HEADER MOTOR PROTEIN 28-AUG-24 9DDZ TITLE CRYSTAL STRUCTURE OF NEISSERIA MENINGITIDIS TONB C-TERMINUS DOMAIN TITLE 2 (GLOBULAR DOMAIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TONB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B; SOURCE 3 ORGANISM_TAXID: 491; SOURCE 4 GENE: TONB, NMB1730; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TONB, TBDTS, PERIPLASM, PMF, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.DUBEY,P.LI,N.NOINAJ REVDAT 1 04-MAR-26 9DDZ 0 JRNL AUTH S.DUBEY,P.LI,N.NOINAJ JRNL TITL CRYSTAL STRUCTURE OF NEISSERIA MENINGITIDIS TONB C-TERMINUS JRNL TITL 2 DOMAIN (GLOBULAR DOMAIN) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (???) 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 2555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 256 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 40.6000 - 2.5900 0.44 1182 132 0.1620 0.2090 REMARK 3 2 3.2400 - 2.5700 0.44 1117 124 0.2839 0.3650 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.80 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 : 0.004 640 REMARK 3 ANGLE : 0.732 870 REMARK 3 CHIRALITY : 0.049 97 REMARK 3 PLANARITY : 0.009 116 REMARK 3 DIHEDRAL : 19.547 232 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 9DDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-23 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 : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1124727 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGSO4 (SALT), 20% W/V PEG 4K REMARK 280 (PRECIPITANT), 10% V/V GLYCEROL (ADDITIVE), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4 REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4 REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4 REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4 REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4 REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4 REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4 REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4 REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4 REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4 REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4 REMARK 290 24555 -Z+1/4,-Y+1/4,-X+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 49.81250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.81250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.81250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.81250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.81250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.81250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 49.81250 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 49.81250 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 49.81250 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 49.81250 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 49.81250 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 49.81250 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 49.81250 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 49.81250 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 49.81250 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 49.81250 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 49.81250 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 49.81250 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 24.90625 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 74.71875 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 24.90625 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 24.90625 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 24.90625 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 74.71875 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 24.90625 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 74.71875 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 24.90625 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 74.71875 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 24.90625 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 74.71875 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 74.71875 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 24.90625 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 74.71875 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 24.90625 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 24.90625 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 24.90625 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 74.71875 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 24.90625 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 24.90625 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 74.71875 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 74.71875 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 74.71875 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 24.90625 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 74.71875 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 24.90625 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 74.71875 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 24.90625 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 24.90625 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 24.90625 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 309 LIES ON A SPECIAL POSITION. 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 193 REMARK 465 SER A 194 REMARK 465 SER A 195 REMARK 465 LYS A 196 REMARK 465 GLY A 197 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 ASN A 198 CG OD1 ND2 REMARK 470 LYS A 276 CG CD CE NZ DBREF 9DDZ A 193 280 UNP P57004 TONB_NEIMB 193 280 SEQRES 1 A 88 GLY SER SER LYS GLY ASN PRO LEU ARG ALA ASN GLY SER SEQRES 2 A 88 ILE PRO ARG PRO ALA TYR PRO THR LEU SER MET GLU ASN SEQRES 3 A 88 ASP GLU GLN GLY THR VAL VAL LEU SER VAL LEU VAL SER SEQRES 4 A 88 PRO GLY GLY HIS VAL GLU SER VAL LYS ILE VAL LYS SER SEQRES 5 A 88 SER GLY PHE SER ARG LEU ASP ASN ALA ALA ARG LYS ALA SEQRES 6 A 88 ALA GLN ASN GLY HIS PHE GLN ALA ASN ALA TRP THR GLU SEQRES 7 A 88 PHE LYS VAL PRO VAL LYS PHE GLU LEU ASN FORMUL 2 HOH *23(H2 O) HELIX 1 AA1 PRO A 212 ASN A 218 1 7 HELIX 2 AA2 PHE A 247 ASN A 260 1 14 SHEET 1 AA1 2 ALA A 202 SER A 205 0 SHEET 2 AA1 2 HIS A 262 ALA A 265 -1 O HIS A 262 N SER A 205 SHEET 1 AA2 3 VAL A 236 LYS A 243 0 SHEET 2 AA2 3 GLY A 222 VAL A 230 -1 N SER A 227 O LYS A 240 SHEET 3 AA2 3 THR A 269 PHE A 277 -1 O PHE A 271 N VAL A 228 CRYST1 99.625 99.625 99.625 90.00 90.00 90.00 P 43 3 2 24 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 0.010038 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010038 0.00000 MASTER 299 0 0 2 5 0 0 6 649 1 0 7 END