HEADER IMMUNE SYSTEM 12-JAN-12 4AEQ TITLE CRYSTAL STRUCTURE OF THE DIMERIC IMMUNITY PROTEIN CMI SOLVED BY DIRECT TITLE 2 METHODS (ARCIMBOLDO) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-M IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 44-141; COMPND 5 SYNONYM: CMI, MICROCIN-M IMMUNITY PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CMI CLONED WITHOUT THE N-TERMINAL HYDROPHOBIC HELIX COMPND 8 FOR EXPRESSION OF THE PROTEIN IN THE CYTOPLASM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IMMUNE SYSTEM, 3D DOMAIN SWAP EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH,S.I.PATZER,R.ALBRECHT,I.USON,V.BRAUN REVDAT 5 20-NOV-24 4AEQ 1 REMARK REVDAT 4 01-MAY-24 4AEQ 1 REMARK REVDAT 3 18-APR-12 4AEQ 1 JRNL REVDAT 2 29-FEB-12 4AEQ 1 AUTHOR JRNL HETATM REVDAT 1 25-JAN-12 4AEQ 0 JRNL AUTH I.USON,S.I.PATZER,D.D.DAYANA RODRIGUEZ,V.BRAUN,K.ZETH JRNL TITL THE CRYSTAL STRUCTURE OF THE DIMERIC COLICIN M IMMUNITY JRNL REF J.STRUCT.BIOL. V. 178 45 2012 JRNL REFN ISSN 1047-8477 JRNL PMID 22366279 JRNL DOI 10.1016/J.JSB.2012.02.004 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 8676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 434 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 28.2267 - 2.7276 0.99 2834 150 0.2029 0.2001 REMARK 3 2 2.7276 - 2.1652 1.00 2757 145 0.1971 0.2316 REMARK 3 3 2.1652 - 1.8916 0.97 2651 139 0.2336 0.2995 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.49 REMARK 3 K_SOL : 0.46 REMARK 3 B_SOL : 63.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.45340 REMARK 3 B22 (A**2) : -2.18710 REMARK 3 B33 (A**2) : 0.73370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 818 REMARK 3 ANGLE : 0.878 1055 REMARK 3 CHIRALITY : 0.064 107 REMARK 3 PLANARITY : 0.003 137 REMARK 3 DIHEDRAL : 15.403 301 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 26:60) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6341 55.4062 5.3832 REMARK 3 T TENSOR REMARK 3 T11: 0.0914 T22: 0.1170 REMARK 3 T33: 0.0991 T12: -0.0009 REMARK 3 T13: 0.0068 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.9803 L22: 1.2080 REMARK 3 L33: 1.3521 L12: -0.3709 REMARK 3 L13: 0.2695 L23: -0.2202 REMARK 3 S TENSOR REMARK 3 S11: 0.0410 S12: 0.0263 S13: 0.0292 REMARK 3 S21: -0.1931 S22: -0.0080 S23: -0.1509 REMARK 3 S31: 0.0503 S32: -0.0412 S33: 0.0146 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 61:115) REMARK 3 ORIGIN FOR THE GROUP (A): 45.3890 57.7333 5.9866 REMARK 3 T TENSOR REMARK 3 T11: 0.0269 T22: 0.0771 REMARK 3 T33: 0.0539 T12: -0.0189 REMARK 3 T13: -0.0012 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.5559 L22: 1.4672 REMARK 3 L33: 3.3951 L12: 0.6785 REMARK 3 L13: -0.2560 L23: 0.3257 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: -0.0468 S13: 0.1668 REMARK 3 S21: -0.3239 S22: 0.0709 S23: 0.0664 REMARK 3 S31: -0.0698 S32: 0.2141 S33: 0.0177 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 4AEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290050937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : SLS REMARK 200 BEAMLINE : X10SA 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15884 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: ALPHA HELIX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% PEG 4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 19.14050 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 19.14050 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 33.02900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.77600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.02900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.77600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.14050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.02900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.77600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.14050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.02900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.77600 REMARK 290 SMTRY3 8 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: 5650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.8 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 66.05800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 19.14050 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 A2020 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 VAL A 19 REMARK 465 PHE A 20 REMARK 465 PHE A 21 REMARK 465 TRP A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 ASP A 25 REMARK 465 ASP A 116 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1116 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XGL RELATED DB: PDB REMARK 900 THE X-RAY STRUCTURE OF THE ESCHERICHIA COLI COLICIN M IMMUNITY REMARK 900 PROTEIN DEMONSTRATES THE PRESENCE OF A DISULPHIDE BRIDGE, WHICH IS REMARK 900 FUNCTIONALLY ESSENTIAL DBREF 4AEQ A 19 116 UNP P18002 IMMM_ECOLX 44 141 SEQRES 1 A 98 VAL PHE PHE TRP SER GLU ASP LYS GLY PRO ALA CYS TYR SEQRES 2 A 98 GLN VAL SER ASP GLU GLN ALA ARG THR PHE VAL LYS ASN SEQRES 3 A 98 ASP TYR LEU GLN ARG MET LYS ARG TRP ASP ASN ASP VAL SEQRES 4 A 98 GLN LEU LEU GLY THR GLU ILE PRO LYS ILE THR TRP GLU SEQRES 5 A 98 LYS ILE GLU ARG SER LEU THR ASP VAL GLU ASP GLU LYS SEQRES 6 A 98 THR LEU LEU VAL PRO PHE LYS ALA GLU GLY PRO ASP GLY SEQRES 7 A 98 LYS ARG MET TYR TYR GLY MET TYR HIS CYS GLU GLU GLY SEQRES 8 A 98 TYR VAL GLU TYR ALA ASN ASP HET PO4 A1116 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *54(H2 O) HELIX 1 1 ALA A 29 VAL A 33 5 5 HELIX 2 2 SER A 34 GLY A 61 1 28 HELIX 3 3 ASP A 78 GLU A 82 5 5 SHEET 1 AA 4 LYS A 66 TRP A 69 0 SHEET 2 AA 4 THR A 84 GLU A 92 -1 O LYS A 90 N THR A 68 SHEET 3 AA 4 LYS A 97 HIS A 105 -1 O ARG A 98 N ALA A 91 SHEET 4 AA 4 TYR A 110 ALA A 114 -1 O TYR A 110 N HIS A 105 SSBOND 1 CYS A 30 CYS A 106 1555 3655 2.06 SITE 1 AC1 4 ARG A 49 TRP A 53 GLU A 112 TYR A 113 CRYST1 66.058 83.552 38.281 90.00 90.00 90.00 C 2 2 21 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 0.015138 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026123 0.00000