HEADER DNA/DNA-BINDING PROTEIN 25-JAN-06 2CDM TITLE THE STRUCTURE OF TRWC COMPLEXED WITH A 27-MER DNA COMPRISING THE TITLE 2 RECOGNITION HAIRPIN AND THE CLEAVAGE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRWC; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-293; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: SELENO METHIONINE DERIVATIVE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*GP*CP*GP*CP*AP*CP*CP*GP*AP*AP COMPND 10 *AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*GP*TP*CP*TP*AP*T)-3'; COMPND 11 CHAIN: B, D; COMPND 12 SYNONYM: ORIT; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSU1621; SOURCE 9 OTHER_DETAILS: FROM THE PLASMID R388; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 562; SOURCE 14 OTHER_DETAILS: FROM THE PLASMID R388 KEYWDS DNA/DNA-BINDING PROTEIN, RELAXASE, BACTERIAL CONJUGATION, DNA KEYWDS 2 TRANSFER, DNA-PROTEIN COMPLEX, DNA-DNA-BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.BOER,S.RUSSI,A.GUASCH,M.LUCAS,A.G.BLANCO,R.PEREZ-LUQUE,M.COLL,F.DE AUTHOR 2 LA CRUZ REVDAT 7 06-NOV-24 2CDM 1 REMARK REVDAT 6 13-DEC-23 2CDM 1 LINK REVDAT 5 24-JAN-18 2CDM 1 SOURCE REVDAT 4 24-FEB-09 2CDM 1 VERSN REVDAT 3 26-JUN-07 2CDM 1 REMARK REVDAT 2 23-JAN-07 2CDM 1 REMARK ATOM MASTER REVDAT 1 31-JUL-06 2CDM 0 JRNL AUTH R.BOER,S.RUSSI,A.GUASCH,M.LUCAS,A.G.BLANCO,R.PEREZ-LUQUE, JRNL AUTH 2 M.COLL,F.DE LA CRUZ JRNL TITL UNVEILING THE MOLECULAR MECHANISM OF A CONJUGATIVE RELAXASE: JRNL TITL 2 THE STRUCTURE OF TRWC COMPLEXED WITH A 27-MER DNA COMPRISING JRNL TITL 3 THE RECOGNITION HAIRPIN AND THE CLEAVAGE SITE. JRNL REF J.MOL.BIOL. V. 358 857 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16540117 JRNL DOI 10.1016/J.JMB.2006.02.018 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.GUASCH,M.LUCAS,G.MONCALIAN,M.CABEZAS,R.PEREZ-LUQUE, REMARK 1 AUTH 2 F.X.GOMIS-RUTH,F.DE LA CRUZ,M.COLL REMARK 1 TITL RECOGNITION AND PROCESSING OF THE ORIGIN OF TRANSFER DNA BY REMARK 1 TITL 2 CONJUGATIVE RELAXASE TRWC REMARK 1 REF NAT.STRUCT.BIOL. V. 10 1002 2003 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 14625590 REMARK 1 DOI 10.1038/NSB1017 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26050 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1377 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4426 REMARK 3 NUCLEIC ACID ATOMS : 971 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.41000 REMARK 3 B12 (A**2) : 0.14000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.720 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.316 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.490 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5582 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7709 ; 1.365 ; 2.177 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 556 ; 5.884 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;35.489 ;23.246 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 842 ;17.945 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;19.990 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 840 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3877 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2270 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3634 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 271 ; 0.153 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 105 ; 0.279 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.138 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2838 ; 0.728 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4378 ; 1.335 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3391 ; 1.421 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3331 ; 2.620 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2CDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1290027443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979269 REMARK 200 MONOCHROMATOR : DIAMOND CRYSTAL (111) REMARK 200 OPTICS : CRYSTALS AND MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27451 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1OSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32 % PEG MME 2000, 0.3 M AMMONIUM REMARK 280 SULPHATE, 0.1 M SODIUM ACETATE PH 4.6, PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.00333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.50167 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 39.75250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.25083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.25417 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 18 TO PHE REMARK 400 ENGINEERED RESIDUE IN CHAIN C, TYR 18 TO PHE 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 GLU A 20 REMARK 465 ASP A 21 REMARK 465 GLY A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 ASP A 25 REMARK 465 TYR A 26 REMARK 465 TYR A 27 REMARK 465 ALA A 28 REMARK 465 LYS A 29 REMARK 465 ASP A 30 REMARK 465 GLY A 31 REMARK 465 ASP A 32 REMARK 465 DG B 1 REMARK 465 DT B 27 REMARK 465 GLU C 20 REMARK 465 ASP C 21 REMARK 465 GLY C 22 REMARK 465 ALA C 23 REMARK 465 ASP C 24 REMARK 465 ASP C 25 REMARK 465 TYR C 26 REMARK 465 TYR C 27 REMARK 465 ALA C 28 REMARK 465 LYS C 29 REMARK 465 ASP C 30 REMARK 465 GLY C 31 REMARK 465 ASP C 32 REMARK 465 DG D 1 REMARK 465 DA D 26 REMARK 465 DT D 27 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 DC B 2 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DC B 2 C3' C2' C1' N1 C2 O2 N3 REMARK 470 DC B 2 C4 N4 C5 C6 REMARK 470 DC D 2 P OP1 OP2 O5' C5' C4' O4' REMARK 470 DC D 2 C3' C2' C1' N1 C2 O2 N3 REMARK 470 DC D 2 C4 N4 C5 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 DT D 25 O HOH D 2006 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC B 2 O3' DG B 3 P -0.115 REMARK 500 DC D 2 O3' DG D 3 P -0.125 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 21 O3' - P - O5' ANGL. DEV. = -17.4 DEGREES REMARK 500 DT B 21 O3' - P - OP2 ANGL. DEV. = -19.6 DEGREES REMARK 500 DT B 21 O3' - P - OP1 ANGL. DEV. = -17.1 DEGREES REMARK 500 DT B 21 OP1 - P - OP2 ANGL. DEV. = 14.3 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC D 6 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC D 7 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG D 12 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG D 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 18 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA D 19 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 21 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT D 23 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT D 25 C4 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 65 66.05 30.01 REMARK 500 LYS A 215 88.19 13.44 REMARK 500 ASP A 216 -15.36 147.17 REMARK 500 SER A 271 89.46 -24.23 REMARK 500 PHE A 292 23.93 -78.59 REMARK 500 GLU C 65 46.72 37.21 REMARK 500 GLN C 159 85.34 -158.67 REMARK 500 LYS C 215 92.09 53.74 REMARK 500 ASP C 216 26.58 -165.68 REMARK 500 LEU C 248 176.55 -59.78 REMARK 500 SER C 271 -179.58 -66.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS C 215 ASP C 216 134.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C1294 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OMH RELATED DB: PDB REMARK 900 CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-FREE REMARK 900 STRUCTURE. REMARK 900 RELATED ID: 1OSB RELATED DB: PDB REMARK 900 CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-FREE REMARK 900 STRUCTURE. REMARK 900 RELATED ID: 1QX0 RELATED DB: PDB REMARK 900 CONJUGATIVE RELAXASE TRWC IN COMPLEX WITH ORIT DNA. METAL-BOUND REMARK 900 STRUCTURE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-293 REMARK 999 T27 DISORDERED AND NOT MODELLED DBREF 2CDM A 1 293 UNP Q47673 Q47673_ECOLI 1 293 DBREF 2CDM B 1 27 PDB 2CDM 2CDM 1 27 DBREF 2CDM C 1 293 UNP Q47673 Q47673_ECOLI 1 293 DBREF 2CDM D 1 27 PDB 2CDM 2CDM 1 27 SEQADV 2CDM PHE A 18 UNP Q47673 TYR 18 ENGINEERED MUTATION SEQADV 2CDM PHE C 18 UNP Q47673 TYR 18 ENGINEERED MUTATION SEQRES 1 A 293 MSE LEU SER HIS MSE VAL LEU THR ARG GLN ASP ILE GLY SEQRES 2 A 293 ARG ALA ALA SER PHE TYR GLU ASP GLY ALA ASP ASP TYR SEQRES 3 A 293 TYR ALA LYS ASP GLY ASP ALA SER GLU TRP GLN GLY LYS SEQRES 4 A 293 GLY ALA GLU GLU LEU GLY LEU SER GLY GLU VAL ASP SER SEQRES 5 A 293 LYS ARG PHE ARG GLU LEU LEU ALA GLY ASN ILE GLY GLU SEQRES 6 A 293 GLY HIS ARG ILE MSE ARG SER ALA THR ARG GLN ASP SER SEQRES 7 A 293 LYS GLU ARG ILE GLY LEU ASP LEU THR PHE SER ALA PRO SEQRES 8 A 293 LYS SER VAL SER LEU GLN ALA LEU VAL ALA GLY ASP ALA SEQRES 9 A 293 GLU ILE ILE LYS ALA HIS ASP ARG ALA VAL ALA ARG THR SEQRES 10 A 293 LEU GLU GLN ALA GLU ALA ARG ALA GLN ALA ARG GLN LYS SEQRES 11 A 293 ILE GLN GLY LYS THR ARG ILE GLU THR THR GLY ASN LEU SEQRES 12 A 293 VAL ILE GLY LYS PHE ARG HIS GLU THR SER ARG GLU ARG SEQRES 13 A 293 ASP PRO GLN LEU HIS THR HIS ALA VAL ILE LEU ASN MSE SEQRES 14 A 293 THR LYS ARG SER ASP GLY GLN TRP ARG ALA LEU LYS ASN SEQRES 15 A 293 ASP GLU ILE VAL LYS ALA THR ARG TYR LEU GLY ALA VAL SEQRES 16 A 293 TYR ASN ALA GLU LEU ALA HIS GLU LEU GLN LYS LEU GLY SEQRES 17 A 293 TYR GLN LEU ARG TYR GLY LYS ASP GLY ASN PHE ASP LEU SEQRES 18 A 293 ALA HIS ILE ASP ARG GLN GLN ILE GLU GLY PHE SER LYS SEQRES 19 A 293 ARG THR GLU GLN ILE ALA GLU TRP TYR ALA ALA ARG GLY SEQRES 20 A 293 LEU ASP PRO ASN SER VAL SER LEU GLU GLN LYS GLN ALA SEQRES 21 A 293 ALA LYS VAL LEU SER ARG ALA LYS LYS THR SER VAL ASP SEQRES 22 A 293 ARG GLU ALA LEU ARG ALA GLU TRP GLN ALA THR ALA LYS SEQRES 23 A 293 GLU LEU GLY ILE ASP PHE SER SEQRES 1 B 27 DG DC DG DC DA DC DC DG DA DA DA DG DG SEQRES 2 B 27 DT DG DC DG DT DA DT DT DG DT DC DT DA SEQRES 3 B 27 DT SEQRES 1 C 293 MSE LEU SER HIS MSE VAL LEU THR ARG GLN ASP ILE GLY SEQRES 2 C 293 ARG ALA ALA SER PHE TYR GLU ASP GLY ALA ASP ASP TYR SEQRES 3 C 293 TYR ALA LYS ASP GLY ASP ALA SER GLU TRP GLN GLY LYS SEQRES 4 C 293 GLY ALA GLU GLU LEU GLY LEU SER GLY GLU VAL ASP SER SEQRES 5 C 293 LYS ARG PHE ARG GLU LEU LEU ALA GLY ASN ILE GLY GLU SEQRES 6 C 293 GLY HIS ARG ILE MSE ARG SER ALA THR ARG GLN ASP SER SEQRES 7 C 293 LYS GLU ARG ILE GLY LEU ASP LEU THR PHE SER ALA PRO SEQRES 8 C 293 LYS SER VAL SER LEU GLN ALA LEU VAL ALA GLY ASP ALA SEQRES 9 C 293 GLU ILE ILE LYS ALA HIS ASP ARG ALA VAL ALA ARG THR SEQRES 10 C 293 LEU GLU GLN ALA GLU ALA ARG ALA GLN ALA ARG GLN LYS SEQRES 11 C 293 ILE GLN GLY LYS THR ARG ILE GLU THR THR GLY ASN LEU SEQRES 12 C 293 VAL ILE GLY LYS PHE ARG HIS GLU THR SER ARG GLU ARG SEQRES 13 C 293 ASP PRO GLN LEU HIS THR HIS ALA VAL ILE LEU ASN MSE SEQRES 14 C 293 THR LYS ARG SER ASP GLY GLN TRP ARG ALA LEU LYS ASN SEQRES 15 C 293 ASP GLU ILE VAL LYS ALA THR ARG TYR LEU GLY ALA VAL SEQRES 16 C 293 TYR ASN ALA GLU LEU ALA HIS GLU LEU GLN LYS LEU GLY SEQRES 17 C 293 TYR GLN LEU ARG TYR GLY LYS ASP GLY ASN PHE ASP LEU SEQRES 18 C 293 ALA HIS ILE ASP ARG GLN GLN ILE GLU GLY PHE SER LYS SEQRES 19 C 293 ARG THR GLU GLN ILE ALA GLU TRP TYR ALA ALA ARG GLY SEQRES 20 C 293 LEU ASP PRO ASN SER VAL SER LEU GLU GLN LYS GLN ALA SEQRES 21 C 293 ALA LYS VAL LEU SER ARG ALA LYS LYS THR SER VAL ASP SEQRES 22 C 293 ARG GLU ALA LEU ARG ALA GLU TRP GLN ALA THR ALA LYS SEQRES 23 C 293 GLU LEU GLY ILE ASP PHE SER SEQRES 1 D 27 DG DC DG DC DA DC DC DG DA DA DA DG DG SEQRES 2 D 27 DT DG DC DG DT DA DT DT DG DT DC DT DA SEQRES 3 D 27 DT MODRES 2CDM MSE A 1 MET SELENOMETHIONINE MODRES 2CDM MSE A 5 MET SELENOMETHIONINE MODRES 2CDM MSE A 70 MET SELENOMETHIONINE MODRES 2CDM MSE A 169 MET SELENOMETHIONINE MODRES 2CDM MSE C 1 MET SELENOMETHIONINE MODRES 2CDM MSE C 5 MET SELENOMETHIONINE MODRES 2CDM MSE C 70 MET SELENOMETHIONINE MODRES 2CDM MSE C 169 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 5 8 HET MSE A 70 8 HET MSE A 169 8 HET MSE C 1 8 HET MSE C 5 8 HET MSE C 70 8 HET MSE C 169 8 HET SO4 A1294 5 HET SO4 C1294 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *237(H2 O) HELIX 1 1 GLN A 10 ILE A 12 5 3 HELIX 2 2 GLY A 38 LEU A 44 1 7 HELIX 3 3 ASP A 51 ALA A 60 1 10 HELIX 4 4 PRO A 91 VAL A 100 1 10 HELIX 5 5 ASP A 103 ARG A 124 1 22 HELIX 6 6 ASN A 182 LYS A 187 1 6 HELIX 7 7 ALA A 188 LEU A 207 1 20 HELIX 8 8 ASP A 225 GLY A 231 1 7 HELIX 9 9 SER A 233 ARG A 246 1 14 HELIX 10 10 SER A 254 SER A 265 1 12 HELIX 11 11 ASP A 273 GLY A 289 1 17 HELIX 12 12 GLN C 10 ILE C 12 5 3 HELIX 13 13 GLY C 38 GLU C 43 1 6 HELIX 14 14 ASP C 51 GLY C 61 1 11 HELIX 15 15 PRO C 91 VAL C 100 1 10 HELIX 16 16 ASP C 103 ARG C 124 1 22 HELIX 17 17 ASN C 182 LYS C 187 1 6 HELIX 18 18 ALA C 188 LEU C 207 1 20 HELIX 19 19 ASP C 225 GLY C 231 1 7 HELIX 20 20 SER C 233 ARG C 246 1 14 HELIX 21 21 SER C 254 GLN C 259 1 6 HELIX 22 22 GLN C 259 LEU C 264 1 6 HELIX 23 23 ASP C 273 LEU C 288 1 16 SHEET 1 AA 5 LEU A 2 THR A 8 0 SHEET 2 AA 5 ARG A 81 SER A 89 -1 N ILE A 82 O LEU A 7 SHEET 3 AA 5 PRO A 158 LEU A 167 -1 O THR A 162 N PHE A 88 SHEET 4 AA 5 ILE A 145 THR A 152 -1 O GLY A 146 N VAL A 165 SHEET 5 AA 5 SER A 34 GLN A 37 -1 O GLU A 35 N LYS A 147 SHEET 1 AB 2 GLN A 126 ILE A 131 0 SHEET 2 AB 2 LYS A 134 THR A 139 -1 O LYS A 134 N ILE A 131 SHEET 1 AC 2 THR A 170 LYS A 171 0 SHEET 2 AC 2 TRP A 177 ARG A 178 -1 O ARG A 178 N THR A 170 SHEET 1 AD 2 LEU A 211 GLY A 214 0 SHEET 2 AD 2 ASN A 218 LEU A 221 -1 O ASN A 218 N GLY A 214 SHEET 1 CA 5 LEU C 2 THR C 8 0 SHEET 2 CA 5 ARG C 81 SER C 89 -1 N ILE C 82 O LEU C 7 SHEET 3 CA 5 PRO C 158 LEU C 167 -1 O THR C 162 N PHE C 88 SHEET 4 CA 5 ILE C 145 THR C 152 -1 O GLY C 146 N VAL C 165 SHEET 5 CA 5 SER C 34 GLN C 37 -1 O GLU C 35 N LYS C 147 SHEET 1 CB 2 GLN C 126 ILE C 131 0 SHEET 2 CB 2 LYS C 134 THR C 139 -1 O LYS C 134 N ILE C 131 SHEET 1 CC 2 THR C 170 LYS C 171 0 SHEET 2 CC 2 TRP C 177 ARG C 178 -1 O ARG C 178 N THR C 170 SHEET 1 CD 2 LEU C 211 TYR C 213 0 SHEET 2 CD 2 PHE C 219 LEU C 221 -1 O ASP C 220 N ARG C 212 LINK C MSE A 1 N LEU A 2 1555 1555 1.33 LINK C HIS A 4 N MSE A 5 1555 1555 1.32 LINK C MSE A 5 N VAL A 6 1555 1555 1.33 LINK C ILE A 69 N MSE A 70 1555 1555 1.33 LINK C MSE A 70 N ARG A 71 1555 1555 1.33 LINK C ASN A 168 N MSE A 169 1555 1555 1.33 LINK C MSE A 169 N THR A 170 1555 1555 1.33 LINK C MSE C 1 N LEU C 2 1555 1555 1.33 LINK C HIS C 4 N MSE C 5 1555 1555 1.32 LINK C MSE C 5 N VAL C 6 1555 1555 1.33 LINK C ILE C 69 N MSE C 70 1555 1555 1.33 LINK C MSE C 70 N ARG C 71 1555 1555 1.33 LINK C ASN C 168 N MSE C 169 1555 1555 1.33 LINK C MSE C 169 N THR C 170 1555 1555 1.33 SITE 1 AC1 5 HIS A 150 GLU A 151 THR A 152 ARG A 156 SITE 2 AC1 5 HOH A2120 SITE 1 AC2 5 HIS C 150 GLU C 151 THR C 152 ARG C 156 SITE 2 AC2 5 HOH C2097 CRYST1 148.383 148.383 79.505 90.00 90.00 120.00 P 65 12 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 0.006739 0.003891 0.000000 0.00000 SCALE2 0.000000 0.007782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012578 0.00000 HETATM 1 N MSE A 1 -23.485 92.397 -10.135 1.00 33.54 N HETATM 2 CA MSE A 1 -24.406 93.392 -9.527 1.00 33.69 C HETATM 3 C MSE A 1 -23.800 93.937 -8.244 1.00 33.62 C HETATM 4 O MSE A 1 -23.224 93.193 -7.453 1.00 33.61 O HETATM 5 CB MSE A 1 -25.772 92.754 -9.250 1.00 33.71 C HETATM 6 CG MSE A 1 -26.815 93.669 -8.606 1.00 34.44 C HETATM 7 SE MSE A 1 -27.359 95.206 -9.698 0.50 36.18 SE HETATM 8 CE MSE A 1 -27.445 94.314 -11.375 0.50 34.73 C