PDB Short entry for 1OKH HEADER TOXIN 24-JUL-03 1OKH TITLE VISCOTOXIN A3 FROM VISCUM ALBUM L. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VISCOTOXIN A3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VISCOTOXIN A3 CHAIN, RESIDUES 27-72 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VISCUM ALBUM; SOURCE 3 ORGANISM_COMMON: EUROPEAN MISTLETOE; SOURCE 4 ORGANISM_TAXID: 3972; SOURCE 5 ORGAN: LEAVES, STEMS KEYWDS THIONIN, TOXIN, PLANT DEFENSE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.DEBRECZENI,B.GIRMANN,A.ZEECK,G.M.SHELDRICK REVDAT 5 24-JUL-19 1OKH 1 REMARK REVDAT 4 22-MAY-19 1OKH 1 REMARK REVDAT 3 14-DEC-16 1OKH 1 JRNL REMARK VERSN FORMUL REVDAT 3 2 1 SITE MASTER REVDAT 2 24-FEB-09 1OKH 1 VERSN REVDAT 1 04-DEC-03 1OKH 0 JRNL AUTH J.E.DEBRECZENI,B.GIRMANN,A.ZEECK,R.KRATZNER,G.M.SHELDRICK JRNL TITL STRUCTURE OF VISCOTOXIN A3: DISULFIDE LOCATION FROM WEAK SAD JRNL TITL 2 DATA JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 2125 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 14646070 JRNL DOI 10.1107/S0907444903018973 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE 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) : 0.192 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 454 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8893 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.171 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.167 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 393 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 7481 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 666 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 780.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3115 REMARK 3 NUMBER OF RESTRAINTS : 2935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.002 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.293 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.029 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.042 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.021 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL 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 1OKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 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 : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : 8938 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 68.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.250 REMARK 200 R MERGE (I) : 0.08920 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.42 REMARK 200 R MERGE FOR SHELL (I) : 0.38660 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, SHELXE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DATA COLLECTED IN-HOUSE. PHASED USING IN-HOUSE SULFUR- SAD REMARK 200 DATA REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M AM2SO4, 0.05M CACOD. PH=6.5, 30% REMARK 280 PEG8000, 15MM HGCL2, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 23.99750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.29650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.99750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.29650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 A2001 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2004 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2005 LIES ON A SPECIAL POSITION. REMARK 375 HOH B2006 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 TYR B 13 CB - CG - CD2 ANGL. DEV. = -4.1 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 A2004 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH B2005 DISTANCE = 6.80 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1047 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1048 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1047 DBREF 1OKH A 1 46 UNP P01538 THN3_VISAL 27 72 DBREF 1OKH B 1 46 UNP P01538 THN3_VISAL 27 72 SEQRES 1 A 46 LYS SER CYS CYS PRO ASN THR THR GLY ARG ASN ILE TYR SEQRES 2 A 46 ASN ALA CYS ARG LEU THR GLY ALA PRO ARG PRO THR CYS SEQRES 3 A 46 ALA LYS LEU SER GLY CYS LYS ILE ILE SER GLY SER THR SEQRES 4 A 46 CYS PRO SER ASP TYR PRO LYS SEQRES 1 B 46 LYS SER CYS CYS PRO ASN THR THR GLY ARG ASN ILE TYR SEQRES 2 B 46 ASN ALA CYS ARG LEU THR GLY ALA PRO ARG PRO THR CYS SEQRES 3 B 46 ALA LYS LEU SER GLY CYS LYS ILE ILE SER GLY SER THR SEQRES 4 B 46 CYS PRO SER ASP TYR PRO LYS HET PO4 A1047 5 HET SO4 A1048 5 HET PO4 B1047 10 HETNAM PO4 PHOSPHATE ION HETNAM SO4 SULFATE ION FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 SO4 O4 S 2- FORMUL 6 HOH *94(H2 O) HELIX 1 1 ASN A 6 THR A 19 1 14 HELIX 2 2 PRO A 22 GLY A 31 1 10 HELIX 3 3 ASN B 6 THR B 19 1 14 HELIX 4 4 PRO B 22 GLY B 31 1 10 SHEET 1 AA 2 SER A 2 CYS A 3 0 SHEET 2 AA 2 LYS A 33 ILE A 34 -1 O LYS A 33 N CYS A 3 SHEET 1 BA 2 SER B 2 CYS B 3 0 SHEET 2 BA 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 2.01 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.04 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.01 SSBOND 4 CYS B 3 CYS B 40 1555 1555 2.02 SSBOND 5 CYS B 4 CYS B 32 1555 1555 2.01 SSBOND 6 CYS B 16 CYS B 26 1555 1555 2.04 SITE 1 AC1 9 LYS A 1 SER A 2 TYR A 13 ARG A 23 SITE 2 AC1 9 HOH A2021 HOH A2052 HOH A2053 HOH A2054 SITE 3 AC1 9 SER B 42 SITE 1 AC2 8 SER A 38 THR A 39 HOH A2043 ARG B 17 SITE 2 AC2 8 PRO B 22 ARG B 23 PRO B 24 HOH B2030 SITE 1 AC3 3 SER B 2 TYR B 13 ARG B 23 CRYST1 47.995 68.593 25.264 90.00 90.00 90.00 P 21 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 0.020835 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039582 0.00000 MTRIX1 1 0.199860 -0.978370 -0.053390 -0.01244 1 MTRIX2 1 -0.979820 -0.199430 -0.013380 0.50519 1 MTRIX3 1 0.002450 0.054990 -0.998480 30.12263 1