HEADER PLANT PROTEIN 07-DEC-03 1RQW TITLE THAUMATIN STRUCTURE AT 1.05 A RESOLUTION 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: MIRACLE FRUIT; SOURCE 4 ORGANISM_TAXID: 4621 KEYWDS THAUMATIN; X-RAY STRUCTURE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.MA,G.M.SHELDRICK REVDAT 5 03-APR-24 1RQW 1 REMARK REVDAT 4 04-APR-18 1RQW 1 REMARK REVDAT 3 25-APR-12 1RQW 1 REMARK VERSN REVDAT 2 24-FEB-09 1RQW 1 VERSN REVDAT 1 23-DEC-03 1RQW 0 JRNL AUTH Q.MA,G.M.SHELDRICK JRNL TITL THAUMATIN STRUCTURE AT 1.05 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.05 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 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) : 0.127 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.127 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5831 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 116567 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 398 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 17 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.016 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.439 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.063 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.074 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.053 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.028 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.116 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: NULL REMARK 4 REMARK 4 1RQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE M06X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC BLUE CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT, SADABS, XPREP, PROTEUM REMARK 200 PLUS REMARK 200 DATA SCALING SOFTWARE : SAINT, SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116807 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 160.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 FOR THE DATA SET : 37.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.25 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 FOR SHELL : 7.170 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: IN HOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP: 4UL 40MG/ML THAUMATIN (IN DTNB REMARK 280 SATURATED DDH2O) + 2UL WELL SOLUTION [0.05M ADA PH6.8, 0.6M REMARK 280 POTASSIUM SODIUM TARTRATE (WHOSE 2M STOCK SOUTION IS SATURATED REMARK 280 WITH DTNB), 20% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K, PH 6.80 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 75.06250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.92350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.92350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.53125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.92350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.92350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.59375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.92350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.92350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.53125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.92350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.92350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.59375 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 75.06250 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 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 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 A1282 LIES ON A SPECIAL POSITION. 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 NH1 - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP A 70 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 122 CD - NE - CZ ANGL. DEV. = 10.2 DEGREES REMARK 500 CYS A 126 CB - CA - C ANGL. DEV. = 9.6 DEGREES REMARK 500 CYS A 126 CA - CB - SG ANGL. DEV. = 15.5 DEGREES REMARK 500 LYS A 163 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 LYS A 163 O - C - N ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG A 171 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -3.7 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 -139.12 55.91 REMARK 500 CYS A 71 77.77 -114.10 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 1001 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM REMARK 999 I IS USED BECAUSE THE CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE REMARK 999 OF LYS AND ASN. ASP IS USED AT POSITION 113 AS SUGGESTED BY KO ET REMARK 999 AL., ACTA CRYST. D50,813(1994) DBREF 1RQW A 1 207 UNP P02883 THM1_THADA 1 207 SEQADV 1RQW LYS A 46 UNP P02883 ASN 46 SEE REMARK 999 SEQADV 1RQW ASP A 113 UNP P02883 ASN 113 SEE REMARK 999 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 LYS 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 A1001 10 HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 TLA C4 H6 O6 FORMUL 3 HOH *398(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 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 CYS A 193 N ASP A 98 SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.05 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 2.06 SSBOND 5 CYS A 126 CYS A 177 1555 1555 2.06 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.06 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.05 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.03 CISPEP 1 PRO A 83 PRO A 84 0 2.78 SITE 1 AC1 12 ARG A 29 GLU A 35 SER A 36 PHE A 152 SITE 2 AC1 12 TYR A 157 HOH A1016 HOH A1023 HOH A1053 SITE 3 AC1 12 HOH A1068 HOH A1092 HOH A1185 HOH A1190 CRYST1 57.847 57.847 150.125 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 0.017287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017287 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006661 0.00000