HEADER BIOSYNTHETIC PROTEIN 13-JAN-23 8I1M TITLE CRYSTAL STRUCTURE OF OXIDATED APSK1 DOMAIN FROM HUMAN PAPSS1 IN TITLE 2 COMPLEX WITH APS AND ADP CAVEAT 8I1M ADX A 302 HAS WRONG CHIRALITY AT ATOM C2' ADX A 302 HAS CAVEAT 2 8I1M WRONG CHIRALITY AT ATOM C1' COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPSS1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APSK1 DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PAPSS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5'-PHOSPHOSULFATE KINASE 1, APSK1, HUMAN PAPSS1, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHANG,W.Y.SONG,L.ZHANG REVDAT 3 06-NOV-24 8I1M 1 REMARK REVDAT 2 19-JUL-23 8I1M 1 JRNL REVDAT 1 28-JUN-23 8I1M 0 JRNL AUTH L.ZHANG,W.SONG,T.LI,Y.MU,P.ZHANG,J.HU,H.LIN,J.ZHANG,H.GAO, JRNL AUTH 2 L.ZHANG JRNL TITL REDOX SWITCHING MECHANISM OF THE ADENOSINE 5'-PHOSPHOSULFATE JRNL TITL 2 KINASE DOMAIN (APSK2) OF HUMAN PAPS SYNTHASE 2. JRNL REF STRUCTURE V. 31 826 2023 JRNL REFN ISSN 0969-2126 JRNL PMID 37207644 JRNL DOI 10.1016/J.STR.2023.04.012 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.0 REMARK 3 NUMBER OF REFLECTIONS : 15998 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) : 0.182 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 815 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 46.8480 - 3.0879 0.99 3331 171 0.1616 0.1850 REMARK 3 2 3.0879 - 2.4510 0.99 3278 159 0.1892 0.2334 REMARK 3 3 2.4510 - 2.1412 0.96 3143 183 0.1908 0.2628 REMARK 3 4 2.1412 - 1.9454 0.78 2572 123 0.2016 0.2702 REMARK 3 5 1.9454 - 1.8060 0.56 1816 113 0.2155 0.2913 REMARK 3 6 1.8060 - 1.6995 0.33 1043 66 0.2255 0.3337 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.600 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 : 0.006 1587 REMARK 3 ANGLE : 1.035 2159 REMARK 3 CHIRALITY : 0.054 237 REMARK 3 PLANARITY : 0.006 277 REMARK 3 DIHEDRAL : 18.377 962 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 8I1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 180 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 : BL19U1 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.699 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 1.00400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 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 (%) : 56.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46200 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: 2OFX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M HEPES, REMARK 280 PH7.5 AND 2% W/V PEG4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.17600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.68050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.17600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.68050 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 402 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 553 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 ALA A 25 REMARK 465 THR A 26 REMARK 465 ASN A 27 REMARK 465 VAL A 28 REMARK 465 THR A 29 REMARK 465 TYR A 30 REMARK 465 GLN A 31 REMARK 465 ALA A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 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 SER A 133 72.53 41.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 8I1M A 25 227 UNP Q05BW9 Q05BW9_HUMAN 25 227 SEQADV 8I1M ASP A 191 UNP Q05BW9 GLU 191 CONFLICT SEQRES 1 A 203 ALA THR ASN VAL THR TYR GLN ALA HIS HIS VAL SER ARG SEQRES 2 A 203 ASN LYS ARG GLY GLN VAL VAL GLY THR ARG GLY GLY PHE SEQRES 3 A 203 ARG GLY CYS THR VAL TRP LEU THR GLY LEU SER GLY ALA SEQRES 4 A 203 GLY LYS THR THR VAL SER MET ALA LEU GLU GLU TYR LEU SEQRES 5 A 203 VAL CYS HIS GLY ILE PRO CYS TYR THR LEU ASP GLY ASP SEQRES 6 A 203 ASN ILE ARG GLN GLY LEU ASN LYS ASN LEU GLY PHE SER SEQRES 7 A 203 PRO GLU ASP ARG GLU GLU ASN VAL ARG ARG ILE ALA GLU SEQRES 8 A 203 VAL ALA LYS LEU PHE ALA ASP ALA GLY LEU VAL CYS ILE SEQRES 9 A 203 THR SER PHE ILE SER PRO TYR THR GLN ASP ARG ASN ASN SEQRES 10 A 203 ALA ARG GLN ILE HIS GLU GLY ALA SER LEU PRO PHE PHE SEQRES 11 A 203 GLU VAL PHE VAL ASP ALA PRO LEU HIS VAL CYS GLU GLN SEQRES 12 A 203 ARG ASP VAL LYS GLY LEU TYR LYS LYS ALA ARG ALA GLY SEQRES 13 A 203 GLU ILE LYS GLY PHE THR GLY ILE ASP SER ASP TYR GLU SEQRES 14 A 203 LYS PRO GLU ALA PRO GLU LEU VAL LEU LYS THR ASP SER SEQRES 15 A 203 CYS ASP VAL ASN ASP CYS VAL GLN GLN VAL VAL GLU LEU SEQRES 16 A 203 LEU GLN GLU ARG ASP ILE VAL PRO HET ADP A 301 27 HET ADX A 302 27 HET PO4 A 303 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ADX ADENOSINE-5'-PHOSPHOSULFATE HETNAM PO4 PHOSPHATE ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 ADX C10 H14 N5 O10 P S FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *156(H2 O) HELIX 1 AA1 SER A 36 VAL A 44 1 9 HELIX 2 AA2 GLY A 64 HIS A 79 1 16 HELIX 3 AA3 GLY A 88 ARG A 92 1 5 HELIX 4 AA4 SER A 102 ALA A 123 1 22 HELIX 5 AA5 TYR A 135 ALA A 149 1 15 HELIX 6 AA6 PRO A 161 ASP A 169 1 9 HELIX 7 AA7 GLY A 172 ALA A 179 1 8 HELIX 8 AA8 ASP A 208 ARG A 223 1 16 SHEET 1 AA1 5 CYS A 83 ASP A 87 0 SHEET 2 AA1 5 VAL A 126 SER A 130 1 O ILE A 128 N LEU A 86 SHEET 3 AA1 5 CYS A 53 THR A 58 1 N CYS A 53 O CYS A 127 SHEET 4 AA1 5 PHE A 153 VAL A 158 1 O VAL A 156 N TRP A 56 SHEET 5 AA1 5 LEU A 200 LEU A 202 1 O LEU A 202 N PHE A 157 SSBOND 1 CYS A 207 CYS A 212 1555 1555 2.04 CRYST1 114.352 51.361 32.397 90.00 91.94 90.00 C 1 2 1 4 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 0.008745 0.000000 0.000295 0.00000 SCALE2 0.000000 0.019470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030885 0.00000