PDB Short entry for 3C8P HEADER TOXIN 13-FEB-08 3C8P TITLE X-RAY STRUCTURE OF VISCOTOXIN A1 FROM VISCUM ALBUM L. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VISCOTOXIN A1; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VISCUM ALBUM; SOURCE 3 ORGANISM_COMMON: EUROPEAN MISTLETOE; SOURCE 4 ORGANISM_TAXID: 3972 KEYWDS HELIX TURN HELIX, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR A.PAL,J.E.DEBRECZENI,M.SEVVANA,T.GRUENE,B.KAHLE,A.ZEECK, AUTHOR 2 G.M.SHELDRICK REVDAT 3 19-MAY-09 3C8P 1 JRNL REVDAT 2 24-FEB-09 3C8P 1 VERSN REVDAT 1 17-JUN-08 3C8P 0 JRNL AUTH A.PAL,J.E.DEBRECZENI,M.SEVVANA,T.GRUENE,B.KAHLE, JRNL AUTH 2 A.ZEECK,G.M.SHELDRICK JRNL TITL STRUCTURES OF VISCOTOXINS A1 AND B2 FROM EUROPEAN JRNL TITL 2 MISTLETOE SOLVED USING NATIVE DATA ALONE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 985 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18703848 JRNL DOI 10.1107/S0907444908022646 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.150 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.151 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1445 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 29166 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.124 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.125 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1098 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21766 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 674 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 801.79 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7269 REMARK 3 NUMBER OF RESTRAINTS : 8599 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.360 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.072 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.065 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.038 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.108 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MEWS AND KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3C8P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB046481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-04; 08-FEB-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; EMBL/DESY, REMARK 200 HAMBURG REMARK 200 BEAMLINE : NULL; BW7B REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54; 1.00 REMARK 200 MONOCHROMATOR : CU K A CRYSTAL MONOCHROMATOR; REMARK 200 SILICON DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : OSMIC FOCUSSING MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000; MAR REMARK 200 SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29217 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 47.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.08910 REMARK 200 R SYM (I) : 0.03100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.75 REMARK 200 R MERGE FOR SHELL (I) : 0.30380 REMARK 200 R SYM FOR SHELL (I) : 0.30380 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: XPREP, SHELXD, SHELXE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M SODIUM CITRATE, 0.1 M HEPES PH REMARK 280 7.5, VAPOR DIFFUSION, TEMPERATURE 298K, PH 7.50 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 23.58000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.86500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.37000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.86500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.86500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.79000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.86500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.86500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.37000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.86500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.86500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.79000 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 23.58000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A3127 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3135 LIES ON A SPECIAL POSITION. 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 10 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 23 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG B 23 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B3109 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH B3132 DISTANCE = 5.73 ANGSTROMS DBREF 3C8P A 1 46 PDB 3C8P 3C8P 1 46 DBREF 3C8P B 1 46 PDB 3C8P 3C8P 1 46 SEQRES 1 A 46 LYS SER CYS CYS PRO SER THR THR GLY ARG ASN ILE TYR SEQRES 2 A 46 ASN THR CYS ARG LEU THR GLY SER SER ARG GLU THR CYS SEQRES 3 A 46 ALA LYS LEU SER GLY CYS LYS ILE ILE SER ALA SER THR SEQRES 4 A 46 CYS PRO SER ASN TYR PRO LYS SEQRES 1 B 46 LYS SER CYS CYS PRO SER THR THR GLY ARG ASN ILE TYR SEQRES 2 B 46 ASN THR CYS ARG LEU THR GLY SER SER ARG GLU THR CYS SEQRES 3 B 46 ALA LYS LEU SER GLY CYS LYS ILE ILE SER ALA SER THR SEQRES 4 B 46 CYS PRO SER ASN TYR PRO LYS FORMUL 3 HOH *135(H2 O) HELIX 1 1 SER A 6 LEU A 18 1 13 HELIX 2 2 SER A 22 GLY A 31 1 10 HELIX 3 3 SER B 6 THR B 19 1 14 HELIX 4 4 SER B 22 GLY B 31 1 10 SHEET 1 A 2 SER A 2 CYS A 3 0 SHEET 2 A 2 LYS A 33 ILE A 34 -1 O LYS A 33 N CYS A 3 SHEET 1 B 2 SER B 2 CYS B 3 0 SHEET 2 B 2 LYS B 33 ILE B 34 -1 O LYS B 33 N CYS B 3 SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.06 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.03 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.08 SSBOND 4 CYS B 3 CYS B 40 1555 1555 2.07 SSBOND 5 CYS B 4 CYS B 32 1555 1555 2.05 SSBOND 6 CYS B 16 CYS B 26 1555 1555 2.06 CRYST1 65.730 65.730 47.160 90.00 90.00 90.00 P 43 21 2 16 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 0.015214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015214 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021204 0.00000