PDB Short entry for 2I88 HEADER MEMBRANE PROTEIN 01-SEP-06 2I88 TITLE CRYSTAL STRUCTURE OF THE CHANNEL-FORMING DOMAIN OF COLICIN E1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-E1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: DM1187; SOURCE 5 GENE: CEA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSKHY KEYWDS PROTEIN-MEMBRANE INTERACTIONS, TOXIN-MEMBRANE INTERACTIONS, TOXIN KEYWDS 2 STRUCTURE, VOLTAGE-GATED CHANNEL, COLICIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.ELKINS,A.BUNKER,W.A.CRAMER,C.V.STAUFFACHER REVDAT 4 21-FEB-24 2I88 1 REMARK REVDAT 3 24-JAN-18 2I88 1 AUTHOR REMARK REVDAT 2 24-FEB-09 2I88 1 VERSN REVDAT 1 26-SEP-06 2I88 0 JRNL AUTH P.ELKINS,A.BUNKER,W.A.CRAMER,C.V.STAUFFACHER JRNL TITL A MECHANISM FOR TOXIN INSERTION INTO MEMBRANES IS SUGGESTED JRNL TITL 2 BY THE CRYSTAL STRUCTURE OF THE CHANNEL-FORMING DOMAIN OF JRNL TITL 3 COLICIN E1 JRNL REF STRUCTURE V. 5 443 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9083117 JRNL DOI 10.1016/S0969-2126(97)00200-1 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 6684 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 562 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1392 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.89 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I88 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : NULL 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6684 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.12500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES AT PH 6.0 25 MM TRIS-HCL PH REMARK 280 7-8 100 MM NACO OR NANO3 23-27% PEG 3350 VERY SENSITIVE TO REMARK 280 TEMPERATUE STABILIZED BY SLOW ADDITION TO OF PEG 20,000 TO 2-3%, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 43.73000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.73000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.55000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.73000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.55000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 43.73000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.55000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 43.73000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 43.73000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.55000 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 ASN A 332 REMARK 465 LEU A 333 REMARK 465 LYS A 334 REMARK 465 LYS A 335 REMARK 465 ALA A 336 REMARK 465 GLN A 337 REMARK 465 ASN A 338 REMARK 465 ASN A 339 REMARK 465 LEU A 340 REMARK 465 LEU A 341 REMARK 465 ASN A 342 REMARK 465 SER A 343 REMARK 465 GLN A 344 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 ALA A 472 -133.59 47.52 REMARK 500 ASP A 509 -29.44 -8.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 367 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1COL RELATED DB: PDB REMARK 900 REFINED STRUCTURE OF THE PORE-FORMING DOMAIN OF COLICIN A AT 2.4 REMARK 900 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 1A87 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A COLICIN N FRAGMENT SUGGESTS A MODEL FOR REMARK 900 TOXICITY. REMARK 900 RELATED ID: 1CII RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COLICIN IA. REMARK 900 RELATED ID: 1UJW RELATED DB: PDB REMARK 900 THE STRUCTURE OF BTUB WITH BOUND COLICIN E3 R-DOMAIN IMPLIES A REMARK 900 TRANSLOCON DBREF 2I88 A 332 522 UNP P02978 CEA1_ECOLI 332 522 SEQRES 1 A 191 ASN LEU LYS LYS ALA GLN ASN ASN LEU LEU ASN SER GLN SEQRES 2 A 191 ILE LYS ASP ALA VAL ASP ALA THR VAL SER PHE TYR GLN SEQRES 3 A 191 THR LEU THR GLU LYS TYR GLY GLU LYS TYR SER LYS MET SEQRES 4 A 191 ALA GLN GLU LEU ALA ASP LYS SER LYS GLY LYS LYS ILE SEQRES 5 A 191 GLY ASN VAL ASN GLU ALA LEU ALA ALA PHE GLU LYS TYR SEQRES 6 A 191 LYS ASP VAL LEU ASN LYS LYS PHE SER LYS ALA ASP ARG SEQRES 7 A 191 ASP ALA ILE PHE ASN ALA LEU ALA SER VAL LYS TYR ASP SEQRES 8 A 191 ASP TRP ALA LYS HIS LEU ASP GLN PHE ALA LYS TYR LEU SEQRES 9 A 191 LYS ILE THR GLY HIS VAL SER PHE GLY TYR ASP VAL VAL SEQRES 10 A 191 SER ASP ILE LEU LYS ILE LYS ASP THR GLY ASP TRP LYS SEQRES 11 A 191 PRO LEU PHE LEU THR LEU GLU LYS LYS ALA ALA ASP ALA SEQRES 12 A 191 GLY VAL SER TYR VAL VAL ALA LEU LEU PHE SER LEU LEU SEQRES 13 A 191 ALA GLY THR THR LEU GLY ILE TRP GLY ILE ALA ILE VAL SEQRES 14 A 191 THR GLY ILE LEU CYS SER TYR ILE ASP LYS ASN LYS LEU SEQRES 15 A 191 ASN THR ILE ASN GLU VAL LEU GLY ILE FORMUL 2 HOH *22(H2 O) HELIX 1 1 ILE A 345 TYR A 363 1 19 HELIX 2 2 GLY A 364 LYS A 379 1 16 HELIX 3 3 ASN A 385 LYS A 403 1 19 HELIX 4 4 SER A 405 ALA A 417 1 13 HELIX 5 5 SER A 418 LYS A 420 5 3 HELIX 6 6 TYR A 421 LYS A 426 1 6 HELIX 7 7 HIS A 427 LEU A 435 1 9 HELIX 8 8 ASP A 446 GLY A 458 1 13 HELIX 9 9 TRP A 460 ALA A 472 1 13 HELIX 10 10 GLY A 475 GLY A 489 1 15 HELIX 11 11 GLY A 493 ILE A 508 1 16 HELIX 12 12 LYS A 512 ASN A 514 5 3 HELIX 13 13 THR A 515 GLY A 521 1 7 CRYST1 87.460 87.460 59.100 90.00 90.00 90.00 I 4 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 0.011434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016920 0.00000