HEADER NUCLEAR PROTEIN 03-MAR-20 6M3H TITLE CRYSTAL STRUCTURE OF MOUSE HPF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE PARYLATION FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: HPF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 7 PPPARG4; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS COFACTOR, ADP-RIBOSYLATION, DNA DAMAGE RESPONSE, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.H.SUN,C.H.YUN REVDAT 2 29-NOV-23 6M3H 1 REMARK REVDAT 1 03-MAR-21 6M3H 0 JRNL AUTH F.H.SUN,P.ZHAO,N.ZHANG,L.L.KONG,C.C.L.WONG,C.H.YUN JRNL TITL HPF1 REMODELS THE ACTIVE SITE OF PARP1 TO ENABLE THE SERINE JRNL TITL 2 ADP-RIBOSYLATION OF HISTONES. JRNL REF NAT COMMUN V. 12 1028 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33589610 JRNL DOI 10.1038/S41467-021-21302-4 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 39364 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 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 44.3600 - 4.1200 1.00 2895 141 0.1716 0.2198 REMARK 3 2 4.1200 - 3.2700 1.00 2745 151 0.1621 0.1959 REMARK 3 3 3.2700 - 2.8600 1.00 2720 144 0.1854 0.2144 REMARK 3 4 2.8600 - 2.6000 1.00 2695 152 0.1904 0.2265 REMARK 3 5 2.6000 - 2.4100 1.00 2692 140 0.1857 0.2212 REMARK 3 6 2.4100 - 2.2700 1.00 2683 141 0.1849 0.2150 REMARK 3 7 2.2700 - 2.1500 1.00 2663 137 0.1835 0.2097 REMARK 3 8 2.1500 - 2.0600 1.00 2676 145 0.1827 0.2281 REMARK 3 9 2.0600 - 1.9800 1.00 2656 132 0.1834 0.1855 REMARK 3 10 1.9800 - 1.9100 1.00 2627 125 0.1905 0.2442 REMARK 3 11 1.9100 - 1.8500 1.00 2673 138 0.1935 0.2222 REMARK 3 12 1.8500 - 1.8000 1.00 2651 139 0.2046 0.2217 REMARK 3 13 1.8000 - 1.7500 0.98 2578 134 0.2296 0.2808 REMARK 3 14 1.7500 - 1.7100 0.92 2485 106 0.2689 0.3220 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) : 0.165 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.079 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.28 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 : 0.007 2548 REMARK 3 ANGLE : 0.943 3443 REMARK 3 CHIRALITY : 0.064 375 REMARK 3 PLANARITY : 0.005 447 REMARK 3 DIHEDRAL : 19.490 960 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 6M3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-18 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97849 REMARK 200 MONOCHROMATOR : SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39364 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 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 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: 6M3G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-PH8.3, 0.2 M POTASSIUM REMARK 280 CITRATE TRIBASIC MONOHYDRATE, 20% W/V PEG 3350,, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.01550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.33700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.33700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.01550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94750 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: 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 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 VAL A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 LYS A 7 REMARK 465 ARG A 8 REMARK 465 ARG A 9 REMARK 465 THR A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 ALA A 13 REMARK 465 GLY A 14 REMARK 465 PRO A 15 REMARK 465 GLN A 16 REMARK 465 CYS A 17 REMARK 465 GLU A 18 REMARK 465 LYS A 19 REMARK 465 THR A 20 REMARK 465 VAL A 21 REMARK 465 GLU A 22 REMARK 465 VAL A 23 REMARK 465 LYS A 24 REMARK 465 LYS A 25 REMARK 465 SER A 26 REMARK 465 LYS A 27 REMARK 465 PHE A 28 REMARK 465 SER A 29 REMARK 465 GLU A 30 REMARK 465 ALA A 31 REMARK 465 ASP A 32 REMARK 465 VAL A 33 REMARK 465 SER A 34 REMARK 465 SER A 35 REMARK 465 GLY A 346 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 LYS A 58 CD CE NZ REMARK 470 GLU A 66 CD OE1 OE2 REMARK 470 MET A 93 CG SD CE REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 LYS A 124 CD CE NZ REMARK 470 LYS A 233 CD CE NZ REMARK 470 GLU A 262 CG CD OE1 OE2 REMARK 470 LEU A 265 CD1 CD2 REMARK 470 LYS A 266 CD CE NZ 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 THR A 221 171.42 65.93 REMARK 500 ARG A 322 53.92 -108.01 REMARK 500 ASN A 340 63.06 60.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 6M3H A 1 346 UNP Q8CFE2 HPF1_MOUSE 1 346 SEQRES 1 A 346 MET VAL GLY GLY GLY GLY LYS ARG ARG THR ALA GLY ALA SEQRES 2 A 346 GLY PRO GLN CYS GLU LYS THR VAL GLU VAL LYS LYS SER SEQRES 3 A 346 LYS PHE SER GLU ALA ASP VAL SER SER ASP LEU ARG LYS SEQRES 4 A 346 GLU VAL GLU ASN LEU TYR LYS LEU SER LEU PRO GLU ASP SEQRES 5 A 346 PHE TYR HIS PHE TRP LYS PHE CYS GLU GLU LEU ASP PRO SEQRES 6 A 346 GLU LYS PRO ALA ASP ALA LEU ALA THR SER LEU GLY LEU SEQRES 7 A 346 ARG LEU VAL GLY PRO TYR ASP ILE LEU ALA GLY LYS HIS SEQRES 8 A 346 LYS MET LYS LYS LYS PRO THR GLY LEU ASN CYS ASN LEU SEQRES 9 A 346 HIS TRP ARG PHE TYR TYR ASP PRO PRO GLU PHE GLN THR SEQRES 10 A 346 ILE ILE ILE GLY ASP ASN LYS THR GLN TYR HIS MET GLY SEQRES 11 A 346 TYR PHE ARG ASP SER PRO ASP GLU LEU PRO VAL TYR VAL SEQRES 12 A 346 GLY THR ASN GLU ALA LYS LYS ASN CYS ILE ILE ILE GLN SEQRES 13 A 346 ASN GLY ASP ASN VAL PHE ALA ALA ILE LYS LEU PHE LEU SEQRES 14 A 346 MET LYS LYS LEU LYS GLU VAL THR ASP ARG LYS LYS ILE SEQRES 15 A 346 SER ILE LEU LYS ASN ILE ASP GLU LYS LEU THR GLU ALA SEQRES 16 A 346 ALA ARG LYS LEU GLY TYR SER LEU GLU GLN ARG THR VAL SEQRES 17 A 346 LYS MET ARG GLN ARG ASP LYS LYS VAL VAL THR LYS THR SEQRES 18 A 346 PHE HIS GLY ALA GLY LEU VAL VAL PRO VAL ASP LYS ASN SEQRES 19 A 346 ASP VAL GLY TYR ARG GLU LEU PRO GLU THR ASP ALA ASP SEQRES 20 A 346 LEU LYS ARG ILE CYS LYS ALA VAL VAL ASP ALA ALA SER SEQRES 21 A 346 ASP GLU GLU ARG LEU LYS ALA PHE ALA PRO ILE GLN GLU SEQRES 22 A 346 MET MET THR PHE VAL GLN PHE ALA ASN ASP GLU CYS ASP SEQRES 23 A 346 TYR GLY MET GLY LEU GLU LEU GLY MET ASP LEU PHE CYS SEQRES 24 A 346 TYR GLY SER HIS TYR PHE HIS LYS VAL ALA GLY GLN LEU SEQRES 25 A 346 LEU PRO LEU ALA TYR ASN LEU LEU LYS ARG ASP LEU PHE SEQRES 26 A 346 ALA LYS ILE ILE GLU ASP HIS LEU ALA SER ARG SER GLU SEQRES 27 A 346 GLU ASN ILE ASP GLN LEU ALA GLY FORMUL 2 HOH *274(H2 O) HELIX 1 AA1 ASP A 36 LYS A 46 1 11 HELIX 2 AA2 PRO A 50 ASP A 64 1 15 HELIX 3 AA3 LYS A 67 ALA A 71 5 5 HELIX 4 AA4 LEU A 72 GLY A 77 1 6 HELIX 5 AA5 GLY A 82 GLY A 89 1 8 HELIX 6 AA6 LYS A 90 LYS A 94 5 5 HELIX 7 AA7 ASN A 160 LYS A 174 1 15 HELIX 8 AA8 ASP A 178 GLY A 200 1 23 HELIX 9 AA9 THR A 207 LYS A 216 1 10 HELIX 10 AB1 THR A 244 ALA A 258 1 15 HELIX 11 AB2 SER A 260 GLU A 284 1 25 HELIX 12 AB3 TYR A 287 GLY A 301 1 15 HELIX 13 AB4 SER A 302 TYR A 304 5 3 HELIX 14 AB5 PHE A 305 LEU A 320 1 16 HELIX 15 AB6 ARG A 322 SER A 335 1 14 SHEET 1 AA1 5 ARG A 79 LEU A 80 0 SHEET 2 AA1 5 PHE A 115 ILE A 120 -1 O ILE A 120 N ARG A 79 SHEET 3 AA1 5 TYR A 127 PHE A 132 -1 O MET A 129 N ILE A 118 SHEET 4 AA1 5 TYR A 142 GLU A 147 -1 O GLY A 144 N GLY A 130 SHEET 5 AA1 5 ILE A 155 GLN A 156 -1 O ILE A 155 N THR A 145 SHEET 1 AA2 2 VAL A 217 THR A 219 0 SHEET 2 AA2 2 LEU A 227 VAL A 228 -1 O LEU A 227 N VAL A 218 CISPEP 1 LYS A 96 PRO A 97 0 4.98 CRYST1 42.031 79.895 106.674 90.00 90.00 90.00 P 21 21 21 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 0.023792 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009374 0.00000