HEADER UNKNOWN FUNCTION/DNA 24-MAR-18 5ZKL TITLE CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE SP_0782 (RESIDUES 7-79) TITLE 2 IN COMPLEX WITH SINGLE-STRANDED DNA DT12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SP_0782; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE R6; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: ATCC BAA-255 / R6; SOURCE 5 GENE: SPR0690, SP_0782; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, UNKNOWN FUNCTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.LU,S.LI,J.ZHU,Y.YANG,P.GONG REVDAT 4 22-NOV-23 5ZKL 1 REMARK REVDAT 3 22-JAN-20 5ZKL 1 JRNL REVDAT 2 27-NOV-19 5ZKL 1 JRNL REVDAT 1 27-MAR-19 5ZKL 0 JRNL AUTH S.LI,G.LU,X.FANG,T.A.RAMELOT,M.A.KENNEDY,X.ZHOU,P.GONG, JRNL AUTH 2 X.ZHANG,M.LIU,J.ZHU,Y.YANG JRNL TITL STRUCTURAL INSIGHT INTO THE LENGTH-DEPENDENT BINDING OF JRNL TITL 2 SSDNA BY SP_0782 FROM STREPTOCOCCUS PNEUMONIAE, REVEALS A JRNL TITL 3 DIVERGENCE IN THE DNA-BINDING INTERFACE OF PC4-LIKE JRNL TITL 4 PROTEINS. JRNL REF NUCLEIC ACIDS RES. V. 48 432 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 31713614 JRNL DOI 10.1093/NAR/GKZ1045 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 5518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 524 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 23.6278 - 3.0946 1.00 1443 168 0.1729 0.1860 REMARK 3 2 3.0946 - 2.4571 1.00 1440 120 0.1953 0.2521 REMARK 3 3 2.4571 - 2.1467 0.85 1204 128 0.1871 0.2274 REMARK 3 4 2.1467 - 1.9506 0.66 907 108 0.1774 0.2159 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.41 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 : 0.007 628 REMARK 3 ANGLE : 0.785 863 REMARK 3 CHIRALITY : 0.051 93 REMARK 3 PLANARITY : 0.005 98 REMARK 3 DIHEDRAL : 17.096 352 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 5ZKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300005823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 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) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3OBH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 3.4, EVAPORATION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 33.15950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 33.15950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.54150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.15950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.77075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.15950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.31225 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.15950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.15950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.54150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 33.15950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.31225 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 33.15950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 9.77075 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: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 MET A 9 REMARK 465 ALA A 10 REMARK 465 LYS A 77 REMARK 465 GLY A 78 REMARK 465 ASN A 79 REMARK 465 LEU A 80 REMARK 465 GLU A 81 REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 465 DT B 6 REMARK 465 DT B 7 REMARK 465 DT B 8 REMARK 465 DT B 9 REMARK 465 DT B 10 REMARK 465 DT B 11 REMARK 465 DT B 12 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 A 11 CG CD OE1 OE2 REMARK 470 GLN A 70 CG CD OE1 NE2 REMARK 470 DT B 1 O5' C5' REMARK 470 DT B 5 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT B 5 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 5 C7 C6 DBREF 5ZKL A 7 79 UNP Q8DQG2 Q8DQG2_STRR6 7 79 DBREF 5ZKL B 1 12 PDB 5ZKL 5ZKL 1 12 SEQADV 5ZKL MET A 6 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL LEU A 80 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL GLU A 81 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 82 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 83 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 84 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 85 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 86 UNP Q8DQG2 EXPRESSION TAG SEQADV 5ZKL HIS A 87 UNP Q8DQG2 EXPRESSION TAG SEQRES 1 A 82 MET LYS LYS MET ALA GLU PHE THR PHE GLU ILE GLU GLU SEQRES 2 A 82 HIS LEU LEU THR LEU SER GLU ASN GLU LYS GLY TRP THR SEQRES 3 A 82 LYS GLU ILE ASN ARG VAL SER PHE ASN GLY ALA PRO ALA SEQRES 4 A 82 LYS PHE ASP ILE ARG ALA TRP SER PRO ASP HIS THR LYS SEQRES 5 A 82 MET GLY LYS GLY ILE THR LEU SER ASN GLU GLU PHE GLN SEQRES 6 A 82 THR MET VAL ASP ALA PHE LYS GLY ASN LEU GLU HIS HIS SEQRES 7 A 82 HIS HIS HIS HIS SEQRES 1 B 12 DT DT DT DT DT DT DT DT DT DT DT DT FORMUL 3 HOH *49(H2 O) HELIX 1 AA1 SER A 65 PHE A 76 1 12 SHEET 1 AA1 4 PHE A 14 GLU A 25 0 SHEET 2 AA1 4 THR A 31 PHE A 39 -1 O LYS A 32 N LEU A 23 SHEET 3 AA1 4 LYS A 45 TRP A 51 -1 O ARG A 49 N GLU A 33 SHEET 4 AA1 4 MET A 58 LEU A 64 -1 O LEU A 64 N PHE A 46 CRYST1 66.319 66.319 39.083 90.00 90.00 90.00 I 41 8 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 0.015079 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025587 0.00000