HEADER TOXIN 10-JUL-01 1IQ9
TITLE CRYSTAL STRUCTURE AT 1.8 A OF TOXIN A FROM NAJA NIGRICOLLIS VENOM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-NEUROTOXIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: SHORT NEUROTOXIN 1
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: NAJA NIGRICOLLIS;
SOURCE 3 ORGANISM_COMMON: SPITTING COBRA;
SOURCE 4 ORGANISM_TAXID: 8654
KEYWDS NEUROTOXIN, THREE FINGERS FOLD, TOXIN
EXPDTA X-RAY DIFFRACTION
AUTHOR R.MENEZ,M.H.LE DU,A.MENEZ
REVDAT 4 27-DEC-23 1IQ9 1 REMARK
REVDAT 3 25-DEC-19 1IQ9 1 REMARK
REVDAT 2 24-FEB-09 1IQ9 1 VERSN
REVDAT 1 25-NOV-03 1IQ9 0
JRNL AUTH B.GILQUIN,M.BOURGOIN,R.MENEZ,M.H.LE DU,D.SERVENT,
JRNL AUTH 2 S.ZINN-JUSTIN,A.MENEZ
JRNL TITL MOTIONS AND STRUCTURAL VARIABILITY WITHIN TOXINS:
JRNL TITL 2 IMPLICATION FOR THEIR USE AS SCAFFOLDS FOR PROTEIN
JRNL TITL 3 ENGINEERING
JRNL REF PROTEIN SCI. V. 12 266 2003
JRNL REFN ISSN 0961-8368
JRNL PMID 12538890
JRNL DOI 10.1110/PS.0227703
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 7347
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 SET) : 0.190
REMARK 3 FREE R VALUE : 0.240
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 368
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 469
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 5
REMARK 3 SOLVENT ATOMS : 61
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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1IQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUL-01.
REMARK 100 THE DEPOSITION ID IS D_1000005173.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-DEC-98
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 4.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419
REMARK 200 MONOCHROMATOR : GRAPHITE
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 : 7347
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9
REMARK 200 DATA REDUNDANCY : 10.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.09000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69
REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4
REMARK 200 DATA REDUNDANCY IN SHELL : 8.00
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.67400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.170
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.49
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, AMMONIUM SULFATE,
REMARK 280 HEXANE DIOL, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 291.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.75000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.45000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.45000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.12500
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.45000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.45000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.37500
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.45000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.45000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.12500
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.45000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.45000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.37500
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 36.75000
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 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 SER A 8 -115.94 45.47
REMARK 500 ASN A 60 38.76 -90.71
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 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1NEA RELATED DB: PDB
REMARK 900 1NEA CONTAINS SOLUTION STRUCTURE OF TOXIN A FROM NAJA NIGRICOLLIS
REMARK 900 VENOM
DBREF 1IQ9 A 1 61 UNP P01426 NXS1_NAJPA 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 PRO GLY GLU THR ASN CYS TYR LYS LYS
SEQRES 3 A 61 VAL TRP ARG ASP HIS ARG GLY THR ILE ILE GLU ARG GLY
SEQRES 4 A 61 CYS GLY CYS PRO THR VAL LYS PRO GLY ILE LYS LEU ASN
SEQRES 5 A 61 CYS CYS THR THR ASP LYS CYS ASN ASN
HET SO4 A 201 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2-
FORMUL 3 HOH *61(H2 O)
SHEET 1 A 2 GLU A 2 HIS A 4 0
SHEET 2 A 2 THR A 14 THR A 16 -1 O LYS A 15 N CYS A 3
SHEET 1 B 3 GLY A 33 CYS A 40 0
SHEET 2 B 3 CYS A 23 ASP A 30 -1 N TYR A 24 O GLY A 39
SHEET 3 B 3 LYS A 50 CYS A 54 -1 O LYS A 50 N VAL A 27
SSBOND 1 CYS A 3 CYS A 23 1555 1555 2.03
SSBOND 2 CYS A 17 CYS A 40 1555 1555 1.99
SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.02
SSBOND 4 CYS A 54 CYS A 59 1555 1555 2.02
SITE 1 AC1 8 LYS A 15 TYR A 24 HIS A 31 ARG A 32
SITE 2 AC1 8 GLY A 39 CYS A 40 HOH A 113 HOH A 129
CRYST1 40.900 40.900 73.500 90.00 90.00 90.00 P 43 21 2 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 0.024450 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024450 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013605 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
