HEADER NEUROTOXIN 16-JAN-98 1QKD TITLE ERABUTOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERABUTOXIN A; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LATICAUDA SEMIFASCIATA; SOURCE 3 ORGANISM_COMMON: BROAD-BANDED BLUE SEA KRAIT; SOURCE 4 ORGANISM_TAXID: 8631; SOURCE 5 SECRETION: VENOM; SOURCE 6 OTHER_DETAILS: JAPANESE SEA SNAKE KEYWDS NEUROTOXIN, ERABUTOXIN EXPDTA X-RAY DIFFRACTION AUTHOR V.NASTOPOULOS,P.N.KANELLOPOULOS,D.TSERNOGLOU REVDAT 3 09-AUG-23 1QKD 1 REMARK REVDAT 2 24-FEB-09 1QKD 1 VERSN REVDAT 1 16-FEB-99 1QKD 0 JRNL AUTH V.NASTOPOULOS,P.N.KANELLOPOULOS,D.TSERNOGLOU JRNL TITL STRUCTURE OF DIMERIC AND MONOMERIC ERABUTOXIN A REFINED AT JRNL TITL 2 1.5 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 964 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 9757111 JRNL DOI 10.1107/S0907444998005125 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19420 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL 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 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1690 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 : 946 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 25.800 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.170 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 18.130; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.005 ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.013 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 7.220 ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.040 ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR WAS ALSO USED REMARK 4 REMARK 4 1QKD 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_1000175916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-92 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 17.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.20400 REMARK 200 FOR SHELL : 5.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 6EBX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.2 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 27.66000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.38000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.77000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.38000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.66000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.77000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 21 CD GLU A 21 OE2 0.069 REMARK 500 GLU A 56 CD GLU A 56 OE2 0.067 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 ASP B 31 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 31 CB - CG - OD2 ANGL. DEV. = -6.2 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 ASN A 5 14.46 -140.96 REMARK 500 SER A 8 -115.95 37.39 REMARK 500 CYS A 43 81.86 -150.37 REMARK 500 VAL A 59 50.23 37.64 REMARK 500 ASN A 61 40.51 -95.18 REMARK 500 ASN A 61 37.87 -95.18 REMARK 500 SER B 8 -120.10 36.73 REMARK 500 ASP B 31 -160.58 -104.57 REMARK 500 CYS B 43 81.45 -150.54 REMARK 500 GLU B 56 58.93 -119.73 REMARK 500 VAL B 59 47.83 36.52 REMARK 500 ASN B 61 34.69 -96.44 REMARK 500 ASN B 61 34.43 -96.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QKD A 1 62 UNP P60775 NXSA_LATSE 22 83 DBREF 1QKD B 1 62 UNP P60775 NXSA_LATSE 22 83 SEQRES 1 A 62 ARG ILE CYS PHE ASN HIS GLN SER SER GLN PRO GLN THR SEQRES 2 A 62 THR LYS THR CYS SER PRO GLY GLU SER SER CYS TYR ASN SEQRES 3 A 62 LYS GLN TRP SER ASP PHE ARG GLY THR ILE ILE GLU ARG SEQRES 4 A 62 GLY CYS GLY CYS PRO THR VAL LYS PRO GLY ILE LYS LEU SEQRES 5 A 62 SER CYS CYS GLU SER GLU VAL CYS ASN ASN SEQRES 1 B 62 ARG ILE CYS PHE ASN HIS GLN SER SER GLN PRO GLN THR SEQRES 2 B 62 THR LYS THR CYS SER PRO GLY GLU SER SER CYS TYR ASN SEQRES 3 B 62 LYS GLN TRP SER ASP PHE ARG GLY THR ILE ILE GLU ARG SEQRES 4 B 62 GLY CYS GLY CYS PRO THR VAL LYS PRO GLY ILE LYS LEU SEQRES 5 B 62 SER CYS CYS GLU SER GLU VAL CYS ASN ASN FORMUL 3 HOH *206(H2 O) SHEET 1 A 2 ILE A 2 PHE A 4 0 SHEET 2 A 2 THR A 14 THR A 16 -1 N LYS A 15 O CYS A 3 SHEET 1 B 3 GLY A 34 CYS A 41 0 SHEET 2 B 3 CYS A 24 ASP A 31 -1 N ASP A 31 O GLY A 34 SHEET 3 B 3 LYS A 51 CYS A 55 -1 N CYS A 55 O CYS A 24 SHEET 1 C 2 ILE B 2 PHE B 4 0 SHEET 2 C 2 THR B 14 THR B 16 -1 N LYS B 15 O CYS B 3 SHEET 1 D 3 GLY B 34 CYS B 41 0 SHEET 2 D 3 CYS B 24 ASP B 31 -1 N ASP B 31 O GLY B 34 SHEET 3 D 3 LYS B 51 CYS B 55 -1 N CYS B 55 O CYS B 24 SSBOND 1 CYS A 3 CYS A 24 1555 1555 1.95 SSBOND 2 CYS A 17 CYS A 41 1555 1555 2.06 SSBOND 3 CYS A 43 CYS A 54 1555 1555 2.00 SSBOND 4 CYS A 55 CYS A 60 1555 1555 2.03 SSBOND 5 CYS B 3 CYS B 24 1555 1555 1.98 SSBOND 6 CYS B 17 CYS B 41 1555 1555 2.02 SSBOND 7 CYS B 43 CYS B 54 1555 1555 2.00 SSBOND 8 CYS B 55 CYS B 60 1555 1555 2.05 CRYST1 55.320 53.540 40.760 90.00 90.00 90.00 P 21 21 21 8 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 0.018077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024534 0.00000 MTRIX1 1 -0.998000 -0.026400 -0.057900 48.36970 1 MTRIX2 1 -0.063500 0.362600 0.929800 -8.31100 1 MTRIX3 1 -0.003500 0.931600 -0.363500 14.57370 1