HEADER DNA BINDING PROTEIN/DNA 22-FEB-19 6JIP TITLE CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE SP_0782 (RESIDUES 7-79) TITLE 2 IN COMPLEX WITH SINGLE-STRANDED DNA DT6 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*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE (STRAIN ATCC BAA-255 / SOURCE 3 R6); SOURCE 4 ORGANISM_TAXID: 171101; SOURCE 5 STRAIN: ATCC BAA-255 / R6; SOURCE 6 GENE: SPR0690, SP_0782; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.FANG,G.LU,S.LI,J.ZHU,Y.YANG,P.GONG REVDAT 3 27-MAR-24 6JIP 1 REMARK REVDAT 2 22-JAN-20 6JIP 1 JRNL REVDAT 1 27-NOV-19 6JIP 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. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 10889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 566 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 46.9587 - 2.6326 1.00 2639 142 0.1786 0.2012 REMARK 3 2 2.6326 - 2.0896 1.00 2582 166 0.2115 0.2226 REMARK 3 3 2.0896 - 1.8254 0.99 2566 121 0.2088 0.2462 REMARK 3 4 1.8254 - 1.6585 0.98 2536 137 0.2627 0.2674 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.38 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 : 0.005 621 REMARK 3 ANGLE : 0.690 838 REMARK 3 CHIRALITY : 0.050 89 REMARK 3 PLANARITY : 0.005 99 REMARK 3 DIHEDRAL : 14.368 481 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 6JIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300010861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 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) : 0.9789 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 : 10917 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.659 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 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) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 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: NULL 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 (%): 39.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 6.8, 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 33.19150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 33.19150 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.07150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.19150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.53575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.19150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.60725 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.19150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.19150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 21.07150 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 33.19150 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 31.60725 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 33.19150 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 10.53575 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, 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 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 5 REMARK 465 DT B 6 REMARK 465 DT B 7 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 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 DT B 4 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT B 4 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 4 C7 C6 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE B 101 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE B 101 DBREF 6JIP A 7 79 UNP Q8DQG2 Q8DQG2_STRR6 7 79 DBREF 6JIP B 2 7 PDB 6JIP 6JIP 2 7 SEQADV 6JIP MET A 6 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP LEU A 80 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP GLU A 81 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP HIS A 82 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP HIS A 83 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP HIS A 84 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP HIS A 85 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP HIS A 86 UNP Q8DQG2 EXPRESSION TAG SEQADV 6JIP 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 6 DT DT DT DT DT DT HET 1PE A 100 16 HET 1PE B 101 7 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 3 1PE 2(C10 H22 O6) FORMUL 5 HOH *42(H2 O) HELIX 1 AA1 SER A 65 LYS A 77 1 13 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 GLY A 59 N ALA A 50 SITE 1 AC1 4 GLU A 17 ALA A 44 GLU A 67 ASP A 74 SITE 1 AC2 6 GLY A 29 THR A 56 LYS A 57 MET A 58 SITE 2 AC2 6 DT B 3 HOH B 202 CRYST1 66.383 66.383 42.143 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 0.015064 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023729 0.00000