HEADER PLANT PROTEIN 03-SEP-21 7VCG TITLE THAUMATIN PROTECTED BY ALGINATE GEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THAUMATIN-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE, PHRYNIUM DANIELLII; SOURCE 4 ORGANISM_TAXID: 4621 KEYWDS HYDROGEL ALGINATE GEL, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.MUROYAMA,F.TOMOIKE,T.NAGAE,T.OKADA REVDAT 2 29-NOV-23 7VCG 1 REMARK REVDAT 1 07-SEP-22 7VCG 0 JRNL AUTH S.MORITA,H.MUROYAMA,T.ITABASHI,T.NAGAE,S.TAKEUCHI,T.OKADA, JRNL AUTH 2 F.TOMOIKE JRNL TITL POST-CRYSTALLIZATION PROTECTION OF PROTEIN CRYSTALS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 71712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.790 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 28.9700 - 3.0100 1.00 5358 154 0.1590 0.1532 REMARK 3 2 3.0100 - 2.3900 1.00 5108 147 0.1633 0.1717 REMARK 3 3 2.3900 - 2.0900 1.00 5021 144 0.1490 0.1518 REMARK 3 4 2.0900 - 1.9000 1.00 5002 143 0.1350 0.1408 REMARK 3 5 1.9000 - 1.7600 1.00 4966 143 0.1392 0.1774 REMARK 3 6 1.7600 - 1.6600 1.00 4943 141 0.1254 0.1490 REMARK 3 7 1.6600 - 1.5700 1.00 4952 142 0.1241 0.1357 REMARK 3 8 1.5700 - 1.5100 1.00 4939 142 0.1264 0.1565 REMARK 3 9 1.5100 - 1.4500 1.00 4898 140 0.1317 0.1667 REMARK 3 10 1.4500 - 1.4000 1.00 4933 142 0.1407 0.1780 REMARK 3 11 1.4000 - 1.3500 1.00 4897 141 0.1501 0.1583 REMARK 3 12 1.3500 - 1.3200 1.00 4889 140 0.1544 0.1872 REMARK 3 13 1.3200 - 1.2800 1.00 4900 141 0.1672 0.2068 REMARK 3 14 1.2800 - 1.2500 1.00 4906 140 0.1843 0.2499 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) : 0.095 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.13 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 : 0.005 1637 REMARK 3 ANGLE : 0.818 2222 REMARK 3 CHIRALITY : 0.079 236 REMARK 3 PLANARITY : 0.005 294 REMARK 3 DIHEDRAL : 27.901 664 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 7VCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300024006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AICHISR REMARK 200 BEAMLINE : BL2S1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 45.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.22200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.70 REMARK 200 R MERGE FOR SHELL (I) : 0.93700 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: 3ALD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M SODIUM TARTRATE, 0.1 M HEPES, PH REMARK 280 7.5, COUNTER-DIFFUSION, 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 75.11750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.97250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.97250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.55875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.97250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.97250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.67625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.97250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.97250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.55875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.97250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.97250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.67625 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 75.11750 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: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 ASP A 60 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 -138.85 57.79 REMARK 500 CYS A 71 77.75 -113.31 REMARK 500 CYS A 71 77.75 -113.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VCG A 1 206 UNP P02883 THM1_THADA 23 228 SEQRES 1 A 206 ALA THR PHE GLU ILE VAL ASN ARG CYS SER TYR THR VAL SEQRES 2 A 206 TRP ALA ALA ALA SER LYS GLY ASP ALA ALA LEU ASP ALA SEQRES 3 A 206 GLY GLY ARG GLN LEU ASN SER GLY GLU SER TRP THR ILE SEQRES 4 A 206 ASN VAL GLU PRO GLY THR ASN GLY GLY LYS ILE TRP ALA SEQRES 5 A 206 ARG THR ASP CYS TYR PHE ASP ASP SER GLY SER GLY ILE SEQRES 6 A 206 CYS LYS THR GLY ASP CYS GLY GLY LEU LEU ARG CYS LYS SEQRES 7 A 206 ARG PHE GLY ARG PRO PRO THR THR LEU ALA GLU PHE SER SEQRES 8 A 206 LEU ASN GLN TYR GLY LYS ASP TYR ILE ASP ILE SER ASN SEQRES 9 A 206 ILE LYS GLY PHE ASN VAL PRO MET ASP PHE SER PRO THR SEQRES 10 A 206 THR ARG GLY CYS ARG GLY VAL ARG CYS ALA ALA ASP ILE SEQRES 11 A 206 VAL GLY GLN CYS PRO ALA LYS LEU LYS ALA PRO GLY GLY SEQRES 12 A 206 GLY CYS ASN ASP ALA CYS THR VAL PHE GLN THR SER GLU SEQRES 13 A 206 TYR CYS CYS THR THR GLY LYS CYS GLY PRO THR GLU TYR SEQRES 14 A 206 SER ARG PHE PHE LYS ARG LEU CYS PRO ASP ALA PHE SER SEQRES 15 A 206 TYR VAL LEU ASP LYS PRO THR THR VAL THR CYS PRO GLY SEQRES 16 A 206 SER SER ASN TYR ARG VAL THR PHE CYS PRO THR HET TLA A 301 10 HET GOL A 302 6 HET GOL A 303 6 HETNAM TLA L(+)-TARTARIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 TLA C4 H6 O6 FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *234(H2 O) HELIX 1 AA1 ASP A 129 CYS A 134 1 6 HELIX 2 AA2 PRO A 135 LYS A 139 5 5 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 SSBOND 1 CYS A 9 CYS A 204 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 66 1555 1555 2.04 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 2.04 SSBOND 6 CYS A 134 CYS A 145 1555 1555 2.04 SSBOND 7 CYS A 149 CYS A 158 1555 1555 2.04 SSBOND 8 CYS A 159 CYS A 164 1555 1555 2.03 CISPEP 1 PRO A 83 PRO A 84 0 3.96 CRYST1 57.945 57.945 150.235 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 0.017258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006656 0.00000