PDB Short entry for 1DTX HEADER PRESYNAPTIC NEUROTOXIN 29-APR-91 1DTX TITLE CRYSTAL STRUCTURE OF ALPHA-DENDROTOXIN FROM THE GREEN MAMBA VENOM AND TITLE 2 ITS COMPARISON WITH THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN TITLE 3 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-DENDROTOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENDROASPIS ANGUSTICEPS; SOURCE 3 ORGANISM_COMMON: EASTERN GREEN MAMBA; SOURCE 4 ORGANISM_TAXID: 8618 KEYWDS PRESYNAPTIC NEUROTOXIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SKARZYNSKI REVDAT 3 25-DEC-19 1DTX 1 SEQRES LINK REVDAT 2 24-FEB-09 1DTX 1 VERSN REVDAT 1 15-JAN-92 1DTX 0 JRNL AUTH T.SKARZYNSKI JRNL TITL CRYSTAL STRUCTURE OF ALPHA-DENDROTOXIN FROM THE GREEN MAMBA JRNL TITL 2 VENOM AND ITS COMPARISON WITH THE STRUCTURE OF BOVINE JRNL TITL 3 PANCREATIC TRYPSIN INHIBITOR. JRNL REF J.MOL.BIOL. V. 224 671 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1373774 JRNL DOI 10.1016/0022-2836(92)90552-U REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.J.JOUBERT,N.TALJAARD REMARK 1 TITL THE AMINO ACID SEQUENCES OF TWO PROTEINASE INHIBITOR REMARK 1 TITL 2 HOMOLOGUES FROM DENDROASPIS AUGUSTICEPS VENOM REMARK 1 REF HOPPE-SEYLER'S V. 361 661 1980 REMARK 1 REF 2 Z.PHYSIOL.CHEM. REMARK 1 REFN ISSN 0018-4888 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.169 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 : 477 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 59 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) : 0.027 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.036 ; 0.020 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.049 ; 0.040 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.023 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.186 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.271 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.220 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.400 ; 10.000 REMARK 3 STAGGERED (DEGREES) : 23.100; 15.000 REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.400 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.180 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DTX 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_1000172938. 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 (%): 47.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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 36.76500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.57500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 11.57500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.76500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.53000 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 PCA A 1 CB CG CD OE REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 LYS A 28 CD CE NZ REMARK 470 ARG A 34 CD NE CZ NH1 NH2 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 ARG A 3 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 3 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 11 CD - NE - CZ ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 15 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 GLN A 27 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 46 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 GLU A 51 CG - CD - OE1 ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 60 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 61 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 62 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 63 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 64 DBREF 1DTX A 2 59 UNP P00980 IVBII_DENAN 2 59 SEQRES 1 A 59 PCA PRO ARG ARG LYS LEU CYS ILE LEU HIS ARG ASN PRO SEQRES 2 A 59 GLY ARG CYS TYR ASP LYS ILE PRO ALA PHE TYR TYR ASN SEQRES 3 A 59 GLN LYS LYS LYS GLN CYS GLU ARG PHE ASP TRP SER GLY SEQRES 4 A 59 CYS GLY GLY ASN SER ASN ARG PHE LYS THR ILE GLU GLU SEQRES 5 A 59 CYS ARG ARG THR CYS ILE GLY MODRES 1DTX PCA A 1 GLN PYROGLUTAMIC ACID HET PCA A 1 4 HET SO4 A 60 5 HET SO4 A 61 5 HET SO4 A 62 5 HET SO4 A 63 5 HET SO4 A 64 5 HETNAM PCA PYROGLUTAMIC ACID HETNAM SO4 SULFATE ION FORMUL 1 PCA C5 H7 N O3 FORMUL 2 SO4 5(O4 S 2-) FORMUL 7 HOH *59(H2 O) HELIX 1 H1 ILE A 50 ILE A 58 1 9 SHEET 1 S1 2 LYS A 19 GLN A 27 0 SHEET 2 S1 2 GLN A 31 SER A 38 -1 SSBOND 1 CYS A 7 CYS A 57 1555 1555 2.01 SSBOND 2 CYS A 16 CYS A 40 1555 1555 2.09 SSBOND 3 CYS A 32 CYS A 53 1555 1555 2.01 LINK C PCA A 1 N PRO A 2 1555 1555 1.34 SITE 1 AC1 6 ARG A 3 ARG A 4 ARG A 15 CYS A 40 SITE 2 AC1 6 GLY A 41 HOH A 84 SITE 1 AC2 6 ASN A 12 GLY A 14 ARG A 15 GLY A 41 SITE 2 AC2 6 GLY A 42 HOH A 65 SITE 1 AC3 5 HIS A 10 LYS A 30 ILE A 50 ARG A 54 SITE 2 AC3 5 HOH A 72 SITE 1 AC4 5 ARG A 4 LYS A 5 TRP A 37 HOH A 73 SITE 2 AC4 5 HOH A 96 SITE 1 AC5 5 TYR A 17 TRP A 37 ARG A 46 PHE A 47 SITE 2 AC5 5 LYS A 48 CRYST1 73.530 39.060 23.150 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 0.013600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.043197 0.00000 HETATM 1 N PCA A 1 16.207 -7.425 8.244 1.00 35.23 N HETATM 2 CA PCA A 1 16.175 -6.019 8.805 1.00 35.13 C HETATM 3 C PCA A 1 14.890 -5.752 9.585 1.00 33.49 C HETATM 4 O PCA A 1 14.563 -6.517 10.541 1.00 35.33 O