HEADER TOXIN 24-SEP-04 1WQ9 TITLE CRYSTAL STRUCTURE OF VR-1, A VEGF-F FROM A SNAKE VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VR-1, VEGF-F; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: VR-1, VEGF-F SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII RUSSELLII; SOURCE 3 ORGANISM_TAXID: 31159; SOURCE 4 STRAIN: RUSSELLII; SOURCE 5 SECRETION: VENOM; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII RUSSELLII; SOURCE 8 ORGANISM_TAXID: 31159; SOURCE 9 STRAIN: RUSSELLII; SOURCE 10 SECRETION: VENOM KEYWDS SNAKE VENOM, VASCULAR ENDOTHELIAL GROWTH FACTOR, VEGF, VEGF-F, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.SUTO,Y.YAMAZAKI,T.MORITA,H.MIZUNO REVDAT 3 25-DEC-19 1WQ9 1 SEQRES LINK REVDAT 2 24-FEB-09 1WQ9 1 VERSN REVDAT 1 07-DEC-04 1WQ9 0 JRNL AUTH K.SUTO,Y.YAMAZAKI,T.MORITA,H.MIZUNO JRNL TITL CRYSTAL STRUCTURES OF NOVEL VASCULAR ENDOTHELIAL GROWTH JRNL TITL 2 FACTORS (VEGF) FROM SNAKE VENOMS: INSIGHT INTO SELECTIVE JRNL TITL 3 VEGF BINDING TO KINASE INSERT DOMAIN-CONTAINING RECEPTOR BUT JRNL TITL 4 NOT TO FMS-LIKE TYROSINE KINASE-1. JRNL REF J.BIOL.CHEM. V. 280 2126 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15542594 JRNL DOI 10.1074/JBC.M411395200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.YAMAZAKI,K.TAKANI,H.ATODA,T.MORITA REMARK 1 TITL SNAKE VENOM VASCULAR ENDOTHELIAL GROWTH FACTORS (VEGFS) REMARK 1 TITL 2 EXHIBIT POTENT ACTIVITY THROUGH THEIR SPECIFIC RECOGNITION REMARK 1 TITL 3 OF KDR (VEGF RECEPTOR 2) REMARK 1 REF J.BIOL.CHEM. V. 278 51985 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 14600159 REMARK 1 DOI 10.1074/JBC.C300454200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 213927.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 15189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 747 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2439 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : -2.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.160 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.210 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.000 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 37.99 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : BUFFER.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : BUFFER.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000023876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-03; 17-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B; BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000; 1.0722, 1.0715, 1.0925 REMARK 200 MONOCHROMATOR : SILICON, GELMANIUM; SILICON REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, TRIS-HCL, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 45.17400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.48050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.17400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.48050 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS DIMERIC FORM IN A ASYMMETRIC REMARK 300 UNIT. 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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: 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 B 32 -20.04 -147.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WQ8 RELATED DB: PDB REMARK 900 VAMMIN, A VEGF-F FROM A SNAKE VENOM DBREF 1WQ9 A 2 95 UNP P67861 TXVE_DABRR 2 95 DBREF 1WQ9 B 2 95 UNP P67861 TXVE_DABRR 2 95 SEQRES 1 A 96 GLU VAL ARG PRO PHE LEU ASP VAL TYR GLN ARG SER ALA SEQRES 2 A 96 CYS GLN THR ARG GLU THR LEU VAL SER ILE LEU GLN GLU SEQRES 3 A 96 HIS PRO ASP GLU ILE SER ASP ILE PHE ARG PRO SER CYS SEQRES 4 A 96 VAL ALA VAL LEU ARG CYS SER GLY CYS CYS THR ASP GLU SEQRES 5 A 96 SER MET LYS CYS THR PRO VAL GLY LYS HIS THR ALA ASP SEQRES 6 A 96 ILE GLN ILE MET ARG MET ASN PRO ARG THR HIS SER SER SEQRES 7 A 96 LYS MET GLU VAL MET LYS PHE MET GLU HIS THR ALA CYS SEQRES 8 A 96 GLU CYS ARG PRO ALA SEQRES 1 B 96 PCA VAL ARG PRO PHE LEU ASP VAL TYR GLN ARG SER ALA SEQRES 2 B 96 CYS GLN THR ARG GLU THR LEU VAL SER ILE LEU GLN GLU SEQRES 3 B 96 HIS PRO ASP GLU ILE SER ASP ILE PHE ARG PRO SER CYS SEQRES 4 B 96 VAL ALA VAL LEU ARG CYS SER GLY CYS CYS THR ASP GLU SEQRES 5 B 96 SER MET LYS CYS THR PRO VAL GLY LYS HIS THR ALA ASP SEQRES 6 B 96 ILE GLN ILE MET ARG MET ASN PRO ARG THR HIS SER SER SEQRES 7 B 96 LYS MET GLU VAL MET LYS PHE MET GLU HIS THR ALA CYS SEQRES 8 B 96 GLU CYS ARG PRO ALA MODRES 1WQ9 PCA B 1 GLN PYROGLUTAMIC ACID HET PCA B 1 8 HETNAM PCA PYROGLUTAMIC ACID FORMUL 2 PCA C5 H7 N O3 FORMUL 3 HOH *143(H2 O) HELIX 1 1 PRO A 4 ALA A 13 1 10 HELIX 2 2 ILE A 23 HIS A 27 1 5 HELIX 3 3 PRO B 4 ALA B 13 1 10 HELIX 4 4 ILE B 23 HIS B 27 1 5 SHEET 1 A 2 GLN A 15 SER A 22 0 SHEET 2 A 2 CYS A 39 SER A 46 -1 O VAL A 42 N THR A 19 SHEET 1 B 3 ILE A 34 ARG A 36 0 SHEET 2 B 3 MET A 54 MET A 71 -1 O MET A 71 N ILE A 34 SHEET 3 B 3 SER A 78 PRO A 95 -1 O MET A 83 N ILE A 66 SHEET 1 C 3 ILE A 34 ARG A 36 0 SHEET 2 C 3 MET A 54 MET A 71 -1 O MET A 71 N ILE A 34 SHEET 3 C 3 VAL B 2 ARG B 3 1 O ARG B 3 N ASP A 65 SHEET 1 D 2 GLN B 15 SER B 22 0 SHEET 2 D 2 CYS B 39 SER B 46 -1 O VAL B 42 N THR B 19 SHEET 1 E 3 ILE B 34 ARG B 36 0 SHEET 2 E 3 LYS B 55 MET B 71 -1 O MET B 71 N ILE B 34 SHEET 3 E 3 SER B 78 ARG B 94 -1 O MET B 83 N ILE B 66 SSBOND 1 CYS A 14 CYS A 56 1555 1555 2.03 SSBOND 2 CYS A 39 CYS B 48 1555 1555 2.03 SSBOND 3 CYS A 45 CYS A 91 1555 1555 2.02 SSBOND 4 CYS A 48 CYS B 39 1555 1555 2.04 SSBOND 5 CYS A 49 CYS A 93 1555 1555 2.02 SSBOND 6 CYS B 14 CYS B 56 1555 1555 2.03 SSBOND 7 CYS B 45 CYS B 91 1555 1555 2.02 SSBOND 8 CYS B 49 CYS B 93 1555 1555 2.03 LINK C PCA B 1 N VAL B 2 1555 1555 1.32 CISPEP 1 ARG A 36 PRO A 37 0 -3.52 CISPEP 2 ARG B 36 PRO B 37 0 -4.06 CRYST1 90.348 48.961 54.214 90.00 90.00 90.00 P 21 21 2 4 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 0.011068 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020424 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018445 0.00000