HEADER PLANT PROTEIN 24-AUG-11 3VHG TITLE RECOMBINANT THAUMATIN I AT PH 8.0 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: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X33, SMD1168H; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC6-PRETH KEYWDS THAUMATIN, SWEET-TASTING PROTEIN, THAUMATIN FAMILY, MAINLY BETA, KEYWDS 2 TASTE PROTEIN, SWEET RECEPTOR, ARIL, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MASUDA,B.MIKAMI,N.KITABATAKE,F.TANI REVDAT 2 08-NOV-23 3VHG 1 REMARK REVDAT 1 29-AUG-12 3VHG 0 JRNL AUTH T.MASUDA,B.MIKAMI,F.TANI,N.KITABATAKE JRNL TITL RECOMBINAT THAUMATIN I AT PH 8.0 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.121 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.111 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5339 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 107219 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.113 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.103 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4757 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 90129 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1551 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 453 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1982.2 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1418.4 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 28 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 19410 REMARK 3 NUMBER OF RESTRAINTS : 24492 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.034 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.088 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.074 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.115 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 3VHG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095048. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107219 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.7486 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.115 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: 3VHF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM TRIS-HCL BUFFER, 15% PEG3350, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.81800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.88550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.76400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.88550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.81800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.76400 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: 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: 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 ARG A 29 CD - NE - CZ ANGL. DEV. = 30.9 DEGREES REMARK 500 ARG A 29 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 82 NH1 - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 PHE A 152 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 TYR A 157 CG - CD1 - CE1 ANGL. DEV. = 5.8 DEGREES REMARK 500 CYS A 164 CB - CA - C ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES 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 -135.17 54.78 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 GOL A 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 240 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AL7 RELATED DB: PDB REMARK 900 RECOMBINANT THAUMATIN I (TETRAGONAL FORM) REMARK 900 RELATED ID: 3ALD 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: 3VHF RELATED DB: PDB REMARK 900 PLANT THAUMATIN I DBREF 3VHG 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 GOL A 230 6 HET GOL A 240 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *453(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 PHE A 203 N VAL A 6 SHEET 4 A 5 MET A 112 PRO A 116 -1 N ASP A 113 O THR A 202 SHEET 5 A 5 VAL A 124 CYS A 126 -1 O VAL A 124 N PHE A 114 SHEET 1 B 4 ALA A 23 LEU A 31 0 SHEET 2 B 4 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 B 4 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 B 4 GLY A 64 THR A 68 -1 O ILE A 65 N TYR A 57 SHEET 1 C 6 ALA A 23 LEU A 31 0 SHEET 2 C 6 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 C 6 GLY A 48 PHE A 58 -1 O LYS A 49 N SER A 18 SHEET 4 C 6 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 5 C 6 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 6 C 6 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 2.04 SSBOND 2 CYS A 56 CYS A 66 1555 1555 2.06 SSBOND 3 CYS A 71 CYS A 77 1555 1555 2.03 SSBOND 4 CYS A 121 CYS A 193 1555 1555 2.04 SSBOND 5 CYS A 126 CYS A 177 1555 1555 2.05 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.05 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.01 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.03 CISPEP 1 PRO A 83 PRO A 84 0 3.97 SITE 1 AC1 8 ARG A 29 ARG A 76 HOH A 321 HOH A 352 SITE 2 AC1 8 HOH A 475 HOH A 645 HOH A 647 HOH A 671 SITE 1 AC2 7 PRO A 43 GLY A 44 THR A 45 ASN A 46 SITE 2 AC2 7 HOH A 362 HOH A 433 HOH A 483 CRYST1 43.636 63.528 71.771 90.00 90.00 90.00 P 21 21 21 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 0.022917 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013933 0.00000