HEADER DNA BINDING PROTEIN 10-OCT-25 9YMS TITLE CRYSTAL STRUCTURE OF THE STREPTOCOCCUS MUTANS YBAB HOMOLOG (SMU.394) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOID-ASSOCIATED PROTEIN SMU_394C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MUTANS; SOURCE 3 ORGANISM_TAXID: 1309; SOURCE 4 GENE: SMU_394C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS NUCLEOID-ASSOCIATED PROTEIN, SMU_394C, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,K.P.BATTAILE,I.BISWAS REVDAT 1 21-OCT-26 9YMS 0 JRNL AUTH S.LOVELL,I.BISWAS JRNL TITL CRYSTAL STRUCTURE OF NUCLEOID-ASSOCIATED PROTEIN SMU_394C JRNL TITL 2 FROM STREPTOCOCCUS MUTANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (2.0_5833: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13074 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 666 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 30.1400 - 2.5600 1.00 2593 145 0.1845 0.2176 REMARK 3 2 2.5600 - 2.0400 1.00 2482 143 0.1732 0.2237 REMARK 3 3 2.0400 - 1.7800 1.00 2444 138 0.1474 0.1746 REMARK 3 4 1.7800 - 1.6200 1.00 2484 112 0.1479 0.2322 REMARK 3 5 1.6200 - 1.5000 1.00 2405 128 0.1971 0.2439 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.510 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 : 0.008 614 REMARK 3 ANGLE : 0.871 829 REMARK 3 CHIRALITY : 0.058 102 REMARK 3 PLANARITY : 0.006 108 REMARK 3 DIHEDRAL : 17.395 234 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 9YMS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 42.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.02900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 100 MM TRIS PH REMARK 280 7.0, 200 MM LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 14.31450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.92850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.97450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 14.31450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.92850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.97450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 14.31450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.92850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.97450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 14.31450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 22.92850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.97450 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: 2010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 28.62900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 45.85700 REMARK 350 BIOMT3 2 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 A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 ASN A 3 REMARK 465 MET A 4 REMARK 465 GLN A 5 REMARK 465 ASN A 6 REMARK 465 MET A 7 REMARK 465 MET A 8 REMARK 465 LYS A 9 REMARK 465 GLN A 10 REMARK 465 GLY A 91 REMARK 465 ALA A 92 REMARK 465 PHE A 93 REMARK 465 ALA A 94 REMARK 465 GLY A 95 REMARK 465 LYS A 96 REMARK 465 LEU A 97 REMARK 465 PRO A 98 REMARK 465 PHE A 99 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 GLN A 12 CG CD OE1 NE2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 GLN A 17 CG CD OE1 NE2 DBREF 9YMS A 1 99 UNP Q8DVS3 Y394_STRMU 1 99 SEQADV 9YMS GLY A -2 UNP Q8DVS3 EXPRESSION TAG SEQADV 9YMS SER A -1 UNP Q8DVS3 EXPRESSION TAG SEQADV 9YMS HIS A 0 UNP Q8DVS3 EXPRESSION TAG SEQRES 1 A 102 GLY SER HIS MET MET ASN MET GLN ASN MET MET LYS GLN SEQRES 2 A 102 ALA GLN LYS LEU GLN LYS GLN MET GLU LYS LYS GLN SER SEQRES 3 A 102 GLU LEU ALA SER MET THR PHE VAL GLY LYS SER ALA GLN SEQRES 4 A 102 ASP LEU VAL VAL ALA THR PHE THR GLY ASN LYS LYS LEU SEQRES 5 A 102 VAL SER ILE ASP PHE LYS GLU ALA VAL VAL ASP PRO ASP SEQRES 6 A 102 ASP ARG GLU THR LEU GLN ASP MET THR VAL GLN ALA ILE SEQRES 7 A 102 ASN ASP ALA LEU GLY GLN ILE GLU ASP ALA THR GLN LYS SEQRES 8 A 102 THR MET GLY ALA PHE ALA GLY LYS LEU PRO PHE FORMUL 2 HOH *42(H2 O) HELIX 1 AA1 ALA A 11 SER A 27 1 17 HELIX 2 AA2 ALA A 35 ASP A 37 5 3 HELIX 3 AA3 GLU A 56 VAL A 59 5 4 HELIX 4 AA4 ASP A 63 MET A 90 1 28 SHEET 1 AA1 3 THR A 29 LYS A 33 0 SHEET 2 AA1 3 VAL A 39 THR A 44 -1 O PHE A 43 N PHE A 30 SHEET 3 AA1 3 LEU A 49 PHE A 54 -1 O VAL A 50 N THR A 42 CRYST1 28.629 45.857 119.949 90.00 90.00 90.00 I 2 2 2 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 0.034930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021807 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008337 0.00000 MASTER 255 0 0 4 3 0 0 6 642 1 0 8 END