HEADER SUGAR BINDING PROTEIN 24-JAN-24 8RSD TITLE THAUMATIN MEASURED VIA SERIAL CRYSTALLOGRAPHY FROM A KAPTON HARE-CHIP TITLE 2 (125 MICRON) CAVEAT 8RSD TAR X 501 HAS WRONG CHIRALITY AT ATOM C2 TAR X 501 HAS WRONG CAVEAT 2 8RSD CHIRALITY AT ATOM C3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN I; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: THAUMATIN-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_TAXID: 4621 KEYWDS THAUMATIN, SERIAL CRYSTALLOGRAPHY, SSX, KAPTON HARE-CHIP, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BOSMAN,A.PRESTER,L.VON SOOSTEN,S.DIBENEDETTO,K.BARTELS,S.SUNG,D.VON AUTHOR 2 STETTEN,P.MEHRABI,E.C.SCHULZ REVDAT 1 04-DEC-24 8RSD 0 JRNL AUTH R.BOSMAN,A.PRESTER,L.VON SOOSTEN,S.DIBENEDETTO,K.BARTELS, JRNL AUTH 2 S.SUNG,D.VON STETTEN,P.MEHRABI,G.BLATTER,G.LU,S.BERNHARD, JRNL AUTH 3 M.OSBILD,E.C.SCHULZ JRNL TITL KAPTON-BASED HARE CHIPS FOR FIXED-TARGET SERIAL JRNL TITL 2 CRYSTALLOGRAPHY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 1375 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 54.3000 - 3.6600 1.00 3035 155 0.1327 0.1335 REMARK 3 2 3.6600 - 2.9100 1.00 2871 133 0.1484 0.1888 REMARK 3 3 2.9100 - 2.5400 1.00 2830 130 0.1816 0.2308 REMARK 3 4 2.5400 - 2.3100 1.00 2831 110 0.1725 0.2249 REMARK 3 5 2.3100 - 2.1400 1.00 2778 135 0.1717 0.2028 REMARK 3 6 2.1400 - 2.0200 1.00 2761 153 0.2299 0.2799 REMARK 3 7 2.0200 - 1.9100 1.00 2747 133 0.2329 0.2542 REMARK 3 8 1.9100 - 1.8300 1.00 2743 132 0.2624 0.3147 REMARK 3 9 1.8300 - 1.7600 1.00 2736 137 0.3660 0.3974 REMARK 3 10 1.7600 - 1.7000 0.99 2725 157 0.4928 0.4932 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.294 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.04 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 : 0.012 1653 REMARK 3 ANGLE : 1.201 2252 REMARK 3 CHIRALITY : 0.075 243 REMARK 3 PLANARITY : 0.013 300 REMARK 3 DIHEDRAL : 6.818 242 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 8RSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.10.2 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL 0.10.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 54.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 73.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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 <I/SIGMA(I)> FOR SHELL : 0.590 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICROCRYSTALS WERE FORMED VIA MIXING REMARK 280 PROTEIN SOLUTION WITH PRECIPITANT SOLUTION, 0.1MM KH2PO4 PH 6.5, REMARK 280 1.7M SODIUM TARTRATE WITH A 1:3 RATIO RESPECTIVELY., BATCH MODE, 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 75.45000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.10000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.10000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.17500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.10000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.10000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.17500 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 75.45000 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: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 MET X -21 REMARK 465 ALA X -20 REMARK 465 ALA X -19 REMARK 465 THR X -18 REMARK 465 THR X -17 REMARK 465 CYS X -16 REMARK 465 PHE X -15 REMARK 465 PHE X -14 REMARK 465 PHE X -13 REMARK 465 LEU X -12 REMARK 465 PHE X -11 REMARK 465 PRO X -10 REMARK 465 PHE X -9 REMARK 465 LEU X -8 REMARK 465 LEU X -7 REMARK 465 LEU X -6 REMARK 465 LEU X -5 REMARK 465 THR X -4 REMARK 465 LEU X -3 REMARK 465 SER X -2 REMARK 465 ARG X -1 REMARK 465 ALA X 0 REMARK 465 LEU X 208 REMARK 465 GLU X 209 REMARK 465 LEU X 210 REMARK 465 GLU X 211 REMARK 465 ASP X 212 REMARK 465 GLU X 213 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 ALA X 22 144.59 -174.75 REMARK 500 ASP X 25 -137.20 56.70 REMARK 500 ASP X 59 -165.93 -100.23 REMARK 500 CYS X 71 69.08 -113.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 8RSD X -21 213 UNP P02883 THM1_THADA 1 235 SEQADV 8RSD LYS X 46 UNP P02883 ASN 68 CONFLICT SEQRES 1 X 235 MET ALA ALA THR THR CYS PHE PHE PHE LEU PHE PRO PHE SEQRES 2 X 235 LEU LEU LEU LEU THR LEU SER ARG ALA ALA THR PHE GLU SEQRES 3 X 235 ILE VAL ASN ARG CYS SER TYR THR VAL TRP ALA ALA ALA SEQRES 4 X 235 SER LYS GLY ASP ALA ALA LEU ASP ALA GLY GLY ARG GLN SEQRES 5 X 235 LEU ASN SER GLY GLU SER TRP THR ILE ASN VAL GLU PRO SEQRES 6 X 235 GLY THR LYS GLY GLY LYS ILE TRP ALA ARG THR ASP CYS SEQRES 7 X 235 TYR PHE ASP ASP SER GLY SER GLY ILE CYS LYS THR GLY SEQRES 8 X 235 ASP CYS GLY GLY LEU LEU ARG CYS LYS ARG PHE GLY ARG SEQRES 9 X 235 PRO PRO THR THR LEU ALA GLU PHE SER LEU ASN GLN TYR SEQRES 10 X 235 GLY LYS ASP TYR ILE ASP ILE SER ASN ILE LYS GLY PHE SEQRES 11 X 235 ASN VAL PRO MET ASP PHE SER PRO THR THR ARG GLY CYS SEQRES 12 X 235 ARG GLY VAL ARG CYS ALA ALA ASP ILE VAL GLY GLN CYS SEQRES 13 X 235 PRO ALA LYS LEU LYS ALA PRO GLY GLY GLY CYS ASN ASP SEQRES 14 X 235 ALA CYS THR VAL PHE GLN THR SER GLU TYR CYS CYS THR SEQRES 15 X 235 THR GLY LYS CYS GLY PRO THR GLU TYR SER ARG PHE PHE SEQRES 16 X 235 LYS ARG LEU CYS PRO ASP ALA PHE SER TYR VAL LEU ASP SEQRES 17 X 235 LYS PRO THR THR VAL THR CYS PRO GLY SER SER ASN TYR SEQRES 18 X 235 ARG VAL THR PHE CYS PRO THR ALA LEU GLU LEU GLU ASP SEQRES 19 X 235 GLU HET TAR X 501 10 HETNAM TAR D(-)-TARTARIC ACID FORMUL 2 TAR C4 H6 O6 FORMUL 3 HOH *178(H2 O) HELIX 1 AA1 ASP X 129 CYS X 134 1 6 HELIX 2 AA2 PRO X 135 LYS X 139 5 5 HELIX 3 AA3 ASP X 147 GLN X 153 1 7 HELIX 4 AA4 THR X 154 CYS X 159 1 6 HELIX 5 AA5 THR X 167 CYS X 177 1 11 SHEET 1 AA1 5 SER X 36 ASN X 40 0 SHEET 2 AA1 5 THR X 2 ASN X 7 -1 N ILE X 5 O TRP X 37 SHEET 3 AA1 5 TYR X 199 PHE X 203 1 O VAL X 201 N VAL X 6 SHEET 4 AA1 5 MET X 112 PRO X 116 -1 N SER X 115 O ARG X 200 SHEET 5 AA1 5 VAL X 124 CYS X 126 -1 O VAL X 124 N PHE X 114 SHEET 1 AA2 6 ALA X 23 LEU X 31 0 SHEET 2 AA2 6 VAL X 13 SER X 18 -1 N VAL X 13 O LEU X 31 SHEET 3 AA2 6 GLY X 48 PHE X 58 -1 O LYS X 49 N SER X 18 SHEET 4 AA2 6 LEU X 87 GLN X 94 -1 O ALA X 88 N ILE X 50 SHEET 5 AA2 6 LYS X 97 SER X 103 -1 O LYS X 97 N GLN X 94 SHEET 6 AA2 6 ALA X 180 PHE X 181 1 O PHE X 181 N ILE X 102 SHEET 1 AA3 5 GLY X 64 THR X 68 0 SHEET 2 AA3 5 GLY X 48 PHE X 58 -1 N TYR X 57 O ILE X 65 SHEET 3 AA3 5 LEU X 87 GLN X 94 -1 O ALA X 88 N ILE X 50 SHEET 4 AA3 5 LYS X 97 SER X 103 -1 O LYS X 97 N GLN X 94 SHEET 5 AA3 5 VAL X 191 PRO X 194 -1 O CYS X 193 N ASP X 98 SSBOND 1 CYS X 9 CYS X 204 1555 1555 2.01 SSBOND 2 CYS X 56 CYS X 66 1555 1555 2.03 SSBOND 3 CYS X 71 CYS X 77 1555 1555 2.02 SSBOND 4 CYS X 121 CYS X 193 1555 1555 2.04 SSBOND 5 CYS X 126 CYS X 177 1555 1555 2.03 SSBOND 6 CYS X 134 CYS X 145 1555 1555 2.04 SSBOND 7 CYS X 149 CYS X 158 1555 1555 2.04 SSBOND 8 CYS X 159 CYS X 164 1555 1555 2.03 CISPEP 1 PRO X 83 PRO X 84 0 6.89 CRYST1 58.200 58.200 150.900 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 0.017182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006627 0.00000