HEADER IMMUNE SYSTEM 29-MAR-99 3EIP TITLE CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN INHIBITOR TO A TITLE 2 RIBOSOME-INACTIVATING RNASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (COLICIN E3 IMMUNITY PROTEIN); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ZINC BOUND BETWEEN CYS 47 OF A AND B CHAINS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI STR. K12 SUBSTR.; SOURCE 3 ORGANISM_TAXID: 316407; SOURCE 4 STRAIN: W3110; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI STR. K12 SUBSTR. W3110; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 316407; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: W3110; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: COLE3; SOURCE 9 OTHER_DETAILS: OVEREXPRESSION BY ADDTION OF MITOMYCIN C DURING LOG SOURCE 10 PHASE OF GROWTH KEYWDS RIBONUCLEASE INHIBITOR, COLICIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.LI,D.ZHAO,A.DJEBLI,M.SHOHAM REVDAT 8 27-DEC-23 3EIP 1 REMARK LINK REVDAT 7 13-JUL-11 3EIP 1 VERSN REVDAT 6 24-FEB-09 3EIP 1 VERSN REVDAT 5 01-APR-03 3EIP 1 JRNL REVDAT 4 30-JUN-00 3EIP 3 SOURCE DBREF ATOM REVDAT 3 08-DEC-99 3EIP 3 ATOM REVDAT 2 17-NOV-99 3EIP 1 REMARK REVDAT 1 10-NOV-99 3EIP 0 JRNL AUTH C.LI,D.ZHAO,A.DJEBLI,M.SHOHAM JRNL TITL CRYSTAL STRUCTURE OF COLICIN E3 IMMUNITY PROTEIN: AN JRNL TITL 2 INHIBITOR OF A RIBOSOME-INACTIVATING RNASE. JRNL REF STRUCTURE FOLD.DES. V. 7 1365 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10574790 JRNL DOI 10.1016/S0969-2126(00)80026-X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4A 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 11860 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 SET) : 0.218 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1175 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.78 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 959 REMARK 3 BIN R VALUE (WORKING SET) : 0.2798 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 125 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 : 1386 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.89000 REMARK 3 B22 (A**2) : 2.52500 REMARK 3 B33 (A**2) : -1.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.50000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.580 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 : DENSITY MODIFICATION REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 36.53 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3EIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-93 REMARK 200 TEMPERATURE (KELVIN) : 295.00 REMARK 200 PH : 6.00 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 2.030 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 0.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.56 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M MES REMARK 280 BUFFER, PH 6.0, PH 6.00 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 40.03500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.03500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.86000 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: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 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 SER A 12 -73.97 -77.77 REMARK 500 PHE A 39 -74.06 -63.43 REMARK 500 ASP A 83 104.97 61.53 REMARK 500 SER B 12 -61.12 -98.28 REMARK 500 GLU B 14 12.44 83.29 REMARK 500 PHE B 39 -85.70 -46.76 REMARK 500 ASN B 45 -155.82 -118.90 REMARK 500 ASP B 83 -1.79 64.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 285 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 CYS B 47 SG 172.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 285 DBREF 3EIP A 1 84 UNP P02984 IMM3_ECOLI 2 85 DBREF 3EIP B 1 84 UNP P02984 IMM3_ECOLI 2 85 SEQRES 1 A 84 GLY LEU LYS LEU ASP LEU THR TRP PHE ASP LYS SER THR SEQRES 2 A 84 GLU ASP PHE LYS GLY GLU GLU TYR SER LYS ASP PHE GLY SEQRES 3 A 84 ASP ASP GLY SER VAL MET GLU SER LEU GLY VAL PRO PHE SEQRES 4 A 84 LYS ASP ASN VAL ASN ASN GLY CYS PHE ASP VAL ILE ALA SEQRES 5 A 84 GLU TRP VAL PRO LEU LEU GLN PRO TYR PHE ASN HIS GLN SEQRES 6 A 84 ILE ASP ILE SER ASP ASN GLU TYR PHE VAL SER PHE ASP SEQRES 7 A 84 TYR ARG ASP GLY ASP TRP SEQRES 1 B 84 GLY LEU LYS LEU ASP LEU THR TRP PHE ASP LYS SER THR SEQRES 2 B 84 GLU ASP PHE LYS GLY GLU GLU TYR SER LYS ASP PHE GLY SEQRES 3 B 84 ASP ASP GLY SER VAL MET GLU SER LEU GLY VAL PRO PHE SEQRES 4 B 84 LYS ASP ASN VAL ASN ASN GLY CYS PHE ASP VAL ILE ALA SEQRES 5 B 84 GLU TRP VAL PRO LEU LEU GLN PRO TYR PHE ASN HIS GLN SEQRES 6 B 84 ILE ASP ILE SER ASP ASN GLU TYR PHE VAL SER PHE ASP SEQRES 7 B 84 TYR ARG ASP GLY ASP TRP HET ZN A 285 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *118(H2 O) HELIX 1 1 SER A 30 LEU A 35 1 6 HELIX 2 2 PHE A 39 ASN A 42 1 4 HELIX 3 3 ALA A 52 TYR A 61 1 10 HELIX 4 4 SER B 30 LEU B 35 1 6 HELIX 5 5 LYS B 40 ASN B 42 5 3 HELIX 6 6 ALA B 52 TYR B 61 1 10 SHEET 1 A 4 CYS A 47 ASP A 49 0 SHEET 2 A 4 ASN A 71 TYR A 79 -1 N VAL A 75 O PHE A 48 SHEET 3 A 4 LEU A 2 ASP A 10 -1 N PHE A 9 O GLU A 72 SHEET 4 A 4 PHE A 16 TYR A 21 -1 N GLU A 20 O LEU A 6 SHEET 1 B 4 CYS B 47 ASP B 49 0 SHEET 2 B 4 ASN B 71 TYR B 79 -1 N VAL B 75 O PHE B 48 SHEET 3 B 4 LEU B 2 ASP B 10 -1 N PHE B 9 O GLU B 72 SHEET 4 B 4 PHE B 16 TYR B 21 -1 N GLU B 20 O LEU B 6 LINK SG CYS A 47 ZN ZN A 285 1555 1555 2.59 LINK ZN ZN A 285 SG CYS B 47 1555 1555 2.71 SITE 1 AC1 4 GLY A 46 CYS A 47 HOH A 311 CYS B 47 CRYST1 80.070 53.720 36.250 90.00 93.18 90.00 C 1 2 1 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 0.012489 0.000000 0.000694 0.00000 SCALE2 0.000000 0.018615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027629 0.00000 MTRIX1 1 -0.987580 -0.050270 0.148840 34.51748 1 MTRIX2 1 -0.154730 0.147270 -0.976920 49.62875 1 MTRIX3 1 0.027190 -0.987820 -0.153220 54.27967 1