HEADER DNA BINDING PROTEIN 31-MAR-25 9QQ9 TITLE CRYSTAL STRUCTURE OF THE RELAXASE DOMAIN OF RELPLS20, PROTOTYPE OF TITLE 2 MOBL FAMILY OF RELAXASES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RELAXASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. NATTO; SOURCE 3 ORGANISM_TAXID: 86029; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS BACTERIAL CONJUGATION, DNA BINDING, ANTIBIOTIC RESISTANCE, KEYWDS 2 FIRMICUTES, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.CRESPO,D.R.BOER REVDAT 1 15-APR-26 9QQ9 0 JRNL AUTH I.CRESPO,D.R.BOER JRNL TITL CRYSTAL STRUCTURE OF THE RELAXASE DOMAIN OF RELPLS20, JRNL TITL 2 PROTOTYPE OF MOBL FAMILY OF RELAXASES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 38155 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1843 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 33.0300 - 3.9200 1.00 2976 175 0.1421 0.1677 REMARK 3 2 3.8800 - 3.0900 0.94 2786 134 0.1603 0.1859 REMARK 3 3 3.0900 - 2.7000 1.00 2957 172 0.1817 0.2188 REMARK 3 4 2.7000 - 2.4600 1.00 2981 134 0.1976 0.2083 REMARK 3 5 2.4600 - 2.2800 1.00 2959 167 0.1811 0.2188 REMARK 3 6 2.2800 - 2.1500 0.85 2519 135 0.1821 0.2289 REMARK 3 7 2.1500 - 2.0400 0.78 2300 125 0.1872 0.2166 REMARK 3 8 2.0400 - 1.9500 1.00 2975 140 0.1894 0.2306 REMARK 3 9 1.9500 - 1.8700 0.71 2123 92 0.2098 0.2600 REMARK 3 10 1.8700 - 1.8100 0.99 2935 144 0.2253 0.2320 REMARK 3 11 1.8100 - 1.7500 0.99 2939 149 0.2585 0.2417 REMARK 3 12 1.7500 - 1.7000 1.00 2930 164 0.2979 0.3062 REMARK 3 13 1.7000 - 1.6600 0.98 2932 112 0.3339 0.3453 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.994 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.01 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 : 0.010 1872 REMARK 3 ANGLE : 1.023 2533 REMARK 3 CHIRALITY : 0.067 271 REMARK 3 PLANARITY : 0.007 330 REMARK 3 DIHEDRAL : 20.088 729 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 19.8146 -33.8472 -2.8802 REMARK 3 T TENSOR REMARK 3 T11: 0.2808 T22: 0.2907 REMARK 3 T33: 0.2748 T12: 0.0055 REMARK 3 T13: -0.0237 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.4476 L22: 1.4120 REMARK 3 L33: 1.5353 L12: 0.2206 REMARK 3 L13: 0.6787 L23: 0.7577 REMARK 3 S TENSOR REMARK 3 S11: -0.0924 S12: -0.0574 S13: 0.0646 REMARK 3 S21: -0.1408 S22: 0.0014 S23: 0.0910 REMARK 3 S31: -0.2273 S32: -0.2039 S33: 0.0000 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 9QQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292138494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979190 REMARK 200 MONOCHROMATOR : CHANNEL CUT SI111 REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20220110 REMARK 200 DATA SCALING SOFTWARE : XSCALE 20220110 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38321 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 58.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.62000 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.16 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL OF PROTEIN AT 6MG/ML ADDED TO 1UL REMARK 280 RESERVOIR (100MM TRIS PH9, 22%PEG 6000), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.62500 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.25000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.43750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.06250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.81250 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 ASP A 222 REMARK 465 ARG A 223 REMARK 465 ILE A 224 REMARK 465 ALA A 225 REMARK 465 PRO A 226 REMARK 465 LYS A 227 REMARK 465 GLY A 228 REMARK 465 LEU A 229 REMARK 465 LYS A 230 REMARK 465 PHE A 231 REMARK 465 GLN A 232 DBREF 9QQ9 A 1 232 UNP E9RJ23 E9RJ23_BACNA 1 232 SEQADV 9QQ9 GLY A -1 UNP E9RJ23 EXPRESSION TAG SEQADV 9QQ9 PRO A 0 UNP E9RJ23 EXPRESSION TAG SEQRES 1 A 234 GLY PRO MET ASP SER PRO GLY VAL VAL LEU VAL SER LYS SEQRES 2 A 234 TYR VAL SER GLY LYS SER THR LYS PHE SER LYS TYR VAL SEQRES 3 A 234 ASN TYR ILE ASN ARG ASP GLU ALA VAL ARG THR GLU LYS SEQRES 4 A 234 PHE GLN THR TYR ASN VAL ASN LYS LEU ASP GLY TYR ASN SEQRES 5 A 234 GLN TYR MET GLY ASN PRO GLU LYS SER SER GLY ILE PHE SEQRES 6 A 234 THR GLN HIS LYS ASP SER LEU SER PRO VAL GLU LYS ASN SEQRES 7 A 234 GLN LEU LYS GLU ILE PHE ARG GLN ALA GLN LYS ASN ASP SEQRES 8 A 234 SER VAL MET TRP GLN ASP VAL ILE SER PHE ASP ASN LYS SEQRES 9 A 234 TRP LEU GLU GLU ARG GLY ILE TYR ASN SER GLN THR GLY SEQRES 10 A 234 TRP VAL ASN GLU GLY ALA ILE GLN ASN SER ILE ARG LYS SEQRES 11 A 234 GLY MET GLU VAL LEU LEU ARG GLU GLU GLN LEU GLU GLN SEQRES 12 A 234 SER GLY VAL TRP SER ALA ALA ILE HIS TYR ASN THR ASP SEQRES 13 A 234 ASN ILE HIS VAL HIS ILE ALA LEU VAL GLU PRO ASN PRO SEQRES 14 A 234 THR LYS GLU TYR GLY VAL PHE THR ASN LYS LYS THR GLY SEQRES 15 A 234 GLU VAL TYR GLN ALA ARG ARG GLY ASN ARG LYS LEU LYS SEQRES 16 A 234 THR LEU ASP LYS MET LYS SER LYS VAL ALA ASN THR LEU SEQRES 17 A 234 MET ASP ARG ASP LYS GLU LEU SER LYS ILE SER GLN LEU SEQRES 18 A 234 ILE HIS ASP ARG ILE ALA PRO LYS GLY LEU LYS PHE GLN HET CL A 301 1 HET CL A 302 1 HET CL A 303 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 3(CL 1-) FORMUL 5 HOH *135(H2 O) HELIX 1 AA1 SER A 17 ILE A 27 1 11 HELIX 2 AA2 ASP A 30 LYS A 37 1 8 HELIX 3 AA3 LYS A 37 ASN A 42 1 6 HELIX 4 AA4 SER A 71 ASN A 88 1 18 HELIX 5 AA5 ASN A 101 ARG A 107 1 7 HELIX 6 AA6 ASN A 118 GLU A 137 1 20 HELIX 7 AA7 LYS A 193 LEU A 206 1 14 HELIX 8 AA8 GLU A 212 HIS A 221 1 10 SHEET 1 AA1 5 VAL A 6 VAL A 13 0 SHEET 2 AA1 5 MET A 92 ASP A 100 -1 O GLN A 94 N LYS A 11 SHEET 3 AA1 5 ASN A 155 VAL A 163 -1 O VAL A 158 N ILE A 97 SHEET 4 AA1 5 VAL A 144 TYR A 151 -1 N SER A 146 O ALA A 161 SHEET 5 AA1 5 LYS A 58 SER A 59 -1 N LYS A 58 O TYR A 151 SHEET 1 AA2 2 TYR A 171 THR A 175 0 SHEET 2 AA2 2 VAL A 182 ARG A 186 -1 O TYR A 183 N PHE A 174 CRYST1 100.918 100.918 58.875 90.00 90.00 120.00 P 61 6 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 0.009909 0.005721 0.000000 0.00000 SCALE2 0.000000 0.011442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016985 0.00000 MASTER 245 0 3 8 7 0 0 6 1918 1 0 18 END