HEADER TOXIN 30-AUG-12 4GVB TITLE CRYSTAL STRUCTURE OF THE VIRALLY ENCODED ANTIFUNGAL PROTEIN, KP6, TITLE 2 HETERODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: KP6 KILLER TOXIN SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KP6 ALPHA SUBUNIT; COMPND 5 SYNONYM: VP10; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: KP6 KILLER TOXIN SUBUNIT BETA; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: KP6 BETA SUBUNIT; COMPND 10 SYNONYM: VP12.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: USTILAGO MAYDIS VIRUS P6; SOURCE 3 ORGANISM_COMMON: UMV6; SOURCE 4 ORGANISM_TAXID: 11010; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: USTILAGO MAYDIS VIRUS P6; SOURCE 7 ORGANISM_COMMON: UMV6; SOURCE 8 ORGANISM_TAXID: 11010 KEYWDS ANTIFUNGAL PROTEIN, SECRETED, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SMITH REVDAT 3 13-FEB-13 4GVB 1 JRNL REVDAT 2 23-JAN-13 4GVB 1 JRNL REVDAT 1 19-DEC-12 4GVB 0 JRNL AUTH A.ALLEN,E.CHATT,T.J.SMITH JRNL TITL THE ATOMIC STRUCTURE OF THE VIRALLY ENCODED ANTIFUNGAL JRNL TITL 2 PROTEIN, KP6. JRNL REF J.MOL.BIOL. V. 425 609 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23219466 JRNL DOI 10.1016/J.JMB.2012.11.033 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_353) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.4768 - 3.0776 0.99 3465 165 0.1936 0.2069 REMARK 3 2 3.0776 - 2.4429 0.97 3187 171 0.2157 0.2483 REMARK 3 3 2.4429 - 2.1341 0.85 2754 155 0.2344 0.3128 REMARK 3 4 2.1341 - 1.9390 0.79 2560 134 0.2519 0.2943 REMARK 3 5 1.9390 - 1.8000 0.73 2359 128 0.2897 0.3237 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 50.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.770 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) : 3.70750 REMARK 3 B22 (A**2) : 3.70750 REMARK 3 B33 (A**2) : -7.41510 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1209 REMARK 3 ANGLE : 0.965 1623 REMARK 3 CHIRALITY : 0.075 162 REMARK 3 PLANARITY : 0.004 214 REMARK 3 DIHEDRAL : 12.476 417 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-12. REMARK 100 THE RCSB ID CODE IS RCSB074677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC (BLUE) MIRROR OPTICS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13869 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION CONTAINED 50 MM REMARK 280 TRIS, PH 8.0, 0.7 M AMMONIUM SULFATE, AND 1 MM SODIUM AZIDE. THE REMARK 280 DROPS WERE COMPOSED OF 1:1 RATIO OF RESERVOIR SOLUTION AND 8.2 REMARK 280 MG/ML KP6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 103.76533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.88267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.88267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 103.76533 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 B 131 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 101 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 78 REMARK 465 LYS A 79 REMARK 465 ARG A 80 REMARK 465 GLY B 1 REMARK 465 LYS B 2 REMARK 465 ARG B 3 REMARK 465 ILE B 31 REMARK 465 ASP B 32 REMARK 465 SER B 33 REMARK 465 PHE B 34 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 115 O HOH B 118 1.97 REMARK 500 O HOH A 113 O HOH A 141 2.04 REMARK 500 O THR B 15 O HOH B 132 2.08 REMARK 500 O HOH B 108 O HOH B 112 2.12 REMARK 500 NH1 ARG B 66 O HOH B 152 2.16 REMARK 500 O HOH B 132 O HOH B 143 2.18 REMARK 500 O HOH B 122 O HOH B 124 2.18 REMARK 500 OE1 GLU B 41 O HOH B 138 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 8 -5.98 -142.87 REMARK 500 LYS A 41 -2.74 81.27 REMARK 500 THR B 15 -131.99 -125.61 REMARK 500 ASN B 16 92.57 -31.69 REMARK 500 ASP B 53 51.60 -105.75 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 A 194 DISTANCE = 5.02 ANGSTROMS REMARK 525 HOH A 196 DISTANCE = 6.05 ANGSTROMS DBREF 4GVB A 1 80 UNP P16948 KP6T_UMV6 28 107 DBREF 4GVB B 1 81 UNP P16948 KP6T_UMV6 139 219 SEQRES 1 A 80 ASN ASN ALA PHE CYS ALA GLY PHE GLY LEU SER CYS LYS SEQRES 2 A 80 TRP GLU CYS TRP CYS THR ALA HIS GLY THR GLY ASN GLU SEQRES 3 A 80 LEU ARG TYR ALA THR ALA ALA GLY CYS GLY ASP HIS LEU SEQRES 4 A 80 SER LYS SER TYR TYR ASP ALA ARG ALA GLY HIS CYS LEU SEQRES 5 A 80 PHE SER ASP ASP LEU ARG ASN GLN PHE TYR SER HIS CYS SEQRES 6 A 80 SER SER LEU ASN ASN ASN MET SER CYS ARG SER LEU SER SEQRES 7 A 80 LYS ARG SEQRES 1 B 81 GLY LYS ARG PRO ARG PRO VAL MET CYS GLN CYS VAL ASP SEQRES 2 B 81 THR THR ASN GLY GLY VAL ARG LEU ASP ALA VAL THR ARG SEQRES 3 B 81 ALA ALA CYS SER ILE ASP SER PHE ILE ASP GLY TYR TYR SEQRES 4 B 81 THR GLU LYS ASP GLY PHE CYS ARG ALA LYS TYR SER TRP SEQRES 5 B 81 ASP LEU PHE THR SER GLY GLN PHE TYR GLN ALA CYS LEU SEQRES 6 B 81 ARG TYR SER HIS ALA GLY THR ASN CYS GLN PRO ASP PRO SEQRES 7 B 81 GLN TYR GLU FORMUL 3 HOH *168(H2 O) HELIX 1 1 ASN A 1 GLY A 9 1 9 HELIX 2 2 LEU A 27 GLY A 34 1 8 HELIX 3 3 CYS A 35 LEU A 39 5 5 HELIX 4 4 LEU A 57 LEU A 68 1 12 HELIX 5 5 THR B 15 VAL B 19 5 5 HELIX 6 6 LEU B 21 SER B 30 1 10 HELIX 7 7 THR B 56 SER B 68 1 13 HELIX 8 8 PRO B 78 GLU B 81 5 4 SHEET 1 A 4 TYR A 43 ASP A 45 0 SHEET 2 A 4 HIS A 50 PHE A 53 -1 O LEU A 52 N TYR A 43 SHEET 3 A 4 TRP A 14 THR A 19 -1 N CYS A 16 O CYS A 51 SHEET 4 A 4 ASN A 71 SER A 76 -1 O ASN A 71 N THR A 19 SHEET 1 B 2 VAL B 7 ASP B 13 0 SHEET 2 B 2 ALA B 70 PRO B 76 -1 O GLN B 75 N MET B 8 SHEET 1 C 2 TYR B 38 TYR B 39 0 SHEET 2 C 2 CYS B 46 ARG B 47 -1 O ARG B 47 N TYR B 38 SSBOND 1 CYS A 5 CYS A 12 1555 1555 2.05 SSBOND 2 CYS A 16 CYS A 74 1555 1555 2.03 SSBOND 3 CYS A 18 CYS A 65 1555 1555 2.02 SSBOND 4 CYS A 35 CYS A 51 1555 1555 2.02 SSBOND 5 CYS B 9 CYS B 74 1555 1555 2.04 SSBOND 6 CYS B 11 CYS B 64 1555 1555 2.02 SSBOND 7 CYS B 29 CYS B 46 1555 1555 2.04 CRYST1 44.419 44.419 155.648 90.00 90.00 120.00 P 32 2 1 6 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 0.022513 0.012998 0.000000 0.00000 SCALE2 0.000000 0.025996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006425 0.00000