HEADER PLANT PROTEIN 07-AUG-14 3WXS TITLE THAUMATIN STRUCTURE DETERMINED BY SPRING-8 ANGSTROM COMPACT FREE TITLE 2 ELECTRON LASER (SACLA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN I; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE, MIRACLE FRUIT; SOURCE 4 ORGANISM_TAXID: 4621 KEYWDS THAUMATIN, SWEET-TASTING PROTEIN, THAUMATIN FAMILY, SWEET RECEPTOR, KEYWDS 2 MAINLY BETA, TASTE PROTEIN, ARIL, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MASUDA,E.NANGO,M.SUGAHARA,E.MIZOHATA,T.TANAKA,R.TANAKA,M.SUZUKI, AUTHOR 2 B.MIKAMI,S.IWATA REVDAT 4 20-NOV-24 3WXS 1 REMARK REVDAT 3 08-NOV-23 3WXS 1 REMARK REVDAT 2 24-JAN-18 3WXS 1 JRNL REMARK REVDAT 1 05-NOV-14 3WXS 0 JRNL AUTH M.SUGAHARA,E.MIZOHATA,E.NANGO,M.SUZUKI,T.TANAKA,T.MASUDA, JRNL AUTH 2 R.TANAKA,T.SHIMAMURA,Y.TANAKA,C.SUNO,K.IHARA,D.PAN, JRNL AUTH 3 K.KAKINOUCHI,S.SUGIYAMA,M.MURATA,T.INOUE,K.TONO,C.SONG, JRNL AUTH 4 J.PARK,T.KAMESHIMA,T.HATSUI,Y.JOTI,M.YABASHI,S.IWATA JRNL TITL GREASE MATRIX AS A VERSATILE CARRIER OF PROTEINS FOR SERIAL JRNL TITL 2 CRYSTALLOGRAPHY JRNL REF NAT. METHODS V. 12 61 2015 JRNL REFN ESSN 1548-7105 JRNL PMID 25384243 JRNL DOI 10.1038/NMETH.3172 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 921 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 28.8525 - 3.8234 1.00 2606 140 0.1741 0.1972 REMARK 3 2 3.8234 - 3.0358 1.00 2438 135 0.1469 0.2003 REMARK 3 3 3.0358 - 2.6524 1.00 2424 136 0.1555 0.1900 REMARK 3 4 2.6524 - 2.4100 1.00 2378 129 0.1557 0.2150 REMARK 3 5 2.4100 - 2.2373 1.00 2388 137 0.1468 0.1994 REMARK 3 6 2.2373 - 2.1055 1.00 2371 121 0.1479 0.1894 REMARK 3 7 2.1055 - 2.0000 1.00 2363 123 0.1573 0.2242 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.03 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 : 0.008 1710 REMARK 3 ANGLE : 1.132 2319 REMARK 3 CHIRALITY : 0.042 244 REMARK 3 PLANARITY : 0.004 314 REMARK 3 DIHEDRAL : 13.106 623 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 3WXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000096926. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 296 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 8856 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.23 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MPCCD OCTAL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22712 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 3AL7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M ADA, 1.0M K/NA TARTRATE, PH 7.2, REMARK 280 BATCH METHOD, 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 74.88800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.84950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.84950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.44400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.84950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.84950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.33200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.84950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.84950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.44400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.84950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.84950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.33200 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 74.88800 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 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 480 O HOH A 504 2.16 REMARK 500 O HOH A 469 O HOH A 485 2.17 REMARK 500 NH1 ARG A 175 O HOH A 514 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 ASP A 25 -138.27 55.03 REMARK 500 ASP A 59 -159.85 -87.37 REMARK 500 CYS A 71 73.35 -112.30 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AL7 RELATED DB: PDB REMARK 900 RECOMBINANT THAUMATIN I REMARK 900 RELATED ID: 3ALD RELATED DB: PDB REMARK 900 PLANT THAUMATIN I REMARK 900 RELATED ID: 3VHF RELATED DB: PDB REMARK 900 PLANT THAUMATIN I REMARK 900 RELATED ID: 3AOK RELATED DB: PDB REMARK 900 PLANT THAUMATIN II REMARK 900 RELATED ID: 3WOU RELATED DB: PDB REMARK 900 RECOMBINANT THAUMATIN II DBREF 3WXS A 1 207 UNP A1IIJ1 A1IIJ1_THADA 23 229 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 *166(H2 O) HELIX 1 1 ASP A 129 CYS A 134 1 6 HELIX 2 2 PRO A 135 LYS A 139 5 5 HELIX 3 3 ASP A 147 GLN A 153 1 7 HELIX 4 4 THR A 154 CYS A 159 1 6 HELIX 5 5 THR A 167 CYS A 177 1 11 SHEET 1 A 5 SER A 36 ASN A 40 0 SHEET 2 A 5 THR A 2 ASN A 7 -1 N ILE A 5 O TRP A 37 SHEET 3 A 5 TYR A 199 PHE A 203 1 O VAL A 201 N VAL A 6 SHEET 4 A 5 MET A 112 PRO A 116 -1 N SER A 115 O ARG A 200 SHEET 5 A 5 VAL A 124 CYS A 126 -1 O VAL A 124 N PHE A 114 SHEET 1 B 6 ALA A 23 LEU A 31 0 SHEET 2 B 6 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 B 6 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 B 6 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 5 B 6 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 6 B 6 ALA A 180 PHE A 181 1 O PHE A 181 N ILE A 102 SHEET 1 C 5 GLY A 64 THR A 68 0 SHEET 2 C 5 GLY A 48 PHE A 58 -1 N TYR A 57 O ILE A 65 SHEET 3 C 5 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 4 C 5 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 5 C 5 VAL A 191 PRO A 194 -1 O VAL A 191 N ILE A 100 SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.00 SSBOND 2 CYS A 56 CYS A 66 1555 1555 2.02 SSBOND 3 CYS A 71 CYS A 77 1555 1555 2.01 SSBOND 4 CYS A 121 CYS A 193 1555 1555 2.02 SSBOND 5 CYS A 126 CYS A 177 1555 1555 2.01 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.03 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.02 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.02 CISPEP 1 PRO A 83 PRO A 84 0 4.47 SITE 1 AC1 10 ARG A 29 GLU A 35 SER A 36 PHE A 152 SITE 2 AC1 10 TYR A 157 HOH A 411 HOH A 455 HOH A 527 SITE 3 AC1 10 HOH A 531 HOH A 541 CRYST1 57.699 57.699 149.776 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 0.017331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006677 0.00000