HEADER HYDROLASE 09-JAN-04 1S2O TITLE X-RAY STRUCTURE OF THE SUCROSE-PHOSPHATASE (SPP) FROM SYNECHOCYSTIS TITLE 2 SP. PCC6803 AT 1.40 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCROSE-PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPP; COMPND 5 EC: 3.1.3.24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP.; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: PCC 6803; SOURCE 5 GENE: SPP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB2 KEYWDS PHOSPHOHYDROLASE, HAD SUPERFAMILY, SUCROSE, CYANOBACTERIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FIEULAINE,J.E.LUNN,F.BOREL,J.L.FERRER REVDAT 5 14-FEB-24 1S2O 1 REMARK LINK REVDAT 4 13-JUL-11 1S2O 1 VERSN REVDAT 3 24-FEB-09 1S2O 1 VERSN REVDAT 2 12-JUL-05 1S2O 1 JRNL REVDAT 1 22-FEB-05 1S2O 0 JRNL AUTH S.FIEULAINE,J.E.LUNN,F.BOREL,J.L.FERRER JRNL TITL THE STRUCTURE OF A CYANOBACTERIAL SUCROSE-PHOSPHATASE JRNL TITL 2 REVEALS THE SUGAR TONGS THAT RELEASE FREE SUCROSE IN THE JRNL TITL 3 CELL. JRNL REF PLANT CELL V. 17 2049 2005 JRNL REFN ISSN 1040-4651 JRNL PMID 15937230 JRNL DOI 10.1105/TPC.105.031229 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 45521 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2257 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 348 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.312 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021290. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-03; 19-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : BM30A; ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.483148; 0.934 REMARK 200 MONOCHROMATOR : SI 111; LAUE DIAMOND C111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAFORMATE, NACL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 25.88000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 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 MET A 1 CG SD CE REMARK 470 GLN A 19 CG CD OE1 NE2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ASP A 122 CG OD1 OD2 REMARK 470 GLU A 135 CG CD OE1 OE2 REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 GLN A 168 CG CD OE1 NE2 REMARK 470 GLN A 216 CG CD OE1 NE2 REMARK 470 GLN A 226 CG CD OE1 NE2 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 LEU A 10 -77.11 -94.18 REMARK 500 THR A 13 -78.47 -121.99 REMARK 500 SER A 150 17.95 53.79 REMARK 500 LYS A 152 -33.35 -145.44 REMARK 500 ASP A 219 -165.52 -128.37 REMARK 500 HIS A 229 -138.57 47.07 REMARK 500 LEU A 243 10.53 59.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 245 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 ASP A 11 O 84.3 REMARK 620 3 ASP A 186 OD1 80.0 90.0 REMARK 620 4 HOH A 284 O 167.5 95.1 87.5 REMARK 620 5 HOH A 311 O 84.8 168.7 85.0 94.8 REMARK 620 6 HOH A 317 O 99.1 95.1 174.8 93.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 245 DBREF 1S2O A 1 244 UNP P74325 P74325_SYNY3 1 244 SEQRES 1 A 244 MET ARG GLN LEU LEU LEU ILE SER ASP LEU ASP ASN THR SEQRES 2 A 244 TRP VAL GLY ASP GLN GLN ALA LEU GLU HIS LEU GLN GLU SEQRES 3 A 244 TYR LEU GLY ASP ARG ARG GLY ASN PHE TYR LEU ALA TYR SEQRES 4 A 244 ALA THR GLY ARG SER TYR HIS SER ALA ARG GLU LEU GLN SEQRES 5 A 244 LYS GLN VAL GLY LEU MET GLU PRO ASP TYR TRP LEU THR SEQRES 6 A 244 ALA VAL GLY SER GLU ILE TYR HIS PRO GLU GLY LEU ASP SEQRES 7 A 244 GLN HIS TRP ALA ASP TYR LEU SER GLU HIS TRP GLN ARG SEQRES 8 A 244 ASP ILE LEU GLN ALA ILE ALA ASP GLY PHE GLU ALA LEU SEQRES 9 A 244 LYS PRO GLN SER PRO LEU GLU GLN ASN PRO TRP LYS ILE SEQRES 10 A 244 SER TYR HIS LEU ASP PRO GLN ALA CYS PRO THR VAL ILE SEQRES 11 A 244 ASP GLN LEU THR GLU MET LEU LYS GLU THR GLY ILE PRO SEQRES 12 A 244 VAL GLN VAL ILE PHE SER SER GLY LYS ASP VAL ASP LEU SEQRES 13 A 244 LEU PRO GLN ARG SER ASN LYS GLY ASN ALA THR GLN TYR SEQRES 14 A 244 LEU GLN GLN HIS LEU ALA MET GLU PRO SER GLN THR LEU SEQRES 15 A 244 VAL CYS GLY ASP SER GLY ASN ASP ILE GLY LEU PHE GLU SEQRES 16 A 244 THR SER ALA ARG GLY VAL ILE VAL ARG ASN ALA GLN PRO SEQRES 17 A 244 GLU LEU LEU HIS TRP TYR ASP GLN TRP GLY ASP SER ARG SEQRES 18 A 244 HIS TYR ARG ALA GLN SER SER HIS ALA GLY ALA ILE LEU SEQRES 19 A 244 GLU ALA ILE ALA HIS PHE ASP PHE LEU SER HET MG A 245 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *348(H2 O) HELIX 1 1 ASP A 17 ASP A 30 1 14 HELIX 2 2 ARG A 31 GLY A 33 5 3 HELIX 3 3 SER A 44 GLY A 56 1 13 HELIX 4 4 ASP A 78 GLU A 87 1 10 HELIX 5 5 GLN A 90 GLY A 100 1 11 HELIX 6 6 SER A 108 GLN A 112 5 5 HELIX 7 7 PRO A 127 GLU A 139 1 13 HELIX 8 8 ASN A 162 LEU A 174 1 13 HELIX 9 9 GLU A 177 SER A 179 5 3 HELIX 10 10 SER A 187 ASN A 189 5 3 HELIX 11 11 ASP A 190 GLU A 195 1 6 HELIX 12 12 GLN A 207 GLY A 218 1 12 HELIX 13 13 SER A 228 PHE A 240 1 13 SHEET 1 A 8 GLY A 76 LEU A 77 0 SHEET 2 A 8 GLU A 70 HIS A 73 -1 N HIS A 73 O GLY A 76 SHEET 3 A 8 TYR A 62 THR A 65 -1 N THR A 65 O GLU A 70 SHEET 4 A 8 PHE A 35 ALA A 40 1 N TYR A 39 O LEU A 64 SHEET 5 A 8 LEU A 4 SER A 8 1 N LEU A 6 O TYR A 36 SHEET 6 A 8 THR A 181 GLY A 185 1 O LEU A 182 N ILE A 7 SHEET 7 A 8 ARG A 199 ILE A 202 1 O ARG A 199 N VAL A 183 SHEET 8 A 8 HIS A 222 ARG A 224 1 O TYR A 223 N GLY A 200 SHEET 1 B 4 LEU A 104 PRO A 106 0 SHEET 2 B 4 ILE A 117 LEU A 121 -1 O HIS A 120 N LYS A 105 SHEET 3 B 4 ASP A 153 PRO A 158 -1 O VAL A 154 N TYR A 119 SHEET 4 B 4 VAL A 144 SER A 149 -1 N GLN A 145 O LEU A 157 LINK OD2 ASP A 9 MG MG A 245 1555 1555 2.17 LINK O ASP A 11 MG MG A 245 1555 1555 2.20 LINK OD1 ASP A 186 MG MG A 245 1555 1555 2.30 LINK MG MG A 245 O HOH A 284 1555 1555 2.30 LINK MG MG A 245 O HOH A 311 1555 1555 2.34 LINK MG MG A 245 O HOH A 317 1555 1555 2.53 SITE 1 AC1 6 ASP A 9 ASP A 11 ASP A 186 HOH A 284 SITE 2 AC1 6 HOH A 311 HOH A 317 CRYST1 46.070 51.760 52.140 90.00 101.70 90.00 P 1 21 1 2 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 0.021706 0.000000 0.004495 0.00000 SCALE2 0.000000 0.019320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019586 0.00000