HEADER ANTIMICROBIAL PROTEIN 12-MAR-23 8IOM TITLE CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL CHANNEL-FORMING DOMAIN OF TITLE 2 COLICIN IB COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHANNEL-FORMING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 STRAIN: 3160_NCHU22; SOURCE 5 GENE: CBL31_01480; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE70 KEYWDS PORE-FORMING TOXIN, ANTIBACTERIAL PROTEIN, COLICIN, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.YANG,N.J.HU REVDAT 2 15-NOV-23 8IOM 1 REMARK DBREF SEQADV HELIX REVDAT 2 2 1 ATOM REVDAT 1 05-APR-23 8IOM 0 JRNL AUTH J.YANG JRNL TITL STRUCTURE OF COLICIN IB CHANNEL DOMAIN AT 3.0 ANGSTROMS JRNL TITL 2 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 9151 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 904 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 26.0800 - 5.4400 1.00 1450 157 0.1590 0.1572 REMARK 3 2 5.4300 - 4.3200 1.00 1426 157 0.1709 0.1919 REMARK 3 3 4.3200 - 3.7800 1.00 1438 156 0.1846 0.2121 REMARK 3 4 3.7800 - 3.4300 1.00 1426 155 0.2152 0.2563 REMARK 3 5 3.4300 - 3.1900 0.99 1381 154 0.2591 0.3026 REMARK 3 6 3.1900 - 3.0000 0.79 1126 125 0.2952 0.3316 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) : 0.341 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.30 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 : 0.003 1552 REMARK 3 ANGLE : 0.544 2084 REMARK 3 CHIRALITY : 0.041 235 REMARK 3 PLANARITY : 0.003 266 REMARK 3 DIHEDRAL : 13.334 205 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.1582 -14.7555 -8.5652 REMARK 3 T TENSOR REMARK 3 T11: 0.2333 T22: 0.2940 REMARK 3 T33: 0.2815 T12: 0.0087 REMARK 3 T13: -0.0076 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.0492 L22: 0.8688 REMARK 3 L33: 2.3345 L12: -0.3478 REMARK 3 L13: -0.3961 L23: 0.4046 REMARK 3 S TENSOR REMARK 3 S11: -0.0098 S12: 0.0195 S13: 0.0336 REMARK 3 S21: 0.0632 S22: -0.0277 S23: -0.0472 REMARK 3 S31: -0.0669 S32: -0.1105 S33: 0.0001 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 8IOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300036153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5.2-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11040 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.940 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55600 REMARK 200 R SYM FOR SHELL (I) : 0.39900 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR PRISM SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT: 0.1M SODIUM CHLORIDE, REMARK 280 0.1M SODIUM HEPES PH7.5, 12% W/V PEG 4000, 0.5 MICROLITER 8MG/ML REMARK 280 COLICIN IB C DOMAIN MIX WITH THE SAME VOLUME PRECIPITANT IN THE REMARK 280 DROP COLICIN IB C DOMAIN BUFFER:20MM SODIUM, CITRATE PH5.2, REMARK 280 200MM NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.5K 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 45.99700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 45.99700 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.94800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.99700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.47400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.99700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 85.42200 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 45.99700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.99700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.94800 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 45.99700 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.42200 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 45.99700 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.47400 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 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 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 432 REMARK 465 GLY A 627 REMARK 465 SER A 628 REMARK 465 ARG A 629 REMARK 465 SER A 630 REMARK 465 HIS A 631 REMARK 465 HIS A 632 REMARK 465 HIS A 633 REMARK 465 HIS A 634 REMARK 465 HIS A 635 REMARK 465 HIS A 636 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 509 -159.74 -102.24 REMARK 500 ARG A 548 56.78 -110.64 REMARK 500 ASN A 613 117.44 -163.90 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8IOM A 433 626 UNP A0A200P0K8_SHIFL DBREF2 8IOM A A0A200P0K8 433 626 SEQADV 8IOM MET A 432 UNP A0A200P0K INITIATING METHIONINE SEQADV 8IOM GLY A 627 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM SER A 628 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM ARG A 629 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM SER A 630 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 631 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 632 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 633 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 634 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 635 UNP A0A200P0K EXPRESSION TAG SEQADV 8IOM HIS A 636 UNP A0A200P0K EXPRESSION TAG SEQRES 1 A 205 MET ASN GLN LYS ILE ALA GLU GLU LYS ARG LYS ARG ASP SEQRES 2 A 205 GLU ILE ASN MET VAL LYS ASP ALA ILE LYS LEU THR SER SEQRES 3 A 205 ASP PHE TYR ARG THR ILE TYR ASP GLU PHE GLY LYS GLN SEQRES 4 A 205 ALA SER GLU LEU ALA LYS GLU LEU ALA SER VAL SER GLN SEQRES 5 A 205 GLY LYS GLN ILE LYS SER VAL ASP ASP ALA LEU ASN ALA SEQRES 6 A 205 PHE ASP LYS PHE ARG ASN ASN LEU ASN LYS LYS TYR ASN SEQRES 7 A 205 ILE GLN ASP ARG MET ALA ILE SER LYS ALA LEU GLU ALA SEQRES 8 A 205 ILE ASN GLN VAL HIS MET ALA GLU ASN PHE LYS LEU PHE SEQRES 9 A 205 SER LYS ALA PHE GLY PHE THR GLY LYS VAL ILE ASP ARG SEQRES 10 A 205 TYR ASP VAL ALA VAL GLU LEU GLN LYS ALA VAL LYS THR SEQRES 11 A 205 ASP ASN TRP ARG PRO PHE PHE VAL LYS LEU GLU SER LEU SEQRES 12 A 205 ALA ALA GLY ARG ALA ALA SER ALA VAL THR ALA TRP ALA SEQRES 13 A 205 PHE SER VAL MET LEU GLY THR PRO VAL GLY ILE LEU GLY SEQRES 14 A 205 PHE ALA ILE ILE MET ALA ALA VAL SER ALA LEU VAL ASN SEQRES 15 A 205 ASP LYS PHE ILE GLU GLN VAL ASN LYS LEU ILE GLY ILE SEQRES 16 A 205 GLY SER ARG SER HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASN A 433 GLY A 468 1 36 HELIX 2 AA2 GLY A 468 GLN A 483 1 16 HELIX 3 AA3 SER A 489 ASN A 505 1 17 HELIX 4 AA4 ASN A 509 GLU A 521 1 13 HELIX 5 AA5 ASN A 524 PHE A 539 1 16 HELIX 6 AA6 ARG A 548 ASP A 562 1 15 HELIX 7 AA7 TRP A 564 ALA A 575 1 12 HELIX 8 AA8 ALA A 579 THR A 594 1 16 HELIX 9 AA9 VAL A 596 ASN A 613 1 18 HELIX 10 AB1 ASP A 614 ILE A 624 1 11 CRYST1 91.994 91.994 113.896 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 0.010870 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008780 0.00000