10 20 30 40 50 60 70 80 1IQ9 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 10-JUL-01 1IQ9
TITLE CRYSTAL STRUCTURE AT 1.8 A OF TOXIN A FROM NAJA NIGRICOLLIS TITLE 2 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
EXPDTA X-RAY DIFFRACTION
AUTHOR R.MENEZ,M.H.LE DU,A.MENEZ
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 1
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 : 475 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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-01. REMARK 100 THE RCSB ID CODE IS RCSB005173.
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 : 10.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 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) : 0.09380 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, REMARK 280 TEMPERATURE 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 REMARK 900 NIGRICOLLIS 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