HEADER DNA BINDING PROTEIN 27-JAN-20 5QUN TITLE STRUCTURE OF UNLIGANDED HUMRADA1.6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RADA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS RAD51, RADA, INHIBITION, FBDD, PPI, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MARSH,M.HYVONEN REVDAT 3 06-MAR-24 5QUN 1 REMARK REVDAT 2 12-MAY-21 5QUN 1 REMARK REVDAT 1 03-MAR-21 5QUN 0 JRNL AUTH P.B.BREAR,G.FISCHER,R.ROCABOY,M.MARSH,M.ROSSMANN, JRNL AUTH 2 T.PANTELEJEVS,J.WAGSTAFF,B.K.BLASZCZYK JRNL TITL OPTIMISATION OF CRYSTAL FORMS FOR STRUCTURE-GUIDED DRUG JRNL TITL 2 DISCOVERY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 61278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3072 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 26.3436 - 3.4720 0.97 2854 146 0.1760 0.1959 REMARK 3 2 3.4720 - 2.7568 1.00 2778 172 0.1908 0.2115 REMARK 3 3 2.7568 - 2.4086 1.00 2776 143 0.1977 0.2167 REMARK 3 4 2.4086 - 2.1885 1.00 2745 152 0.2577 0.2757 REMARK 3 5 2.1885 - 2.0317 1.00 2704 179 0.1969 0.2423 REMARK 3 6 2.0317 - 1.9119 0.99 2719 119 0.2876 0.3511 REMARK 3 7 1.9119 - 1.8162 1.00 2725 132 0.2206 0.2239 REMARK 3 8 1.8162 - 1.7372 1.00 2726 150 0.1841 0.2173 REMARK 3 9 1.7372 - 1.6703 1.00 2745 111 0.1671 0.2077 REMARK 3 10 1.6703 - 1.6127 1.00 2705 136 0.1692 0.2153 REMARK 3 11 1.6127 - 1.5622 1.00 2732 130 0.1674 0.2215 REMARK 3 12 1.5622 - 1.5176 1.00 2715 144 0.1808 0.2233 REMARK 3 13 1.5176 - 1.4776 0.97 2612 146 0.2258 0.3178 REMARK 3 14 1.4776 - 1.4416 1.00 2694 133 0.2504 0.2948 REMARK 3 15 1.4416 - 1.4088 1.00 2697 137 0.2529 0.3408 REMARK 3 16 1.4088 - 1.3789 1.00 2666 161 0.2185 0.2542 REMARK 3 17 1.3789 - 1.3513 1.00 2704 140 0.2401 0.3035 REMARK 3 18 1.3513 - 1.3258 1.00 2676 145 0.2544 0.3362 REMARK 3 19 1.3258 - 1.3021 0.72 1932 120 0.3569 0.4752 REMARK 3 20 1.3021 - 1.2800 0.73 1963 96 0.5217 0.6309 REMARK 3 21 1.2800 - 1.2594 0.99 2689 129 0.3009 0.3233 REMARK 3 22 1.2594 - 1.2400 0.99 2649 151 0.3338 0.3632 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.33 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 5QUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1001402428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 26.338 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.723 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.41 REMARK 200 R MERGE FOR SHELL (I) : 1.22100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.410 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 (%): 43.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM NA/K PHOSPATE, 5% PEG1000H, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 20.28250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.64650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.97850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.64650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.28250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.97850 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 107 REMARK 465 GLN A 300 REMARK 465 ALA A 301 REMARK 465 GLY A 302 REMARK 465 PRO A 331 REMARK 465 HIS A 332 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 765 O HOH A 791 2.04 REMARK 500 O HOH A 655 O HOH A 794 2.06 REMARK 500 O HOH A 546 O HOH A 672 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 771 O HOH A 803 1655 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 401 DBREF 5QUN A 107 349 PDB 5QUN 5QUN 107 349 SEQRES 1 A 229 MET ALA THR ILE GLY ARG ILE SER THR GLY SER LYS SER SEQRES 2 A 229 LEU ASP LYS LEU LEU GLY GLY GLY ILE GLU THR GLN ALA SEQRES 3 A 229 ILE THR GLU VAL PHE GLY GLU PHE GLY SER GLY LYS THR SEQRES 4 A 229 GLN LEU ALA HIS THR LEU ALA VAL MET VAL GLN LEU PRO SEQRES 5 A 229 PRO GLU GLU GLY GLY LEU ASN GLY SER VAL MET TRP ILE SEQRES 6 A 229 ASP THR GLU ASN THR PHE ARG PRO GLU ARG ILE ARG GLU SEQRES 7 A 229 ILE ALA GLN ASN ARG GLY LEU ASP PRO ASP GLU VAL LEU SEQRES 8 A 229 LYS HIS ILE ALA TYR ALA ARG ALA PHE ASN SER ASN HIS SEQRES 9 A 229 GLN MET LEU LEU VAL GLN GLN ALA GLU ASP MET ILE LYS SEQRES 10 A 229 GLU LEU LEU ASN THR ASP ARG PRO VAL LYS LEU LEU ILE SEQRES 11 A 229 VAL ASP SER LEU THR SER HIS PHE ARG SER GLU TYR ILE SEQRES 12 A 229 GLY ARG GLY ALA LEU ALA GLU ARG GLN GLN LYS LEU ALA SEQRES 13 A 229 LYS HIS LEU ALA ASP LEU HIS ARG LEU ALA ASN LEU TYR SEQRES 14 A 229 ASP ILE ALA VAL PHE VAL THR ASN GLN VAL GLN ALA GLY SEQRES 15 A 229 HIS ILE LEU ALA HIS SER ALA THR LEU ARG VAL TYR LEU SEQRES 16 A 229 ARG LYS GLY LYS GLY GLY LYS ARG ILE ALA ARG LEU ILE SEQRES 17 A 229 ASP ALA PRO HIS LEU PRO GLU GLY GLU ALA VAL PHE SER SEQRES 18 A 229 ILE THR GLU LYS GLY ILE GLU ASP HET PO4 A 401 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *313(H2 O) HELIX 1 AA1 SER A 117 LEU A 124 1 8 HELIX 2 AA2 GLY A 143 VAL A 155 1 13 HELIX 3 AA3 GLN A 156 LEU A 157 5 2 HELIX 4 AA4 PRO A 158 GLY A 162 5 5 HELIX 5 AA5 ARG A 178 ARG A 189 1 12 HELIX 6 AA6 ASP A 192 HIS A 199 1 8 HELIX 7 AA7 ASN A 207 LEU A 226 1 20 HELIX 8 AA8 THR A 241 TYR A 248 1 8 HELIX 9 AA9 GLY A 252 ASP A 276 1 25 HELIX 10 AB1 LYS A 319 GLY A 321 5 3 SHEET 1 AA1 2 ARG A 112 ILE A 113 0 SHEET 2 AA1 2 ILE A 128 GLU A 129 -1 O ILE A 128 N ILE A 113 SHEET 1 AA2 9 ILE A 200 ARG A 204 0 SHEET 2 AA2 9 SER A 167 ASP A 172 1 N TRP A 170 O ALA A 201 SHEET 3 AA2 9 VAL A 232 ASP A 238 1 O ILE A 236 N ILE A 171 SHEET 4 AA2 9 ALA A 278 GLN A 284 1 O PHE A 280 N LEU A 235 SHEET 5 AA2 9 ALA A 132 GLY A 138 1 N THR A 134 O VAL A 279 SHEET 6 AA2 9 LEU A 311 LYS A 317 1 O VAL A 313 N GLU A 135 SHEET 7 AA2 9 ARG A 323 ILE A 328 -1 O ARG A 326 N TYR A 314 SHEET 8 AA2 9 ALA A 338 THR A 343 -1 O PHE A 340 N ARG A 323 SHEET 9 AA2 9 GLY A 346 GLU A 348 -1 O GLU A 348 N SER A 341 CISPEP 1 ASP A 238 SER A 239 0 4.14 SITE 1 AC1 11 GLU A 139 PHE A 140 GLY A 141 SER A 142 SITE 2 AC1 11 GLY A 143 LYS A 144 THR A 145 HOH A 524 SITE 3 AC1 11 HOH A 559 HOH A 577 HOH A 623 CRYST1 40.565 61.957 87.293 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 0.024652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011456 0.00000