HEADER DNA BINDING PROTEIN 11-FEB-26 10XD TITLE RHODOCOCCUS RUBER DNAA DI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS RUBER; SOURCE 3 ORGANISM_TAXID: 1830; SOURCE 4 GENE: DNAA, RHRU231_590005; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INITIATOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.K.ELLIS,M.A.SCHUMACHER REVDAT 1 03-JUN-26 10XD 0 JRNL AUTH P.K.ELLIS,M.A.SCHUMACHER JRNL TITL STRUCTURES REVEAL DNAA DOMAIN I DIMER CONSERVED ACROSS JRNL TITL 2 ACTINOMYCETES: IMPLICATIONS FOR REPLICATION INITIATION JRNL REF TO BE PUBLISHED JRNL REFN 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 10866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 537 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 31.9500 - 3.1000 0.99 2742 144 0.1586 0.2067 REMARK 3 2 3.0900 - 2.4600 0.97 2581 132 0.2692 0.2816 REMARK 3 3 2.4600 - 2.1500 0.94 2497 126 0.2551 0.2953 REMARK 3 4 2.1500 - 1.9500 0.96 2509 135 0.3200 0.3425 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) : 0.292 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.60 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 : 0.015 724 REMARK 3 ANGLE : 1.407 989 REMARK 3 CHIRALITY : 0.084 113 REMARK 3 PLANARITY : 0.016 129 REMARK 3 DIHEDRAL : 16.210 259 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1384 -5.5089 30.0212 REMARK 3 T TENSOR REMARK 3 T11: 1.2731 T22: 1.9774 REMARK 3 T33: 1.4668 T12: 0.0313 REMARK 3 T13: 0.3899 T23: -0.0513 REMARK 3 L TENSOR REMARK 3 L11: 0.3711 L22: 0.2785 REMARK 3 L33: 0.9400 L12: 0.0010 REMARK 3 L13: -0.5541 L23: 0.1689 REMARK 3 S TENSOR REMARK 3 S11: -0.9619 S12: -1.4167 S13: 1.3963 REMARK 3 S21: 0.9748 S22: 1.2666 S23: 1.6544 REMARK 3 S31: 0.0050 S32: -1.7520 S33: -0.3523 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 7 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.2036 -17.1117 24.5956 REMARK 3 T TENSOR REMARK 3 T11: 0.4551 T22: 0.3828 REMARK 3 T33: 0.3060 T12: 0.0311 REMARK 3 T13: 0.0461 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 6.2639 L22: 5.8906 REMARK 3 L33: 7.4746 L12: 0.9239 REMARK 3 L13: -1.3185 L23: 3.4405 REMARK 3 S TENSOR REMARK 3 S11: -0.6328 S12: -0.6564 S13: 0.0980 REMARK 3 S21: 0.6399 S22: 0.0964 S23: 0.1756 REMARK 3 S31: 0.2556 S32: 0.7286 S33: 0.4177 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8838 -20.2852 19.6217 REMARK 3 T TENSOR REMARK 3 T11: 0.3633 T22: 0.2875 REMARK 3 T33: 0.3583 T12: -0.0419 REMARK 3 T13: -0.0227 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 7.8191 L22: 6.9137 REMARK 3 L33: 6.1943 L12: -1.0141 REMARK 3 L13: -0.0780 L23: 4.6183 REMARK 3 S TENSOR REMARK 3 S11: 0.0865 S12: -0.0303 S13: 0.3622 REMARK 3 S21: 0.0417 S22: -0.2729 S23: 0.1466 REMARK 3 S31: -0.0175 S32: -0.1869 S33: 0.1692 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.0458 -17.1553 31.7030 REMARK 3 T TENSOR REMARK 3 T11: 0.6032 T22: 0.4629 REMARK 3 T33: 0.3936 T12: -0.0722 REMARK 3 T13: 0.1014 T23: -0.1440 REMARK 3 L TENSOR REMARK 3 L11: 7.6312 L22: 7.7569 REMARK 3 L33: 4.2287 L12: -0.4047 REMARK 3 L13: 2.4823 L23: 5.0112 REMARK 3 S TENSOR REMARK 3 S11: -0.0143 S12: -1.2237 S13: 0.7032 REMARK 3 S21: 1.7243 S22: 0.2350 S23: 0.3938 REMARK 3 S31: 0.8403 S32: -0.0180 S33: -0.1639 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 90 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.4545 -17.4531 21.3863 REMARK 3 T TENSOR REMARK 3 T11: 0.5749 T22: 0.3137 REMARK 3 T33: 0.6103 T12: -0.0235 REMARK 3 T13: -0.0732 T23: -0.0631 REMARK 3 L TENSOR REMARK 3 L11: 8.0121 L22: 8.1446 REMARK 3 L33: 4.0982 L12: 0.5386 REMARK 3 L13: 2.4292 L23: 5.3841 REMARK 3 S TENSOR REMARK 3 S11: 0.2208 S12: 0.1206 S13: 1.0099 REMARK 3 S21: -0.3175 S22: -0.6392 S23: 1.0606 REMARK 3 S31: -1.8766 S32: -0.7369 S33: 0.9090 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 10XD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1000301432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-25 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 : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 31.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 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 : 18.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 66.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M AMMONIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, PH 7.0; 0.1M BIS-TRIS PROPANE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 42.18133 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 21.09067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.09067 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 42.18133 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 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.18133 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 178 LIES ON A SPECIAL POSITION. 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 SER A -1 OG REMARK 470 MET A 1 CG SD CE REMARK 470 ASN A 2 CG OD1 ND2 REMARK 470 ASP A 3 CG OD1 OD2 REMARK 470 GLU A 4 CG CD OE1 OE2 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 MET A 1 -150.79 -88.46 REMARK 500 ASN A 2 -125.70 55.79 REMARK 500 ILE A 40 -75.21 -103.15 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 187 DISTANCE = 6.36 ANGSTROMS DBREF1 10XD A 1 90 UNP A0A098BQE3_9NOCA DBREF2 10XD A A0A098BQE3 1 90 SEQADV 10XD GLY A -2 UNP A0A098BQE EXPRESSION TAG SEQADV 10XD SER A -1 UNP A0A098BQE EXPRESSION TAG SEQADV 10XD HIS A 0 UNP A0A098BQE EXPRESSION TAG SEQRES 1 A 93 GLY SER HIS MET ASN ASP GLU PRO ASN ALA LEU ALA ASP SEQRES 2 A 93 VAL TRP PRO ASP VAL VAL ALA GLU LEU THR ALA ASP GLY SEQRES 3 A 93 GLU GLY LEU SER LYS GLY GLN LYS ALA TRP LEU ALA LEU SEQRES 4 A 93 VAL LYS PRO ILE THR LEU ALA GLN GLY PHE ALA LEU LEU SEQRES 5 A 93 SER VAL PRO SER SER PHE ALA GLN GLU ALA ILE GLU ARG SEQRES 6 A 93 ASP LEU ARG GLU PRO ILE LEU ARG ALA LEU HIS ARG THR SEQRES 7 A 93 LEU GLY HIS ARG VAL GLU GLY LEU GLY VAL ARG ILE GLU SEQRES 8 A 93 PRO SER FORMUL 2 HOH *87(H2 O) HELIX 1 AA1 ASN A 6 ALA A 21 1 16 HELIX 2 AA2 ASP A 22 GLY A 25 5 4 HELIX 3 AA3 SER A 27 LEU A 36 1 10 HELIX 4 AA4 SER A 53 ASP A 63 1 11 HELIX 5 AA5 LEU A 64 GLY A 77 1 14 SHEET 1 AA1 3 LYS A 38 ALA A 43 0 SHEET 2 AA1 3 PHE A 46 VAL A 51 -1 O LEU A 48 N ILE A 40 SHEET 3 AA1 3 GLY A 82 ILE A 87 1 O GLY A 84 N LEU A 49 CRYST1 63.904 63.904 63.272 90.00 90.00 120.00 P 32 2 1 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 0.015648 0.009035 0.000000 0.00000 SCALE2 0.000000 0.018069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015805 0.00000 MASTER 330 0 0 5 3 0 0 6 780 1 0 8 END