HEADER ANTIMICROBIAL PROTEIN 16-NOV-22 8HHJ TITLE CRYSTAL STRUCTURE OF THE MAFB2-CTMGI-2B16B6/MAFI2MGI-2B16B6 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAFB2 IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MAFB2 TOXIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 8 ORGANISM_TAXID: 487; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYMORPHIC TOXIN SYSTEM, MAFB2, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.C.HA REVDAT 1 15-NOV-23 8HHJ 0 JRNL AUTH S.H.PARK,S.J.JEONG,S.C.HA JRNL TITL STRUCTURAL BASIS FOR THE TOXIC ACTIVITY OF MAFB2 FROM MAF JRNL TITL 2 GENOMIC ISLAND 2 (MGI-2) IN N. MENINGITIDIS B16B6. JRNL REF SCI REP V. 13 3365 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 36849501 JRNL DOI 10.1038/S41598-023-30528-9 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.11 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) : 28.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 30286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 28.9030 - 3.6130 0.90 1925 136 0.1772 0.1887 REMARK 3 2 3.6130 - 2.8686 0.99 2076 147 0.1757 0.2021 REMARK 3 3 2.8686 - 2.5062 1.00 2075 146 0.1875 0.2067 REMARK 3 4 2.5062 - 2.2772 1.00 2051 145 0.1837 0.2284 REMARK 3 5 2.2772 - 2.1140 0.99 2025 143 0.1716 0.2030 REMARK 3 6 2.1140 - 1.9894 0.99 2042 145 0.1762 0.2034 REMARK 3 7 1.9894 - 1.8898 0.99 2047 144 0.1803 0.2273 REMARK 3 8 1.8898 - 1.8076 0.99 2019 144 0.1809 0.1985 REMARK 3 9 1.8076 - 1.7380 0.98 2013 142 0.1890 0.2355 REMARK 3 10 1.7380 - 1.6780 0.98 2020 143 0.1822 0.2233 REMARK 3 11 1.6780 - 1.6255 0.98 1989 140 0.1894 0.2141 REMARK 3 12 1.6255 - 1.5791 0.98 2011 143 0.1823 0.2187 REMARK 3 13 1.5791 - 1.5375 0.98 1998 140 0.1854 0.2537 REMARK 3 14 1.5375 - 1.5000 0.97 1995 142 0.1991 0.2137 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.420 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 : 0.006 1618 REMARK 3 ANGLE : 0.808 2179 REMARK 3 CHIRALITY : 0.054 234 REMARK 3 PLANARITY : 0.005 283 REMARK 3 DIHEDRAL : 14.268 969 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 8HHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-00 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9734 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30286 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.3000 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 : 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 - 0.3 M MAGNESIUM FORMATE, 25 - REMARK 280 30% POLYETHYLENE GLYCOL (PEG) 3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 39.33350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.89600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.33350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.89600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10080 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 1 REMARK 465 GLY A 2 REMARK 465 ASN A 3 REMARK 465 ILE A 4 REMARK 465 SER A 104 REMARK 465 GLN A 105 REMARK 465 ALA A 106 REMARK 465 LEU A 107 REMARK 465 GLU A 108 REMARK 465 GLY B 267 REMARK 465 HIS B 268 REMARK 465 MET B 269 REMARK 465 ALA B 270 REMARK 465 LYS B 271 REMARK 465 VAL B 272 REMARK 465 LYS B 273 REMARK 465 ASN B 274 REMARK 465 LEU B 275 REMARK 465 THR B 276 REMARK 465 LYS B 277 REMARK 465 ALA B 278 REMARK 465 ALA B 279 REMARK 465 LYS B 280 REMARK 465 PRO B 281 REMARK 465 GLY B 282 REMARK 465 LYS B 283 REMARK 465 ALA B 284 REMARK 465 ALA B 285 REMARK 465 VAL B 286 REMARK 465 SER B 287 REMARK 465 GLY B 288 REMARK 465 ASP B 289 REMARK 465 PHE B 290 REMARK 465 SER B 291 REMARK 465 ASP B 292 REMARK 465 SER B 293 REMARK 465 TYR B 294 REMARK 465 LYS B 295 REMARK 465 HIS B 296 REMARK 465 ASN B 297 REMARK 465 THR B 298 REMARK 465 ALA B 299 REMARK 465 SER B 300 REMARK 465 ARG B 301 REMARK 465 LEU B 302 REMARK 465 SER B 303 REMARK 465 GLN B 304 REMARK 465 SER B 305 REMARK 465 VAL B 306 REMARK 465 ASP B 307 REMARK 465 GLY B 308 REMARK 465 GLU B 309 REMARK 465 MET B 310 REMARK 465 PHE B 311 REMARK 465 GLN B 312 REMARK 465 THR B 313 REMARK 465 ARG B 314 REMARK 465 ASN B 315 REMARK 465 VAL B 316 REMARK 465 ASP B 317 REMARK 465 PHE B 318 REMARK 465 LYS B 319 REMARK 465 ALA B 320 REMARK 465 LYS B 321 REMARK 465 SER B 322 REMARK 465 GLU B 424 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 74 O HOH A 201 2.07 REMARK 500 O HOH A 264 O HOH A 287 2.15 REMARK 500 O HOH B 560 O HOH B 567 2.16 REMARK 500 O HOH A 286 O HOH A 293 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8HHJ A 3 106 UNP A0A0Y5KAW3_NEIME DBREF2 8HHJ A A0A0Y5KAW3 2 105 DBREF1 8HHJ B 270 422 UNP A0A8E3U2Q7_NEIME DBREF2 8HHJ B A0A8E3U2Q7 270 422 SEQADV 8HHJ MET A 1 UNP A0A0Y5KAW INITIATING METHIONINE SEQADV 8HHJ GLY A 2 UNP A0A0Y5KAW EXPRESSION TAG SEQADV 8HHJ LEU A 107 UNP A0A0Y5KAW EXPRESSION TAG SEQADV 8HHJ GLU A 108 UNP A0A0Y5KAW EXPRESSION TAG SEQADV 8HHJ GLY B 267 UNP A0A8E3U2Q EXPRESSION TAG SEQADV 8HHJ HIS B 268 UNP A0A8E3U2Q EXPRESSION TAG SEQADV 8HHJ MET B 269 UNP A0A8E3U2Q EXPRESSION TAG SEQADV 8HHJ ARG B 376 UNP A0A8E3U2Q GLY 376 ENGINEERED MUTATION SEQADV 8HHJ LEU B 423 UNP A0A8E3U2Q EXPRESSION TAG SEQADV 8HHJ GLU B 424 UNP A0A8E3U2Q EXPRESSION TAG SEQRES 1 A 108 MET GLY ASN ILE LEU PRO SER TRP LEU ARG VAL GLY MET SEQRES 2 A 108 ASN ILE ALA MET LEU GLY MET ILE HIS SER ASP ILE ARG SEQRES 3 A 108 LEU ILE THR VAL ASP TYR GLU GLU ARG ARG ARG PHE LEU SEQRES 4 A 108 LYS ILE LYS ASN TYR LEU SER ARG GLU ALA ILE THR GLU SEQRES 5 A 108 ASP HIS GLU ASP MET GLU TYR LEU ILE THR GLU LEU TRP SEQRES 6 A 108 SER MET CYS GLY GLU TYR PHE ASP GLU ALA ASP PHE GLU SEQRES 7 A 108 CYS ILE TYR SER ASN HIS SER SER MET GLU LEU ASN GLN SEQRES 8 A 108 ILE ASN GLY ALA VAL PHE ARG ARG LYS GLU LEU ILE SER SEQRES 9 A 108 GLN ALA LEU GLU SEQRES 1 B 158 GLY HIS MET ALA LYS VAL LYS ASN LEU THR LYS ALA ALA SEQRES 2 B 158 LYS PRO GLY LYS ALA ALA VAL SER GLY ASP PHE SER ASP SEQRES 3 B 158 SER TYR LYS HIS ASN THR ALA SER ARG LEU SER GLN SER SEQRES 4 B 158 VAL ASP GLY GLU MET PHE GLN THR ARG ASN VAL ASP PHE SEQRES 5 B 158 LYS ALA LYS SER ILE GLY THR LYS ILE HIS ASP GLY ALA SEQRES 6 B 158 GLN GLY LYS HIS ILE SER GLY HIS ARG ASN TYR ILE GLU SEQRES 7 B 158 GLY LYS SER THR LEU ASN GLN ASN ILE ASN PRO GLN GLU SEQRES 8 B 158 LEU LEU ASN GLY ILE HIS SER GLY ALA TYR PRO VAL ILE SEQRES 9 B 158 SER LYS GLY ALA ARG ARG ASN PRO VAL VAL ASP PHE GLY SEQRES 10 B 158 TYR PRO ILE GLY SER ASP GLY LYS SER GLY LEU SER THR SEQRES 11 B 158 ASN PHE GLY THR ILE HIS SER GLY LYS ASN GLY VAL HIS SEQRES 12 B 158 ILE VAL PRO ALA ASN PRO LYS THR ILE LYS LYS VAL GLN SEQRES 13 B 158 LEU GLU FORMUL 3 HOH *178(H2 O) HELIX 1 AA1 PRO A 6 MET A 17 1 12 HELIX 2 AA2 ILE A 50 GLY A 69 1 20 HELIX 3 AA3 SER A 85 GLN A 91 1 7 HELIX 4 AA4 HIS B 328 GLY B 333 1 6 HELIX 5 AA5 LYS B 334 ILE B 336 5 3 HELIX 6 AA6 ASN B 354 SER B 364 1 11 HELIX 7 AA7 ALA B 374 ARG B 376 5 3 HELIX 8 AA8 ASN B 414 LYS B 420 1 7 SHEET 1 AA1 4 GLU A 74 TYR A 81 0 SHEET 2 AA1 4 PHE A 38 LEU A 45 1 N LEU A 45 O ILE A 80 SHEET 3 AA1 4 ILE A 25 GLU A 33 -1 N GLU A 33 O PHE A 38 SHEET 4 AA1 4 ALA A 95 ARG A 98 -1 O VAL A 96 N ILE A 28 SHEET 1 AA2 3 THR B 348 LEU B 349 0 SHEET 2 AA2 3 GLY B 387 SER B 388 -1 O SER B 388 N THR B 348 SHEET 3 AA2 3 SER B 395 THR B 396 -1 O THR B 396 N GLY B 387 SHEET 1 AA3 4 VAL B 369 LYS B 372 0 SHEET 2 AA3 4 PRO B 378 ASP B 381 -1 O VAL B 379 N ILE B 370 SHEET 3 AA3 4 PHE B 398 GLY B 404 -1 O ILE B 401 N PRO B 378 SHEET 4 AA3 4 GLY B 407 PRO B 412 -1 O GLY B 407 N GLY B 404 CRYST1 78.667 39.792 65.547 90.00 109.16 90.00 C 1 2 1 4 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 0.012712 0.000000 0.004418 0.00000 SCALE2 0.000000 0.025131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016151 0.00000