYS A 63 1555 1555 2.05 CISPEP 1 THR A 6 PRO A 7 0 2.12 CRYST1 25.170 75.580 35.860 90.00 90.00 90.00 P 21 21 21 4 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 0.039730 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027886 0.00000