HEADER HYDROLASE 17-JAN-24 8RPT TITLE CRYSTAL STRUCTURE OF HUMAN DNPH1 MUTANT- D80A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: C-MYC-RESPONSIVE PROTEIN RCL; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DNPH1, C6ORF108, RCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE ACTIVITY, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DEVI,R.G.DA SILVA REVDAT 1 20-NOV-24 8RPT 0 JRNL AUTH A.E.CARBERRY,S.DEVI,D.J.HARRISON,R.G.DA SILVA JRNL TITL HUMAN 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1: THE JRNL TITL 2 CATALYTIC ROLES OF TYR24 AND ASP80. JRNL REF CHEMBIOCHEM V. 25 00047 2024 JRNL REFN ESSN 1439-7633 JRNL PMID 38350003 JRNL DOI 10.1002/CBIC.202400047 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 936 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 47.6000 - 3.7300 1.00 2820 103 0.1715 0.1849 REMARK 3 2 3.7200 - 2.9600 1.00 2641 159 0.1622 0.2068 REMARK 3 3 2.9600 - 2.5800 1.00 2631 127 0.1851 0.2262 REMARK 3 4 2.5800 - 2.3500 1.00 2626 118 0.1845 0.2355 REMARK 3 5 2.3500 - 2.1800 1.00 2585 132 0.1774 0.2326 REMARK 3 6 2.1800 - 2.0500 1.00 2578 160 0.1970 0.2657 REMARK 3 7 2.0500 - 1.9500 0.99 2536 137 0.2240 0.2960 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.010 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 : 0.007 NULL REMARK 3 ANGLE : 0.871 NULL REMARK 3 CHIRALITY : 0.055 323 REMARK 3 PLANARITY : 0.012 400 REMARK 3 DIHEDRAL : 8.901 333 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 8RPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6199 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19407 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 47.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 16.80 REMARK 200 R MERGE (I) : 0.18200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.50 REMARK 200 R MERGE FOR SHELL (I) : 1.47600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 % PEG 4000, 100 MM SODIUM ACETATE PH REMARK 280 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.79200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.60450 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.79200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.60450 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: 4910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLU B 67 REMARK 465 GLU B 68 REMARK 465 GLY A 18 REMARK 465 ILE A 29 REMARK 465 ARG A 30 REMARK 465 GLY A 31 REMARK 465 ARG A 65 REMARK 465 GLY A 66 REMARK 465 GLU A 67 REMARK 465 GLU A 68 REMARK 465 ALA A 160 REMARK 465 ASP A 161 REMARK 465 PRO A 162 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 ARG B 30 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 33 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 122 CG CD OE1 NE2 REMARK 470 ASP B 161 CG OD1 OD2 REMARK 470 ARG A 33 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 ASP A 35 CG OD1 OD2 REMARK 470 ARG A 36 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 SER B 128 132.12 -38.09 REMARK 500 SER B 138 -72.68 -134.44 REMARK 500 SER A 138 -83.82 -127.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RPS RELATED DB: PDB DBREF 8RPT B 20 162 UNP O43598 DNPH1_HUMAN 20 162 DBREF 8RPT A 20 162 UNP O43598 DNPH1_HUMAN 20 162 SEQADV 8RPT GLY B 18 UNP O43598 EXPRESSION TAG SEQADV 8RPT MET B 19 UNP O43598 EXPRESSION TAG SEQADV 8RPT ALA B 80 UNP O43598 ASP 80 ENGINEERED MUTATION SEQADV 8RPT GLY A 18 UNP O43598 EXPRESSION TAG SEQADV 8RPT MET A 19 UNP O43598 EXPRESSION TAG SEQADV 8RPT ALA A 80 UNP O43598 ASP 80 ENGINEERED MUTATION SEQRES 1 B 145 GLY MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG SEQRES 2 B 145 GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SEQRES 3 B 145 SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS SEQRES 4 B 145 VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA SEQRES 5 B 145 ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ALA LEU GLU SEQRES 6 B 145 TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR SEQRES 7 B 145 GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA SEQRES 8 B 145 VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE ARG PRO SEQRES 9 B 145 GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA SEQRES 10 B 145 ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR GLU GLU SEQRES 11 B 145 GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA SEQRES 12 B 145 ASP PRO SEQRES 1 A 145 GLY MET ARG PRO ALA LEU TYR PHE CYS GLY SER ILE ARG SEQRES 2 A 145 GLY GLY ARG GLU ASP ARG THR LEU TYR GLU ARG ILE VAL SEQRES 3 A 145 SER ARG LEU ARG ARG PHE GLY THR VAL LEU THR GLU HIS SEQRES 4 A 145 VAL ALA ALA ALA GLU LEU GLY ALA ARG GLY GLU GLU ALA SEQRES 5 A 145 ALA GLY GLY ASP ARG LEU ILE HIS GLU GLN ALA LEU GLU SEQRES 6 A 145 TRP LEU GLN GLN ALA ASP VAL VAL VAL ALA GLU VAL THR SEQRES 7 A 145 GLN PRO SER LEU GLY VAL GLY TYR GLU LEU GLY ARG ALA SEQRES 8 A 145 VAL ALA PHE ASN LYS ARG ILE LEU CYS LEU PHE ARG PRO SEQRES 9 A 145 GLN SER GLY ARG VAL LEU SER ALA MET ILE ARG GLY ALA SEQRES 10 A 145 ALA ASP GLY SER ARG PHE GLN VAL TRP ASP TYR GLU GLU SEQRES 11 A 145 GLY GLU VAL GLU ALA LEU LEU ASP ARG TYR PHE GLU ALA SEQRES 12 A 145 ASP PRO HET CL B 201 1 HET CL B 202 1 HET PEG B 203 7 HET EDO B 204 4 HET EDO B 205 4 HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET CL A 206 1 HET PEG A 207 7 HET EDO A 208 4 HET EDO A 209 4 HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CL 8(CL 1-) FORMUL 5 PEG 2(C4 H10 O3) FORMUL 6 EDO 4(C2 H6 O2) FORMUL 17 HOH *145(H2 O) HELIX 1 AA1 GLY B 32 ARG B 47 1 16 HELIX 2 AA2 THR B 54 GLY B 63 1 10 HELIX 3 AA3 ALA B 64 GLY B 66 5 3 HELIX 4 AA4 GLY B 71 ALA B 87 1 17 HELIX 5 AA5 SER B 98 PHE B 111 1 14 HELIX 6 AA6 ARG B 120 GLY B 124 5 5 HELIX 7 AA7 SER B 128 GLY B 133 1 6 HELIX 8 AA8 GLU B 149 ASP B 161 1 13 HELIX 9 AA9 ARG A 33 ARG A 47 1 15 HELIX 10 AB1 GLU A 55 GLU A 61 1 7 HELIX 11 AB2 GLY A 71 ALA A 87 1 17 HELIX 12 AB3 SER A 98 PHE A 111 1 14 HELIX 13 AB4 ARG A 120 GLY A 124 5 5 HELIX 14 AB5 SER A 128 GLY A 133 1 6 HELIX 15 AB6 GLU A 146 GLY A 148 5 3 HELIX 16 AB7 GLU A 149 GLU A 159 1 11 SHEET 1 AA1 5 THR B 51 LEU B 53 0 SHEET 2 AA1 5 ALA B 22 CYS B 26 1 N LEU B 23 O THR B 51 SHEET 3 AA1 5 VAL B 89 GLU B 93 1 O GLU B 93 N CYS B 26 SHEET 4 AA1 5 ARG B 114 PHE B 119 1 O LEU B 118 N ALA B 92 SHEET 5 AA1 5 PHE B 140 ASP B 144 1 O TRP B 143 N CYS B 117 SHEET 1 AA2 5 THR A 51 THR A 54 0 SHEET 2 AA2 5 ALA A 22 CYS A 26 1 N LEU A 23 O THR A 51 SHEET 3 AA2 5 VAL A 89 GLU A 93 1 O VAL A 91 N CYS A 26 SHEET 4 AA2 5 ARG A 114 PHE A 119 1 O LEU A 118 N ALA A 92 SHEET 5 AA2 5 PHE A 140 ASP A 144 1 O GLN A 141 N CYS A 117 CRYST1 56.481 65.584 69.209 90.00 90.00 90.00 P 2 21 21 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 0.017705 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014449 0.00000