PDB Short entry for 2DJH HEADER HYDROLASE 03-APR-06 2DJH TITLE CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL RIBONUCLEASE TITLE 2 DOMAIN OF COLICIN E5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-E5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL RIBONUCLEASE DOMAIN, RESIDUES 2-116; COMPND 5 SYNONYM: FRAGMENT; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: RR1; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBR328 KEYWDS ALPHA/BETA PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAJIMA,S.INOUE,T.OGAWA,T.NONAKA,K.OHSAWA,H.MASAKI REVDAT 2 24-FEB-09 2DJH 1 VERSN REVDAT 1 23-JAN-07 2DJH 0 JRNL AUTH S.YAJIMA,S.INOUE,T.OGAWA,T.NONAKA,K.OHSAWA,H.MASAKI JRNL TITL STRUCTURAL BASIS FOR SEQUENCE-DEPENDENT JRNL TITL 2 RECOGNITION OF COLICIN E5 TRNASE BY MIMICKING THE JRNL TITL 3 MRNA-TRNA INTERACTION JRNL REF NUCLEIC ACIDS RES. V. 34 6074 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 17099236 JRNL DOI 10.1093/NAR/GKL729 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.46 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) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7399 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) : 0.198 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 395 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1723 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 115 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 749 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 105 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.85 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 2DJH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-06. REMARK 100 THE RCSB ID CODE IS RCSB025486. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 38.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04600 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2DFX; CHAIN_ID E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 20MM TRISCL, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.29000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.29000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.36000 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: 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 ALA A 2 REMARK 465 GLU A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 ASN A 7 REMARK 465 ASP A 8 REMARK 465 GLU A 9 REMARK 465 LEU A 10 REMARK 465 ALA A 11 REMARK 465 LYS A 12 REMARK 465 ASN A 13 REMARK 465 LYS A 14 REMARK 465 GLY A 15 REMARK 465 ASN A 112 REMARK 465 LYS A 113 REMARK 465 ASN A 114 REMARK 465 ASP A 115 REMARK 465 GLN A 116 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 52 -165.96 -165.73 REMARK 500 ASN A 69 57.44 -151.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 3PD A 117 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PD A 117 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UM3 A 118 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DFX RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH THE INHIBITOR PROTEIN DBREF 2DJH A 2 116 UNP P18000 CEA5_ECOLI 66 180 SEQRES 1 A 115 ALA GLU GLY LYS LEU ASN ASP GLU LEU ALA LYS ASN LYS SEQRES 2 A 115 GLY LYS ILE PRO GLY LEU LYS ILE ASP GLN LYS ILE ARG SEQRES 3 A 115 GLY GLN MET PRO GLU ARG GLY TRP THR GLU ASP ASP ILE SEQRES 4 A 115 LYS ASN THR VAL SER ASN GLY ALA THR GLY THR SER PHE SEQRES 5 A 115 ASP LYS ARG SER PRO LYS LYS THR PRO PRO ASP TYR LEU SEQRES 6 A 115 GLY ARG ASN ASP PRO ALA THR VAL TYR GLY SER PRO GLY SEQRES 7 A 115 LYS TYR VAL VAL VAL ASN ASP ARG THR GLY GLU VAL THR SEQRES 8 A 115 GLN ILE SER ASP LYS THR ASP PRO GLY TRP VAL ASP ASP SEQRES 9 A 115 SER ARG ILE GLN TRP GLY ASN LYS ASN ASP GLN HET 3PD A 117 22 HET UM3 A 118 20 HETNAM 3PD 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9- HETNAM 2 3PD DIHYDRO-6H-PURIN-6-ONE HETNAM UM3 2'-DEOXYURIDINE 3'-MONOPHOSPHATE HETSYN 3PD 2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE FORMUL 2 3PD C10 H14 N5 O7 P FORMUL 2 UM3 C9 H13 N2 O8 P FORMUL 3 HOH *105(H2 O) HELIX 1 1 ASP A 23 MET A 30 1 8 HELIX 2 2 THR A 36 ASN A 46 1 11 HELIX 3 3 SER A 57 THR A 61 5 5 SHEET 1 A 5 VAL A 91 ILE A 94 0 SHEET 2 A 5 LYS A 80 ASN A 85 -1 N VAL A 83 O GLN A 93 SHEET 3 A 5 ASP A 70 SER A 77 -1 N THR A 73 O VAL A 84 SHEET 4 A 5 GLY A 50 ASP A 54 -1 N ASP A 54 O ASP A 70 SHEET 5 A 5 GLN A 109 TRP A 110 -1 O GLN A 109 N THR A 51 LINK P 3PD A 117 O5' UM3 A 118 1555 1555 1.60 CISPEP 1 PRO A 62 PRO A 63 0 0.13 SITE 1 AC1 14 LYS A 25 GLN A 29 ARG A 33 PHE A 53 SITE 2 AC1 14 LYS A 55 GLN A 93 TRP A 102 VAL A 103 SITE 3 AC1 14 SER A 106 ARG A 107 GLN A 109 UM3 A 118 SITE 4 AC1 14 HOH A 122 HOH A 167 SITE 1 AC2 16 SER A 52 PHE A 53 ASP A 54 LYS A 55 SITE 2 AC2 16 ARG A 56 SER A 57 LYS A 60 VAL A 83 SITE 3 AC2 16 THR A 92 GLN A 93 ASP A 105 ARG A 107 SITE 4 AC2 16 GLN A 109 3PD A 117 HOH A 165 HOH A 177 CRYST1 29.190 48.720 62.580 90.00 90.00 90.00 P 21 21 21 4 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 0.034258 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015980 0.00000