10 20 30 40 50 60 70 80 1TFO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN/TOXIN INHIBITOR 27-MAY-04 1TFO
TITLE RIBONUCLEASE FROM ESCHERICHIA COLI COMPLEXED WITH ITS TITLE 2 INHIBITOR PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COLICIN D IMMUNITY PROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: IMMD; MICROCIN D IMMUNITY PROTEIN; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: INHIBITOR PROTEIN
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562; SOURCE 11 GENE: CDI; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS PROTEIN-PROTEIN COMPLEX, TOXIN/TOXIN INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.YAJIMA,K.NAKANISHI,K.TAKAHASHI,T.OGAWA,Y.KEZUKA,M.HIDAKA, AUTHOR 2 T.NONAKA,K.OHSAWA,H.MASAKI
REVDAT 2 24-FEB-09 1TFO 1 VERSN REVDAT 1 01-MAR-05 1TFO 0
JRNL AUTH S.YAJIMA,K.NAKANISHI,K.TAKAHASHI,T.OGAWA,M.HIDAKA, JRNL AUTH 2 Y.KEZUKA,T.NONAKA,K.OHSAWA,H.MASAKI JRNL TITL RELATION BETWEEN TRNASE ACTIVITY AND THE STRUCTURE JRNL TITL 2 OF COLICIN D ACCORDING TO X-RAY CRYSTALLOGRAPHY JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 322 966 2004 JRNL REFN ISSN 0006-291X JRNL PMID 15336558 JRNL DOI 10.1016/J.BBRC.2004.07.206
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.40 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11367 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) : 0.258 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 568 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 : 1533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 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 1TFO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB022608.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11367 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, GLYCEROL, DTT, REMARK 280 HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 74.65350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.08550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.08550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.32675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.08550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.08550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 111.98025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.08550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.08550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.32675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.08550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.08550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 111.98025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.65350 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, 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 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 B 2 REMARK 465 HIS B 89 REMARK 465 HIS B 90 REMARK 465 HIS B 91 REMARK 465 HIS B 92
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 ASP A 596 81.05 -63.94 REMARK 500 ASP A 619 108.87 -51.97 REMARK 500 LYS A 653 -89.84 1.20 REMARK 500 LEU A 676 -60.42 -101.05 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TFK RELATED DB: PDB REMARK 900 SAME PROTEIN EXCEPT MISSING 10 RESIDUES AT THE N-TERMINAL
DBREF 1TFO A 595 697 UNP P17998 CEAD_ECOLI 595 697 DBREF 1TFO B 2 87 UNP P11899 IMMD_ECOLI 2 87
SEQADV 1TFO HIS B 88 UNP P11899 EXPRESSION TAG SEQADV 1TFO HIS B 89 UNP P11899 EXPRESSION TAG SEQADV 1TFO HIS B 90 UNP P11899 EXPRESSION TAG SEQADV 1TFO HIS B 91 UNP P11899 EXPRESSION TAG SEQADV 1TFO HIS B 92 UNP P11899 EXPRESSION TAG
SEQRES 1 A 103 LEU ASP SER GLY ARG PHE SER ARG LYS GLN LEU ASP LYS SEQRES 2 A 103 LYS TYR LYS HIS ALA GLY ASP PHE GLY ILE SER ASP THR SEQRES 3 A 103 LYS LYS ASN ARG GLU THR LEU THR LYS PHE ARG ASP ALA SEQRES 4 A 103 ILE GLU GLU HIS LEU SER ASP LYS ASP THR VAL GLU LYS SEQRES 5 A 103 GLY THR TYR ARG ARG GLU LYS GLY SER LYS VAL TYR PHE SEQRES 6 A 103 ASN PRO ASN THR MET ASN VAL VAL ILE ILE LYS SER ASN SEQRES 7 A 103 GLY GLU PHE LEU SER GLY TRP LYS ILE ASN PRO ASP ALA SEQRES 8 A 103 ASP ASN GLY ARG ILE TYR LEU GLU THR GLY GLU LEU SEQRES 1 B 91 ASN LYS MET ALA MET ILE ASP LEU ALA LYS LEU PHE LEU SEQRES 2 B 91 ALA SER LYS ILE THR ALA ILE GLU PHE SER GLU ARG ILE SEQRES 3 B 91 CYS VAL GLU ARG ARG ARG LEU TYR GLY VAL LYS ASP LEU SEQRES 4 B 91 SER PRO ASN ILE LEU ASN CYS GLY GLU GLU LEU PHE MET SEQRES 5 B 91 ALA ALA GLU ARG PHE GLU PRO ASP ALA ASP ARG ALA ASN SEQRES 6 B 91 TYR GLU ILE ASP ASP ASN GLY LEU LYS VAL GLU VAL ARG SEQRES 7 B 91 SER ILE LEU GLU LYS PHE LYS LEU HIS HIS HIS HIS HIS
FORMUL 3 HOH *28(H2 O)
HELIX 1 1 SER A 601 TYR A 609 1 9 HELIX 2 2 LYS A 610 GLY A 616 5 7 HELIX 3 3 ASN A 623 ASP A 640 1 18 HELIX 4 4 ALA A 685 GLY A 695 1 11 HELIX 5 5 MET B 4 ALA B 15 1 12 HELIX 6 6 THR B 19 TYR B 35 1 17 HELIX 7 7 SER B 41 ARG B 57 1 17 HELIX 8 8 ASP B 70 PHE B 85 1 16
SHEET 1 A 4 VAL A 644 GLU A 645 0 SHEET 2 A 4 LYS A 656 ASN A 660 -1 O PHE A 659 N VAL A 644 SHEET 3 A 4 ASN A 665 ILE A 669 -1 O ILE A 669 N LYS A 656 SHEET 4 A 4 PHE A 675 LYS A 680 -1 O SER A 677 N ILE A 668
CRYST1 56.171 56.171 149.307 90.00 90.00 90.00 P 41 21 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 0.017803 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017803 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006698 0.00000