HEADER TRANSFERASE 22-DEC-23 8XJQ TITLE CRYSTAL STRUCTURE OF A SULFOTRANSFERASE S4 IN COMPLEX WITH PAP AND TITLE 2 PNPS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SULFOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.8.2.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BAMBUSICOLA THORACICUS; SOURCE 3 ORGANISM_COMMON: CHINESE BAMBOO-PARTRIDGE; SOURCE 4 ORGANISM_TAXID: 9083; SOURCE 5 GENE: CIB84_007067; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PAP, SULFOTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GAO,H.WANG,Y.Y.CHEN,S.Y.YANG,L.YIN,W.D.LIU,J.S.LI REVDAT 1 25-DEC-24 8XJQ 0 JRNL AUTH J.GAO,H.WANG,Y.Y.CHEN,S.Y.YANG,L.YIN,W.D.LIU,J.S.LI JRNL TITL CRYSTAL STRUCTURE OF A SULFOTRANSFERASE S4 IN COMPLEX WITH JRNL TITL 2 PAP AND PNPS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.78 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 42216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2112 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 43.3500 - 3.8400 1.00 4298 226 0.1656 0.1951 REMARK 3 2 3.8300 - 3.0400 1.00 4089 215 0.1650 0.1649 REMARK 3 3 3.0400 - 2.6600 1.00 4029 213 0.1817 0.2035 REMARK 3 4 2.6600 - 2.4200 1.00 4000 210 0.1819 0.2313 REMARK 3 5 2.4200 - 2.2400 1.00 3988 210 0.1798 0.2254 REMARK 3 6 2.2400 - 2.1100 1.00 3948 208 0.1830 0.2205 REMARK 3 7 2.1100 - 2.0000 1.00 3953 208 0.1887 0.1994 REMARK 3 8 2.0000 - 1.9200 1.00 3965 208 0.1997 0.2402 REMARK 3 9 1.9200 - 1.8400 1.00 3934 208 0.2079 0.2534 REMARK 3 10 1.8400 - 1.7800 0.99 3900 206 0.2498 0.2944 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.510 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 : 0.013 2518 REMARK 3 ANGLE : 1.157 3429 REMARK 3 CHIRALITY : 0.078 354 REMARK 3 PLANARITY : 0.012 440 REMARK 3 DIHEDRAL : 7.405 366 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 8XJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-23 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 : SSRF REMARK 200 BEAMLINE : BL17UM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42303 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 43.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 27.70 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 16.20 REMARK 200 R MERGE FOR SHELL (I) : 0.97000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M (NH4)2SO4, 0.1 M MES PH 6.0, 1% REMARK 280 DEXTRAN SULFATE SODIUM SALT 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 70.06200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.02250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.02250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.09300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.02250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.02250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.03100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.02250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.02250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.09300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.02250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.02250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.03100 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 70.06200 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: 850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 684 LIES ON A SPECIAL POSITION. 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 A 1 REMARK 465 ALA A 2 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 GLU A 68 CG CD OE1 OE2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 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 TYR A 170 0.14 80.50 REMARK 500 ASP A 200 86.75 -156.38 REMARK 500 LYS A 259 -40.74 -136.78 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8XJQ A 1 296 UNP A0A2P4SYK2_BAMTH DBREF2 8XJQ A A0A2P4SYK2 1 296 SEQRES 1 A 296 MET ALA THR VAL ASP ARG TYR LEU ARG GLN PRO TRP SER SEQRES 2 A 296 VAL VAL HIS GLY ILE PRO MET VAL CYS ALA PHE ALA PRO SEQRES 3 A 296 ASN TRP GLU ARG VAL ASP ASN PHE GLN SER ARG PRO GLU SEQRES 4 A 296 ASP ILE VAL VAL ALA THR PHE PRO LYS SER GLY THR THR SEQRES 5 A 296 TRP VAL SER GLU ILE VAL ASP MET ILE LEU GLN GLY GLY SEQRES 6 A 296 ASP PRO GLU LYS CYS LYS ARG ASP ALA ILE VAL ASN ARG SEQRES 7 A 296 VAL PRO MET LEU GLU PHE ALA ALA PRO GLY GLU MET PRO SEQRES 8 A 296 THR GLY SER GLU VAL LEU ALA THR MET PRO SER PRO ARG SEQRES 9 A 296 VAL VAL LYS SER HIS LEU PRO ALA HIS ILE LEU PRO LYS SEQRES 10 A 296 SER PHE TRP ASP ASN GLY CYS LYS ILE ILE TYR VAL GLY SEQRES 11 A 296 ARG ASN ALA LYS ASP VAL ALA VAL SER PHE TYR HIS PHE SEQRES 12 A 296 ASP LEU MET ASN LYS PHE GLU GLN HIS PRO GLY THR TRP SEQRES 13 A 296 ASP GLN TYR LEU GLU ALA PHE MET ALA GLY LYS VAL ALA SEQRES 14 A 296 TYR GLY SER TRP PHE ASP HIS VAL ARG GLY TYR TRP GLU SEQRES 15 A 296 ARG ARG GLN GLU HIS PRO ILE LEU TYR LEU PHE TYR GLU SEQRES 16 A 296 ASP MET LYS GLU ASP LEU ARG ARG GLU ILE THR LYS VAL SEQRES 17 A 296 ALA GLN PHE LEU GLY GLN GLU LEU THR GLU VAL ALA LEU SEQRES 18 A 296 ASP ALA ILE ALA HIS HIS THR SER PHE GLU ALA MET ARG SEQRES 19 A 296 ASP ASN PRO SER THR ASN TYR SER THR VAL PRO SER HIS SEQRES 20 A 296 LEU MET ASP HIS GLY VAL SER PRO PHE MET ARG LYS GLY SEQRES 21 A 296 ILE THR GLY ASP TRP LYS ASN HIS PHE THR VAL ALA GLN SEQRES 22 A 296 ASN ALA HIS PHE ASP GLN TYR TYR ALA GLN LYS MET ALA SEQRES 23 A 296 GLY THR ASP LEU ARG PHE ARG THR GLU ILE HET NPO A 301 10 HET PPS A 302 31 HET 4NS A 303 14 HET NPO A 304 10 HETNAM NPO P-NITROPHENOL HETNAM PPS 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE HETNAM 4NS 4-NITROPHENYL SULFATE HETSYN 4NS 4-NITROPHENYL HYDROGEN SULFATE FORMUL 2 NPO 2(C6 H5 N O3) FORMUL 3 PPS C10 H15 N5 O13 P2 S FORMUL 4 4NS C6 H5 N O6 S FORMUL 6 HOH *292(H2 O) HELIX 1 AA1 THR A 3 LEU A 8 5 6 HELIX 2 AA2 VAL A 21 ALA A 25 5 5 HELIX 3 AA3 TRP A 28 ASN A 33 1 6 HELIX 4 AA4 GLY A 50 GLN A 63 1 14 HELIX 5 AA5 ASP A 66 LYS A 71 1 6 HELIX 6 AA6 ALA A 74 VAL A 79 1 6 HELIX 7 AA7 THR A 92 THR A 99 1 8 HELIX 8 AA8 PRO A 111 LEU A 115 5 5 HELIX 9 AA9 PRO A 116 ASN A 122 1 7 HELIX 10 AB1 ASN A 132 ASN A 147 1 16 HELIX 11 AB2 THR A 155 ALA A 165 1 11 HELIX 12 AB3 SER A 172 ARG A 184 1 13 HELIX 13 AB4 GLN A 185 HIS A 187 5 3 HELIX 14 AB5 TYR A 194 ASP A 200 1 7 HELIX 15 AB6 ASP A 200 LEU A 212 1 13 HELIX 16 AB7 THR A 217 THR A 228 1 12 HELIX 17 AB8 SER A 229 ASN A 236 1 8 HELIX 18 AB9 ASP A 264 PHE A 269 1 6 HELIX 19 AC1 THR A 270 MET A 285 1 16 SHEET 1 AA1 2 SER A 13 VAL A 15 0 SHEET 2 AA1 2 ILE A 18 MET A 20 -1 O ILE A 18 N VAL A 15 SHEET 1 AA2 4 VAL A 105 SER A 108 0 SHEET 2 AA2 4 ILE A 41 THR A 45 1 N ILE A 41 O VAL A 106 SHEET 3 AA2 4 LYS A 125 GLY A 130 1 O ILE A 127 N VAL A 42 SHEET 4 AA2 4 ILE A 189 PHE A 193 1 O LEU A 192 N TYR A 128 CISPEP 1 SER A 102 PRO A 103 0 -0.34 CRYST1 78.045 78.045 140.124 90.00 90.00 90.00 P 43 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 0.012813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007137 0.00000