HEADER DNA BINDING PROTEIN 24-FEB-23 8IIS TITLE MSMUDGX H109S/R184A DOUBLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-4 URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.27; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 ATCC: 700084; SOURCE 6 GENE: MSMEG_0265; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET14B KEYWDS UDGX, H109S, R184A, MUTANT, PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.AROLI REVDAT 3 29-MAY-24 8IIS 1 REMARK REVDAT 2 02-AUG-23 8IIS 1 JRNL REVDAT 1 21-JUN-23 8IIS 0 JRNL AUTH S.AROLI,E.J.WOO,B.GOPAL,U.VARSHNEY JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSES OF UDGX: INSIGHTS INTO JRNL TITL 2 THE ACTIVE SITE POCKET ARCHITECTURE AND ITS EVOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 51 6554 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37283083 JRNL DOI 10.1093/NAR/GKAD486 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.2 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 24272 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1215 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 23.4800 - 3.3500 0.88 2407 116 0.1670 0.1547 REMARK 3 2 3.3500 - 2.6600 0.99 2671 152 0.1696 0.1958 REMARK 3 3 2.6600 - 2.3200 0.99 2654 132 0.1568 0.1667 REMARK 3 4 2.3200 - 2.1100 0.98 2604 130 0.1470 0.1635 REMARK 3 5 2.1100 - 1.9600 0.97 2610 132 0.1338 0.1469 REMARK 3 6 1.9600 - 1.8400 0.96 2563 128 0.1368 0.1705 REMARK 3 7 1.8400 - 1.7500 0.96 2528 131 0.1338 0.1687 REMARK 3 8 1.7500 - 1.6800 0.95 2514 162 0.1380 0.1793 REMARK 3 9 1.6800 - 1.6100 0.94 2506 132 0.1478 0.1958 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.070 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 : 0.019 1643 REMARK 3 ANGLE : 1.746 2238 REMARK 3 CHIRALITY : 0.115 256 REMARK 3 PLANARITY : 0.012 298 REMARK 3 DIHEDRAL : 6.025 237 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 8IIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8-7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.05900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 16.80 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 (%): 43.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM CITRATE TRIBASIC PH7.0, REMARK 280 0.1M BIS-TRIS PROPANE PH7.0, MICROBATCH, TEMPERATURE 295K 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 25.82500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 16 CG CD OE1 OE2 REMARK 470 ARG A 31 NH1 NH2 REMARK 470 ASP A 81 OD2 REMARK 470 ASP A 83 OD1 OD2 REMARK 470 ARG A 84 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 85 CG OD1 OD2 REMARK 470 GLU A 189 CG CD OE1 OE2 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 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 SF4 A 301 S1 120.6 REMARK 620 3 SF4 A 301 S2 105.0 107.0 REMARK 620 4 SF4 A 301 S4 115.1 102.1 106.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 27 SG REMARK 620 2 SF4 A 301 S1 119.1 REMARK 620 3 SF4 A 301 S3 101.3 105.5 REMARK 620 4 SF4 A 301 S4 122.2 102.4 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S1 108.3 REMARK 620 3 SF4 A 301 S2 108.2 106.0 REMARK 620 4 SF4 A 301 S3 121.7 108.3 103.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 SF4 A 301 S2 113.2 REMARK 620 3 SF4 A 301 S3 114.8 104.1 REMARK 620 4 SF4 A 301 S4 111.8 106.4 105.6 REMARK 620 N 1 2 3 DBREF 8IIS A 1 207 UNP A0QP43 A0QP43_MYCS2 1 207 SEQADV 8IIS GLY A -7 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS LEU A -6 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS VAL A -5 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS PRO A -4 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS ARG A -3 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS GLY A -2 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS SER A -1 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS HIS A 0 UNP A0QP43 EXPRESSION TAG SEQADV 8IIS SER A 109 UNP A0QP43 HIS 109 ENGINEERED MUTATION SEQADV 8IIS ALA A 184 UNP A0QP43 ARG 184 ENGINEERED MUTATION SEQRES 1 A 215 GLY LEU VAL PRO ARG GLY SER HIS MET ALA GLY ALA GLN SEQRES 2 A 215 ASP PHE VAL PRO HIS THR ALA ASP LEU ALA GLU LEU ALA SEQRES 3 A 215 ALA ALA ALA GLY GLU CYS ARG GLY CYS GLY LEU TYR ARG SEQRES 4 A 215 ASP ALA THR GLN ALA VAL PHE GLY ALA GLY GLY ARG SER SEQRES 5 A 215 ALA ARG ILE MET MET ILE GLY GLU GLN PRO GLY ASP LYS SEQRES 6 A 215 GLU ASP LEU ALA GLY LEU PRO PHE VAL GLY PRO ALA GLY SEQRES 7 A 215 ARG LEU LEU ASP ARG ALA LEU GLU ALA ALA ASP ILE ASP SEQRES 8 A 215 ARG ASP ALA LEU TYR VAL THR ASN ALA VAL LYS HIS PHE SEQRES 9 A 215 LYS PHE THR ARG ALA ALA GLY GLY LYS ARG ARG ILE SER SEQRES 10 A 215 LYS THR PRO SER ARG THR GLU VAL VAL ALA CYS ARG PRO SEQRES 11 A 215 TRP LEU ILE ALA GLU MET THR SER VAL GLU PRO ASP VAL SEQRES 12 A 215 VAL VAL LEU LEU GLY ALA THR ALA ALA LYS ALA LEU LEU SEQRES 13 A 215 GLY ASN ASP PHE ARG VAL THR GLN HIS ARG GLY GLU VAL SEQRES 14 A 215 LEU HIS VAL ASP ASP VAL PRO GLY ASP PRO ALA LEU VAL SEQRES 15 A 215 ALA THR VAL HIS PRO SER SER LEU LEU ALA GLY PRO LYS SEQRES 16 A 215 GLU GLU ARG GLU SER ALA PHE ALA GLY LEU VAL ASP ASP SEQRES 17 A 215 LEU ARG VAL ALA ALA ASP VAL HET SF4 A 301 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *205(H2 O) HELIX 1 AA1 GLY A -2 ALA A 2 5 5 HELIX 2 AA2 ALA A 4 VAL A 8 5 5 HELIX 3 AA3 ASP A 13 GLY A 22 1 10 HELIX 4 AA4 CYS A 27 ARG A 31 5 5 HELIX 5 AA5 GLY A 55 GLY A 62 1 8 HELIX 6 AA6 GLY A 67 ALA A 80 1 14 HELIX 7 AA7 ASP A 83 ASP A 85 5 3 HELIX 8 AA8 SER A 113 GLU A 132 1 20 HELIX 9 AA9 GLY A 140 GLY A 149 1 10 HELIX 10 AB1 ARG A 153 HIS A 157 5 5 HELIX 11 AB2 HIS A 178 LEU A 183 5 6 HELIX 12 AB3 PRO A 186 ASP A 206 1 21 SHEET 1 AA1 4 LEU A 87 ASN A 91 0 SHEET 2 AA1 4 ILE A 47 GLY A 51 1 N MET A 49 O TYR A 88 SHEET 3 AA1 4 VAL A 135 LEU A 139 1 O VAL A 137 N MET A 48 SHEET 4 AA1 4 ALA A 172 THR A 176 1 O VAL A 174 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 SER A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE3 SF4 A 301 1555 1555 2.32 LINK SG CYS A 27 FE2 SF4 A 301 1555 1555 2.31 LINK ND1 HIS A 95 FE4 SF4 A 301 1555 1555 2.32 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.25 CRYST1 36.360 51.650 54.580 90.00 105.00 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 0.027503 0.000000 0.007369 0.00000 SCALE2 0.000000 0.019361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018968 0.00000