HEADER PLANT PROTEIN 08-APR-18 6G89 TITLE THAUMATIN SOLVED BY NATIVE SAD FROM A DATASET COLLECTED IN 0.6 SECOND TITLE 2 WITH JUNGFRAU DETECTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN I; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: THAUMATIN-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE; SOURCE 4 ORGANISM_TAXID: 4621 KEYWDS NATIVE-SAD, JUNGFRAU, INTEGRATING DETECTOR, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.LEONARSKI,V.OLIERIC,L.VERA,S.REDFORD,M.WANG REVDAT 2 24-OCT-18 6G89 1 JRNL REVDAT 1 01-AUG-18 6G89 0 JRNL AUTH F.LEONARSKI,S.REDFORD,A.MOZZANICA,C.LOPEZ-CUENCA, JRNL AUTH 2 E.PANEPUCCI,K.NASS,D.OZEROV,L.VERA,V.OLIERIC,D.BUNTSCHU, JRNL AUTH 3 R.SCHNEIDER,G.TINTI,E.FROEJDH,K.DIEDERICHS,O.BUNK,B.SCHMITT, JRNL AUTH 4 M.WANG JRNL TITL FAST AND ACCURATE DATA COLLECTION FOR MACROMOLECULAR JRNL TITL 2 CRYSTALLOGRAPHY USING THE JUNGFRAU DETECTOR. JRNL REF NAT. METHODS V. 15 799 2018 JRNL REFN ESSN 1548-7105 JRNL PMID 30275593 JRNL DOI 10.1038/S41592-018-0143-7 REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.3 REMARK 3 NUMBER OF REFLECTIONS : 16460 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 819 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 37.8179 - 4.2850 0.98 3121 163 0.1739 0.1997 REMARK 3 2 4.2850 - 3.4018 0.97 3058 164 0.1524 0.2134 REMARK 3 3 3.4018 - 2.9720 0.97 3090 165 0.1729 0.2364 REMARK 3 4 2.9720 - 2.7003 0.95 2984 152 0.1746 0.2324 REMARK 3 5 2.7003 - 2.5068 0.78 2481 124 0.1821 0.2356 REMARK 3 6 2.5068 - 2.3591 0.29 907 51 0.2036 0.3248 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.140 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 : 0.009 1616 REMARK 3 ANGLE : 0.920 2198 REMARK 3 CHIRALITY : 0.067 235 REMARK 3 PLANARITY : 0.005 290 REMARK 3 DIHEDRAL : 14.273 602 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 6G89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.0667 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16463 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 37.813 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.3 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 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 : 9.650 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD, CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% SODIUM POTASSIUM TARTRATE, 100 MM REMARK 280 BIS-TRIS PROPANE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 74.96350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.91600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.91600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.48175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.91600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.91600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.44525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.91600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.91600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.48175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.91600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.91600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.44525 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 74.96350 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: 340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR C 99 CG CD1 CD2 CE1 CE2 CZ OH 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 C 25 -141.72 52.01 REMARK 500 ARG C 29 146.47 -175.19 REMARK 500 ASP C 55 60.54 60.13 REMARK 500 CYS C 71 73.42 -119.62 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 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA C 302 DBREF 6G89 C 1 206 UNP P02883 THM1_THADA 23 228 SEQRES 1 C 206 ALA THR PHE GLU ILE VAL ASN ARG CYS SER TYR THR VAL SEQRES 2 C 206 TRP ALA ALA ALA SER LYS GLY ASP ALA ALA LEU ASP ALA SEQRES 3 C 206 GLY GLY ARG GLN LEU ASN SER GLY GLU SER TRP THR ILE SEQRES 4 C 206 ASN VAL GLU PRO GLY THR ASN GLY GLY LYS ILE TRP ALA SEQRES 5 C 206 ARG THR ASP CYS TYR PHE ASP ASP SER GLY SER GLY ILE SEQRES 6 C 206 CYS LYS THR GLY ASP CYS GLY GLY LEU LEU ARG CYS LYS SEQRES 7 C 206 ARG PHE GLY ARG PRO PRO THR THR LEU ALA GLU PHE SER SEQRES 8 C 206 LEU ASN GLN TYR GLY LYS ASP TYR ILE ASP ILE SER ASN SEQRES 9 C 206 ILE LYS GLY PHE ASN VAL PRO MET ASP PHE SER PRO THR SEQRES 10 C 206 THR ARG GLY CYS ARG GLY VAL ARG CYS ALA ALA ASP ILE SEQRES 11 C 206 VAL GLY GLN CYS PRO ALA LYS LEU LYS ALA PRO GLY GLY SEQRES 12 C 206 GLY CYS ASN ASP ALA CYS THR VAL PHE GLN THR SER GLU SEQRES 13 C 206 TYR CYS CYS THR THR GLY LYS CYS GLY PRO THR GLU TYR SEQRES 14 C 206 SER ARG PHE PHE LYS ARG LEU CYS PRO ASP ALA PHE SER SEQRES 15 C 206 TYR VAL LEU ASP LYS PRO THR THR VAL THR CYS PRO GLY SEQRES 16 C 206 SER SER ASN TYR ARG VAL THR PHE CYS PRO THR HET TLA C 301 14 HET TLA C 302 14 HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 TLA 2(C4 H6 O6) FORMUL 4 HOH *150(H2 O) HELIX 1 AA1 PRO C 135 LYS C 139 5 5 HELIX 2 AA2 ASP C 147 GLN C 153 1 7 HELIX 3 AA3 THR C 154 CYS C 159 1 6 HELIX 4 AA4 THR C 167 CYS C 177 1 11 SHEET 1 AA1 5 SER C 36 ASN C 40 0 SHEET 2 AA1 5 THR C 2 ASN C 7 -1 N ILE C 5 O TRP C 37 SHEET 3 AA1 5 TYR C 199 PHE C 203 1 O PHE C 203 N VAL C 6 SHEET 4 AA1 5 MET C 112 PRO C 116 -1 N SER C 115 O ARG C 200 SHEET 5 AA1 5 VAL C 124 CYS C 126 -1 O CYS C 126 N MET C 112 SHEET 1 AA2 4 ALA C 23 LEU C 31 0 SHEET 2 AA2 4 VAL C 13 SER C 18 -1 N VAL C 13 O LEU C 31 SHEET 3 AA2 4 GLY C 48 PHE C 58 -1 O LYS C 49 N SER C 18 SHEET 4 AA2 4 GLY C 64 THR C 68 -1 O ILE C 65 N TYR C 57 SHEET 1 AA3 6 ALA C 23 LEU C 31 0 SHEET 2 AA3 6 VAL C 13 SER C 18 -1 N VAL C 13 O LEU C 31 SHEET 3 AA3 6 GLY C 48 PHE C 58 -1 O LYS C 49 N SER C 18 SHEET 4 AA3 6 LEU C 87 GLN C 94 -1 O ALA C 88 N ILE C 50 SHEET 5 AA3 6 LYS C 97 SER C 103 -1 O LYS C 97 N GLN C 94 SHEET 6 AA3 6 VAL C 191 PRO C 194 -1 O VAL C 191 N ILE C 100 SSBOND 1 CYS C 9 CYS C 204 1555 1555 2.03 SSBOND 2 CYS C 56 CYS C 66 1555 1555 2.05 SSBOND 3 CYS C 71 CYS C 77 1555 1555 2.04 SSBOND 4 CYS C 121 CYS C 193 1555 1555 2.05 SSBOND 5 CYS C 126 CYS C 177 1555 1555 2.03 SSBOND 6 CYS C 134 CYS C 145 1555 1555 2.03 SSBOND 7 CYS C 149 CYS C 158 1555 1555 2.02 SSBOND 8 CYS C 159 CYS C 164 1555 1555 2.03 CISPEP 1 PRO C 83 PRO C 84 0 5.54 SITE 1 AC1 9 ARG C 29 GLU C 35 SER C 36 PHE C 152 SITE 2 AC1 9 TYR C 157 HOH C 410 HOH C 422 HOH C 448 SITE 3 AC1 9 HOH C 473 SITE 1 AC2 7 GLY C 96 LYS C 97 ALA C 136 PRO C 194 SITE 2 AC2 7 GLY C 195 HOH C 453 HOH C 454 CRYST1 57.832 57.832 149.927 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 0.017291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006670 0.00000