HEADER BACTERIOCIN 04-NOV-97 1AYI TITLE COLICIN E7 IMMUNITY PROTEIN IM7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN E IMMUNITY PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IM7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: JM109; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS BACTERIOCIN, E COLICINS, PROTEIN-PROTEIN INTERACTIONS, DNASE KEYWDS 2 INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR C.A.DENNIS,R.A.PAUPTIT,R.WALLIS,R.JAMES,G.R.MOORE,C.KLEANTHOUS REVDAT 4 03-APR-24 1AYI 1 REMARK REVDAT 3 07-FEB-24 1AYI 1 REMARK REVDAT 2 24-FEB-09 1AYI 1 VERSN REVDAT 1 28-JAN-98 1AYI 0 JRNL AUTH C.A.DENNIS,H.VIDELER,R.A.PAUPTIT,R.WALLIS,R.JAMES,G.R.MOORE, JRNL AUTH 2 C.KLEANTHOUS JRNL TITL A STRUCTURAL COMPARISON OF THE COLICIN IMMUNITY PROTEINS IM7 JRNL TITL 2 AND IM9 GIVES NEW INSIGHTS INTO THE MOLECULAR DETERMINANTS JRNL TITL 3 OF IMMUNITY-PROTEIN SPECIFICITY. JRNL REF BIOCHEM.J. V.T 1) 183 1998 JRNL REFN ISSN 0264-6021 JRNL PMID 9639578 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 5000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 670 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.60 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.500 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR WAS USED INITIALLY TO REFINE THE REMARK 3 VERY INCOMPLETE STARTING MODEL FROM MOLECULAR REPLACEMENT. THE REMARK 3 REFINEMENT USING SIMULATED ANNEALING AND POSITIONAL REFINEMENT REMARK 3 DID NOT DECREASE THE FREE R VALUE. AT THIS STAGE, REFINEMENT BY REMARK 3 MAXIMUM LIKELIHOOD METHOD WAS STARTED. REMARK 4 REMARK 4 1AYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : MARSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 10 ALIGNED NMR STRUCTURES OF COLICIN E9 IMMUNITY REMARK 200 PROTEIN IM9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: USING THE HANGING DROP METHOD, PROTEIN REMARK 280 (10MG/ML) WAS CRYSTALLISED BY MIXING AN EQUAL VOLUME OF PROTEIN REMARK 280 WITH A SOLUTION CONTAINING 55% SATURATED DI-AMMONIUM PHOSPHATE REMARK 280 AND 200MM TRIS PH7.2. THE DROP WAS EQUILIBRATED AGAINST A WELL REMARK 280 CONTAINING 100% SATURATED DI-AMMONIUM PHOSPHATE AT ROOM REMARK 280 TEMPERATURE., VAPOR DIFFUSION - HANGING DROP, VAPOR DIFFUSION, REMARK 280 HANGING DROP 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 22.31500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.33850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.59350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.33850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.59350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.33850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.59350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.33850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.59350 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 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 87 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 MET A 1 CG SD CE REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 SER A 58 OG REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 LYS A 81 CG CD CE NZ DBREF 1AYI A 1 87 UNP Q03708 IMM7_ECOLI 1 87 SEQRES 1 A 87 MET GLU LEU LYS ASN SER ILE SER ASP TYR THR GLU ALA SEQRES 2 A 87 GLU PHE VAL GLN LEU LEU LYS GLU ILE GLU LYS GLU ASN SEQRES 3 A 87 VAL ALA ALA THR ASP ASP VAL LEU ASP VAL LEU LEU GLU SEQRES 4 A 87 HIS PHE VAL LYS ILE THR GLU HIS PRO ASP GLY THR ASP SEQRES 5 A 87 LEU ILE TYR TYR PRO SER ASP ASN ARG ASP ASP SER PRO SEQRES 6 A 87 GLU GLY ILE VAL LYS GLU ILE LYS GLU TRP ARG ALA ALA SEQRES 7 A 87 ASN GLY LYS PRO GLY PHE LYS GLN GLY FORMUL 2 HOH *34(H2 O) HELIX 1 I GLU A 12 LYS A 24 1 13 HELIX 2 II ASP A 32 THR A 45 1 14 HELIX 3 III THR A 51 TYR A 56 5 6 HELIX 4 IV GLU A 66 ASN A 79 1 14 CRYST1 44.630 50.677 75.187 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 0.022406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013300 0.00000