HEADER PLANT PROTEIN 26-MAY-16 5K7Q TITLE MICROED STRUCTURE OF THAUMATIN AT 2.5 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: THAUMATIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THAUMATIN I SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THAUMATOCOCCUS DANIELLII; SOURCE 3 ORGANISM_COMMON: KATEMFE; SOURCE 4 ORGANISM_TAXID: 4621 KEYWDS SWEET PROTEIN, PLANT PROTEIN EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ,F.E.REYES, AUTHOR 2 M.R.SAWAYA,D.CASCIO,D.EISENBERG,T.GONEN REVDAT 4 22-AUG-18 5K7Q 1 REMARK REVDAT 3 18-JUL-18 5K7Q 1 REMARK ATOM REVDAT 2 12-APR-17 5K7Q 1 JRNL REVDAT 1 05-APR-17 5K7Q 0 JRNL AUTH M.J.DE LA CRUZ,J.HATTNE,D.SHI,P.SEIDLER,J.RODRIGUEZ, JRNL AUTH 2 F.E.REYES,M.R.SAWAYA,D.CASCIO,S.C.WEISS,S.K.KIM,C.S.HINCK, JRNL AUTH 3 A.P.HINCK,G.CALERO,D.EISENBERG,T.GONEN JRNL TITL ATOMIC-RESOLUTION STRUCTURES FROM FRAGMENTED PROTEIN JRNL TITL 2 CRYSTALS WITH THE CRYOEM METHOD MICROED. JRNL REF NAT. METHODS V. 14 399 2017 JRNL REFN ESSN 1548-7105 JRNL PMID 28192420 JRNL DOI 10.1038/NMETH.4178 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 8898 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 453 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 27.7333 - 3.6040 0.93 2910 170 0.1959 0.2384 REMARK 3 2 3.6040 - 2.8615 0.96 2845 148 0.2636 0.3127 REMARK 3 3 2.8615 - 2.5001 0.92 2690 135 0.3408 0.3898 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.740 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 1595 REMARK 3 ANGLE : 0.462 2168 REMARK 3 CHIRALITY : 0.039 230 REMARK 3 PLANARITY : 0.004 285 REMARK 3 DIHEDRAL : 12.505 960 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 5K7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221818. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 12786 REMARK 240 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 240 RESOLUTION RANGE LOW (A) : 27.730 REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : 81.5 REMARK 240 DATA REDUNDANCY : 4.000 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :2.11 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :2.17 REMARK 240 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 240 DATA REDUNDANCY IN SHELL : 2.50 REMARK 240 R MERGE FOR SHELL (I) : 0.86400 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL 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 75.15350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.05900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.05900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.57675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.05900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.05900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 112.73025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.05900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.05900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.57675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.05900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.05900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 112.73025 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 75.15350 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU A 42 OG1 THR A 45 2.17 REMARK 500 OG SER A 182 OD2 ASP A 186 2.19 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 -125.97 58.69 REMARK 500 ASP A 55 70.46 53.59 REMARK 500 CYS A 71 65.82 -113.18 REMARK 500 ASN A 109 -38.23 -141.44 REMARK 500 CYS A 204 70.49 55.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 317 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 318 DISTANCE = 6.39 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8219 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8216 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8217 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8218 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8220 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8221 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-8222 RELATED DB: EMDB REMARK 900 RELATED ID: 5K7N RELATED DB: PDB REMARK 900 RELATED ID: 5K7O RELATED DB: PDB REMARK 900 RELATED ID: 5K7P RELATED DB: PDB REMARK 900 RELATED ID: 5K7R RELATED DB: PDB REMARK 900 RELATED ID: 5K7S RELATED DB: PDB REMARK 900 RELATED ID: 5K7T RELATED DB: PDB DBREF 5K7Q 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 FORMUL 2 HOH *18(H2 O) HELIX 1 AA1 ASP A 147 GLN A 153 1 7 HELIX 2 AA2 THR A 154 CYS A 159 1 6 HELIX 3 AA3 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 ARG A 29 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 ARG A 29 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 SER A 91 -1 O PHE A 90 N GLY A 48 SHEET 5 AA3 6 LYS A 97 SER A 103 -1 O TYR A 99 N SER A 91 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 2.03 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 1.13 CRYST1 58.118 58.118 150.307 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 0.017206 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017206 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006653 0.00000