HEADER VIRAL PROTEIN 29-JAN-26 10ON TITLE CRYSTAL FORM TWO OF THE ROSEOPHAGE RDJLF1 GAPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAPR-LIKE DNA-BINDING DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: E, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSEOBACTER PHAGE RDJL PHI 1; SOURCE 3 ORGANISM_TAXID: 562742; SOURCE 4 GENE: RDJLPHI1_GP30; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NAP, NUCLEOID ASSOCIATED PROTEIN, GAPR, PHAGE, RDJLF1, NAP POISON, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 1 30-SEP-26 10ON 0 JRNL AUTH M.A.SCHUMACHER JRNL TITL CRYSTAL FORM TWO OF THE ROSEOPHAGE RDJLF1 GAPR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 4751 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 47.1200 - 4.3300 0.98 1517 169 0.2154 0.2435 REMARK 3 2 4.3300 - 3.4300 0.98 1413 157 0.2116 0.2716 REMARK 3 3 3.4300 - 3.0000 0.95 1346 149 0.2625 0.3455 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.180 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 1202 REMARK 3 ANGLE : 1.013 1614 REMARK 3 CHIRALITY : 0.053 174 REMARK 3 PLANARITY : 0.011 218 REMARK 3 DIHEDRAL : 13.863 464 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): 14.1631 13.7094 10.5061 REMARK 3 T TENSOR REMARK 3 T11: 0.3149 T22: 0.3022 REMARK 3 T33: 0.2848 T12: -0.0299 REMARK 3 T13: 0.0279 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 4.6319 L22: 4.2194 REMARK 3 L33: 1.2131 L12: -4.2571 REMARK 3 L13: 0.9554 L23: -0.8954 REMARK 3 S TENSOR REMARK 3 S11: 0.3173 S12: 0.3361 S13: 0.1746 REMARK 3 S21: -0.2929 S22: -0.3458 S23: -0.1987 REMARK 3 S31: 0.0609 S32: 0.0980 S33: 0.0321 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 10ON COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1000304731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-19 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4753 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE PH 6.0, 2 MM REMARK 280 CACL2, 1.8 M AMMONIUM SULPHATE, 0.5 MM SPERMINE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 91.20400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.38700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.38700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.60200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.38700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.38700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 136.80600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.38700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.38700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.60200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.38700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.38700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 136.80600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 91.20400 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: 3850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 E -2 REMARK 465 SER E -1 REMARK 465 HIS E 0 REMARK 465 MET E 1 REMARK 465 ASN E 2 REMARK 465 VAL E 3 REMARK 465 ASN E 4 REMARK 465 GLN E 80 REMARK 465 LYS E 81 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 VAL A 3 REMARK 465 ASN A 4 REMARK 465 GLN A 80 REMARK 465 LYS A 81 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 GLU E 29 CG CD OE1 OE2 REMARK 470 GLN A 33 CG CD OE1 NE2 REMARK 470 LYS A 63 CG 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 ASP E 57 6.70 -68.08 REMARK 500 ARG E 59 42.83 -142.24 REMARK 500 LEU A 60 100.87 -163.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 211 DISTANCE = 6.82 ANGSTROMS DBREF 10ON E 1 81 UNP F4YXP1 F4YXP1_9CAUD 1 81 DBREF 10ON A 1 81 UNP F4YXP1 F4YXP1_9CAUD 1 81 SEQADV 10ON GLY E -2 UNP F4YXP1 EXPRESSION TAG SEQADV 10ON SER E -1 UNP F4YXP1 EXPRESSION TAG SEQADV 10ON HIS E 0 UNP F4YXP1 EXPRESSION TAG SEQADV 10ON GLY A -2 UNP F4YXP1 EXPRESSION TAG SEQADV 10ON SER A -1 UNP F4YXP1 EXPRESSION TAG SEQADV 10ON HIS A 0 UNP F4YXP1 EXPRESSION TAG SEQRES 1 E 84 GLY SER HIS MET ASN VAL ASN ARG ASP TYR ASP GLN LEU SEQRES 2 E 84 ARG ALA TYR LEU SER LEU LEU VAL GLU LEU GLU CYS GLN SEQRES 3 E 84 ILE ASP GLU ILE ASN GLU ALA LYS GLY GLN ALA PHE ARG SEQRES 4 E 84 GLU ALA LYS ALA CYS GLY PHE PRO ARG ASP VAL VAL ARG SEQRES 5 E 84 ASP LEU LEU ARG MET LYS GLN ASP GLY ARG LEU ASP ASP SEQRES 6 E 84 LYS ASP VAL PRO SER ALA PHE GLU GLY ILE LEU ASP ALA SEQRES 7 E 84 ARG GLY ILE ALA GLN LYS SEQRES 1 A 84 GLY SER HIS MET ASN VAL ASN ARG ASP TYR ASP GLN LEU SEQRES 2 A 84 ARG ALA TYR LEU SER LEU LEU VAL GLU LEU GLU CYS GLN SEQRES 3 A 84 ILE ASP GLU ILE ASN GLU ALA LYS GLY GLN ALA PHE ARG SEQRES 4 A 84 GLU ALA LYS ALA CYS GLY PHE PRO ARG ASP VAL VAL ARG SEQRES 5 A 84 ASP LEU LEU ARG MET LYS GLN ASP GLY ARG LEU ASP ASP SEQRES 6 A 84 LYS ASP VAL PRO SER ALA PHE GLU GLY ILE LEU ASP ALA SEQRES 7 A 84 ARG GLY ILE ALA GLN LYS HET SO4 E 101 5 HET SO4 A 101 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *21(H2 O) HELIX 1 AA1 ASP E 6 ALA E 40 1 35 HELIX 2 AA2 PRO E 44 ASP E 57 1 14 HELIX 3 AA3 ASP E 61 LYS E 63 5 3 HELIX 4 AA4 ASP E 64 ARG E 76 1 13 HELIX 5 AA5 ASP A 6 GLY A 42 1 37 HELIX 6 AA6 PRO A 44 ASP A 57 1 14 HELIX 7 AA7 ASP A 64 ARG A 76 1 13 CRYST1 48.774 48.774 182.408 90.00 90.00 90.00 P 41 21 2 16 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 0.020503 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005482 0.00000 CONECT 1185 1186 1187 1188 1189 CONECT 1186 1185 CONECT 1187 1185 CONECT 1188 1185 CONECT 1189 1185 CONECT 1190 1191 1192 1193 1194 CONECT 1191 1190 CONECT 1192 1190 CONECT 1193 1190 CONECT 1194 1190 MASTER 293 0 2 7 0 0 0 6 1213 2 10 14 END