HEADER PLANT PROTEIN 09-MAR-19 6O8A TITLE THAUMATIN NATIVE-SAD STRUCTURE DETERMINED AT 5 KEV FROM MICROCRYSTALS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THAUMATIN I; COMPND 5 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: THAUMATOCOCCUS DANIELLII; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4621 KEYWDS MICROCRYSTAL, MICRODIFFRACTION, NATIVE-SAD, LOW ENERGY, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.GUO,P.ZHU,M.R.FUCHS,W.SHI,B.ANDI,Y.GAO,W.A.HENDRICKSON,S.MCSWEENEY, AUTHOR 2 Q.LIU REVDAT 3 18-DEC-19 6O8A 1 REMARK REVDAT 2 31-JUL-19 6O8A 1 JRNL REVDAT 1 08-MAY-19 6O8A 0 JRNL AUTH G.GUO,P.ZHU,M.R.FUCHS,W.SHI,B.ANDI,Y.GAO,W.A.HENDRICKSON, JRNL AUTH 2 S.MCSWEENEY,Q.LIU JRNL TITL SYNCHROTRON MICROCRYSTAL NATIVE-SAD PHASING AT A LOW ENERGY. JRNL REF IUCRJ V. 6 532 2019 JRNL REFN ESSN 2052-2525 JRNL PMID 31316798 JRNL DOI 10.1107/S2052252519004536 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 737 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 37.8540 - 4.4444 1.00 2830 146 0.1489 0.1496 REMARK 3 2 4.4444 - 3.5285 1.00 2869 130 0.1421 0.1815 REMARK 3 3 3.5285 - 3.0827 1.00 2840 153 0.1829 0.2290 REMARK 3 4 3.0827 - 2.8009 1.00 2789 167 0.2293 0.2568 REMARK 3 5 2.8009 - 2.6002 1.00 2839 141 0.3401 0.3687 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.070 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 : 0.002 1603 REMARK 3 ANGLE : 0.435 2178 REMARK 3 CHIRALITY : 0.039 232 REMARK 3 PLANARITY : 0.003 286 REMARK 3 DIHEDRAL : 12.151 962 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 1:207) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7195 16.5942 -4.9837 REMARK 3 T TENSOR REMARK 3 T11: 0.1525 T22: 0.1281 REMARK 3 T33: 0.1628 T12: 0.0008 REMARK 3 T13: -0.0056 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 1.2680 L22: 0.5392 REMARK 3 L33: 1.3693 L12: -0.0016 REMARK 3 L13: 0.3187 L23: 0.1219 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: -0.0288 S13: -0.0762 REMARK 3 S21: 0.0342 S22: 0.0083 S23: 0.0095 REMARK 3 S31: 0.0972 S32: -0.0038 S33: -0.0155 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 6O8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000240207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.479 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8435 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 323.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M SODIUM TARTRATE, 100 MM ADA, REMARK 280 PH6.5, VAPOR DIFFUSION, SITTING 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 75.22250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.84900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.84900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.61125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.84900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.84900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.83375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.84900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.84900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.61125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.84900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.84900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.83375 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 75.22250 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: 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 -131.09 59.28 REMARK 500 CYS A 71 70.24 -110.13 REMARK 500 ASN A 109 -39.64 -133.58 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 6O8A A 1 207 UNP P02883 THM1_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 ASN 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 *94(H2 O) HELIX 1 AA1 PRO A 135 LYS A 139 5 5 HELIX 2 AA2 ASP A 147 GLN A 153 1 7 HELIX 3 AA3 THR A 154 CYS A 159 1 6 HELIX 4 AA4 TYR A 169 CYS A 177 1 9 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 6 ALA A 23 LEU A 31 0 SHEET 2 AA2 6 VAL A 13 SER A 18 -1 N VAL A 13 O LEU A 31 SHEET 3 AA2 6 GLY A 48 TRP A 51 -1 O LYS A 49 N SER A 18 SHEET 4 AA2 6 LEU A 87 GLN A 94 -1 O ALA A 88 N ILE A 50 SHEET 5 AA2 6 LYS A 97 SER A 103 -1 O LYS A 97 N GLN A 94 SHEET 6 AA2 6 ALA A 180 PHE A 181 1 O PHE A 181 N ILE A 102 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 TRP A 51 -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 THR A 54 PHE A 58 0 SHEET 2 AA4 2 GLY A 64 THR A 68 -1 O ILE A 65 N TYR A 57 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 2.03 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 2.03 CISPEP 1 PRO A 83 PRO A 84 0 3.68 SITE 1 AC1 7 ARG A 29 GLU A 35 SER A 36 PHE A 152 SITE 2 AC1 7 TYR A 157 HOH A 401 HOH A 404 CRYST1 57.698 57.698 150.445 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 0.017332 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006647 0.00000