HEADER PLANT PROTEIN 27-JAN-15 4XVB TITLE RECOMBINANT THAUMATIN IN THE PRESENCE OF 1.5M PST AT 293K COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE; SOURCE 4 ORGANISM_TAXID: 4621; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X-33; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC6 KEYWDS THAUMATIN, SWEET-TASTING PROTEIN, THAUMATIN FAMILY, SWEET RECEPTOR, KEYWDS 2 PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MASUDA,K.OKUBO,B.MIKAMI REVDAT 2 05-FEB-20 4XVB 1 REMARK REVDAT 1 03-FEB-16 4XVB 0 JRNL AUTH T.MASUDA,K.OKUBO,B.MIKAMI JRNL TITL STRUCTURE OF THE RECOMBINANT THAUMATIN IN THE PRESENCE OF JRNL TITL 2 PST AT ROOM TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 41460 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.110 REMARK 3 R VALUE (WORKING SET) : 0.109 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2074 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 27.9472 - 3.7462 1.00 2869 152 0.1105 0.1109 REMARK 3 2 3.7462 - 2.9746 1.00 2705 143 0.1254 0.1359 REMARK 3 3 2.9746 - 2.5989 1.00 2670 139 0.1403 0.1655 REMARK 3 4 2.5989 - 2.3614 1.00 2630 140 0.1290 0.1438 REMARK 3 5 2.3614 - 2.1922 1.00 2633 138 0.1081 0.1377 REMARK 3 6 2.1922 - 2.0630 1.00 2621 137 0.0996 0.1267 REMARK 3 7 2.0630 - 1.9597 1.00 2592 137 0.0877 0.1120 REMARK 3 8 1.9597 - 1.8744 1.00 2612 137 0.0821 0.1240 REMARK 3 9 1.8744 - 1.8023 1.00 2583 137 0.0868 0.1098 REMARK 3 10 1.8023 - 1.7401 1.00 2592 136 0.0820 0.1252 REMARK 3 11 1.7401 - 1.6857 1.00 2589 136 0.0778 0.1159 REMARK 3 12 1.6857 - 1.6375 1.00 2572 136 0.0810 0.1036 REMARK 3 13 1.6375 - 1.5944 1.00 2563 134 0.0870 0.1256 REMARK 3 14 1.5944 - 1.5555 1.00 2588 136 0.0924 0.1638 REMARK 3 15 1.5555 - 1.5202 1.00 2567 136 0.0998 0.1539 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.010 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 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 : 0.006 1826 REMARK 3 ANGLE : 1.100 2493 REMARK 3 CHIRALITY : 0.044 257 REMARK 3 PLANARITY : 0.005 346 REMARK 3 DIHEDRAL : 12.204 684 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 4XVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41551 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 68.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M ADA, 1.5M K-NA TARTRATE, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 75.80450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.24350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.90225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.24350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.24350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.70675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.24350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.24350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.90225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.24350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.24350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.70675 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 75.80450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 A 512 O HOH A 518 2.06 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 ASP A 25 -137.06 55.95 REMARK 500 CYS A 71 72.71 -112.15 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 TLA A 301 DBREF 4XVB A 1 207 UNP Q8RVT0 Q8RVT0_THADA 1 207 SEQRES 1 A 207 ALA THR PHE GLU ILE VAL ASN ARG CYS SER TYR THR VAL SEQRES 2 A 207 TRP ALA ALA ALA SER LYS GLY ASP ALA ALA LEU ASP ALA SEQRES 3 A 207 GLY GLY ARG GLN LEU ASN SER GLY GLU SER TRP THR ILE SEQRES 4 A 207 ASN VAL GLU PRO GLY THR ASN GLY GLY LYS ILE TRP ALA SEQRES 5 A 207 ARG THR ASP CYS TYR PHE ASP ASP SER GLY SER GLY ILE SEQRES 6 A 207 CYS LYS THR GLY ASP CYS GLY GLY LEU LEU ARG CYS LYS SEQRES 7 A 207 ARG PHE GLY ARG PRO PRO THR THR LEU ALA GLU PHE SER SEQRES 8 A 207 LEU ASN GLN TYR GLY LYS ASP TYR ILE ASP ILE SER ASN SEQRES 9 A 207 ILE LYS GLY PHE ASN VAL PRO MET ASP PHE SER PRO THR SEQRES 10 A 207 THR ARG GLY CYS ARG GLY VAL ARG CYS ALA ALA ASP ILE SEQRES 11 A 207 VAL GLY GLN CYS PRO ALA LYS LEU LYS ALA PRO GLY GLY SEQRES 12 A 207 GLY CYS ASN ASP ALA CYS THR VAL PHE GLN THR SER GLU SEQRES 13 A 207 TYR CYS CYS THR THR GLY LYS CYS GLY PRO THR GLU TYR SEQRES 14 A 207 SER ARG PHE PHE LYS ARG LEU CYS PRO ASP ALA PHE SER SEQRES 15 A 207 TYR VAL LEU ASP LYS PRO THR THR VAL THR CYS PRO GLY SEQRES 16 A 207 SER SER ASN TYR ARG VAL THR PHE CYS PRO THR ALA HET TLA A 301 10 HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 TLA C4 H6 O6 FORMUL 3 HOH *163(H2 O) HELIX 1 AA1 ASP A 129 CYS A 134 1 6 HELIX 2 AA2 PRO A 135 LYS A 137 5 3 HELIX 3 AA3 ASP A 147 GLN A 153 1 7 HELIX 4 AA4 THR A 154 CYS A 159 1 6 HELIX 5 AA5 THR A 167 CYS A 177 1 11 SHEET 1 AA1 5 SER A 36 ASN A 40 0 SHEET 2 AA1 5 THR A 2 ASN A 7 -1 N ILE A 5 O TRP A 37 SHEET 3 AA1 5 TYR A 199 PHE A 203 1 O VAL A 201 N VAL A 6 SHEET 4 AA1 5 MET A 112 PRO A 116 -1 N SER A 115 O ARG A 200 SHEET 5 AA1 5 VAL A 124 CYS A 126 -1 O VAL A 124 N PHE A 114 SHEET 1 AA2 4 ALA A 23 LEU A 31 0 SHEET 2 AA2 4 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 AA2 4 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 AA2 4 GLY A 64 THR A 68 -1 O ILE A 65 N TYR A 57 SHEET 1 AA3 6 ALA A 23 LEU A 31 0 SHEET 2 AA3 6 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 AA3 6 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 AA3 6 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 5 AA3 6 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 6 AA3 6 VAL A 191 PRO A 194 -1 O CYS A 193 N ASP A 98 SHEET 1 AA4 2 LYS A 139 ALA A 140 0 SHEET 2 AA4 2 GLY A 144 CYS A 145 -1 O GLY A 144 N ALA A 140 SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.02 SSBOND 2 CYS A 56 CYS A 66 1555 1555 2.02 SSBOND 3 CYS A 71 CYS A 77 1555 1555 2.03 SSBOND 4 CYS A 121 CYS A 193 1555 1555 2.03 SSBOND 5 CYS A 126 CYS A 177 1555 1555 2.03 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.03 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.03 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.01 CISPEP 1 PRO A 83 PRO A 84 0 5.05 SITE 1 AC1 8 ARG A 29 GLU A 35 SER A 36 TYR A 157 SITE 2 AC1 8 HOH A 419 HOH A 427 HOH A 430 HOH A 529 CRYST1 58.487 58.487 151.609 90.00 90.00 90.00 P 41 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 0.017098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006596 0.00000