PDB Short entry for 2DPD HEADER DNA BINDING PROTEIN/DNA 09-MAY-06 2DPD TITLE CRYSTAL STRUCTURE OF THE REPLICATION TERMINATION PROTEIN IN COMPLEX TITLE 2 WITH A PSEUDOSYMMETRIC B-SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*AP*AP*TP*GP*TP*TP*CP*AP COMPND 3 *TP*AP*G)-3'; COMPND 4 CHAIN: D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*TP*AP*TP*GP*AP*AP*CP*AP*TP*TP*AP*TP*GP*TP*TP*CP*AP COMPND 8 *TP*AP*G)-3'; COMPND 9 CHAIN: E; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: REPLICATION TERMINATION PROTEIN; COMPND 13 CHAIN: A, B; COMPND 14 SYNONYM: REPLICATION TERMINATOR PROTEIN; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 7 ORGANISM_TAXID: 1423; SOURCE 8 GENE: RTP; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET-3 KEYWDS WINGED-HELIX PROTEIN-DNA COMPLEX, REPLICATION TERMINATION, FORK KEYWDS 2 ARREST MECHANISM, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.P.VIVIAN,J.WILCE,M.C.J.WILCE REVDAT 4 25-OCT-23 2DPD 1 REMARK REVDAT 3 10-NOV-21 2DPD 1 SEQADV REVDAT 2 24-FEB-09 2DPD 1 VERSN REVDAT 1 15-MAY-07 2DPD 0 JRNL AUTH J.P.VIVIAN,J.WILCE,M.C.J.WILCE JRNL TITL CRYSTAL STRUCTURE OF THE REPLICATION TERMINATION PROTEIN IN JRNL TITL 2 COMPLEX WITH A PSEUDOSYMMETRIC B-SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.17 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) : 3.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 11048 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 654 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) : 3.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 745 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1939 REMARK 3 NUCLEIC ACID ATOMS : 855 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 96.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.87000 REMARK 3 B22 (A**2) : -2.87000 REMARK 3 B33 (A**2) : 4.31000 REMARK 3 B12 (A**2) : -1.44000 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): 0.792 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.455 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.393 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 49.763 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.890 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2925 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4097 ; 1.718 ; 2.363 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 230 ; 6.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;32.637 ;24.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;22.023 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1821 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1404 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1901 ; 0.324 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.177 ; 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): 42 ; 0.280 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 71 1 REMARK 3 1 B 8 B 71 1 REMARK 3 2 A 89 A 122 1 REMARK 3 2 B 89 B 122 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 823 ; 0.05 ; 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000025685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11638 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1F4K WITH RESIDUES 71 TO 89 OF EACH REMARK 200 MONOMER OMITTED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% MPD, 75MM SODIUM ACETATE PH 4.6, REMARK 280 20MM CALCIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 55.18433 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 110.36867 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 0.00000 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 55.18433 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 110.36867 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.18433 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 110.36867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 55.18433 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 110.36867 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 300 REMARK: THIS STRUCTURE REPRESENTS ONE DIMER OF THE FUNCTIONAL REMARK 300 TERMINATION COMPLEX WHICH COMPRISES A DIMER OF DIMERS 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 ARG A 6 REMARK 465 SER A 7 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 REMARK 465 LYS B 5 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 N LYS B 74 O HOH B 128 2.19 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 D 1 O3' DC D 1 C3' -0.044 REMARK 500 DA E 9 O3' DA E 9 C3' -0.043 REMARK 500 DA E 18 O3' DA E 18 C3' -0.043 REMARK 500 GLN A 83 CD GLN A 83 OE1 0.136 REMARK 500 GLN A 83 CD GLN A 83 NE2 0.159 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 D 1 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DA D 3 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DA D 3 C1' - O4' - C4' ANGL. DEV. = -7.9 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG D 5 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG D 5 C1' - O4' - C4' ANGL. DEV. = -12.3 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 DC D 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT D 10 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT D 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA D 11 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA D 12 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT D 13 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DT D 13 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT D 13 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 DT D 13 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT D 15 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT D 19 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DT D 19 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC E 1 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DA E 3 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DG E 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA E 9 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT E 10 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT E 11 C3' - C2' - C1' ANGL. DEV. = -7.4 DEGREES REMARK 500 DT E 11 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 DA E 12 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA E 12 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DT E 13 O4' - C1' - N1 ANGL. DEV. = 10.4 DEGREES REMARK 500 DT E 13 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT E 13 C5 - C4 - O4 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT E 15 C4 - C5 - C7 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT E 15 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT E 16 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT E 16 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 DA E 18 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 DA E 20 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA E 20 O4' - C1' - N9 ANGL. DEV. = 1.9 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 THR A 9 5.49 54.25 REMARK 500 PHE A 11 -141.35 -82.12 REMARK 500 LYS A 46 -47.90 -27.43 REMARK 500 GLU A 47 -72.43 -57.95 REMARK 500 LYS A 74 33.40 -92.61 REMARK 500 VAL A 75 -174.39 -58.67 REMARK 500 LYS A 81 -151.47 -110.94 REMARK 500 LEU A 82 69.30 -152.44 REMARK 500 LYS A 91 -61.39 -95.70 REMARK 500 SER B 8 35.41 -72.66 REMARK 500 THR B 9 2.02 53.92 REMARK 500 PHE B 11 -144.18 -83.51 REMARK 500 LYS B 46 -44.92 -25.53 REMARK 500 VAL B 75 -168.41 -119.07 REMARK 500 GLU B 78 -97.09 -117.55 REMARK 500 LYS B 81 -158.61 -143.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F4K RELATED DB: PDB REMARK 900 THE SAME COMPLEX SOLVED IN A DIFFERENT SPACE GROUP REMARK 900 RELATED ID: 1BM9 RELATED DB: PDB REMARK 900 WILD-TYPE APO-STRUCTURE REMARK 900 RELATED ID: 1J0R RELATED DB: PDB REMARK 900 APO-STRUCTURE DBREF 2DPD A 1 122 UNP P68732 RTP_BACSU 1 122 DBREF 2DPD B 1 122 UNP P68732 RTP_BACSU 1 122 DBREF 2DPD D 1 21 PDB 2DPD 2DPD 1 21 DBREF 2DPD E 1 21 PDB 2DPD 2DPD 1 21 SEQADV 2DPD SER A 110 UNP P68732 CYS 110 ENGINEERED MUTATION SEQADV 2DPD SER B 110 UNP P68732 CYS 110 ENGINEERED MUTATION SEQRES 1 D 21 DC DT DA DT DG DA DA DC DA DT DA DA DT SEQRES 2 D 21 DG DT DT DC DA DT DA DG SEQRES 1 E 21 DC DT DA DT DG DA DA DC DA DT DT DA DT SEQRES 2 E 21 DG DT DT DC DA DT DA DG SEQRES 1 A 122 MET LYS GLU GLU LYS ARG SER SER THR GLY PHE LEU VAL SEQRES 2 A 122 LYS GLN ARG ALA PHE LEU LYS LEU TYR MET ILE THR MET SEQRES 3 A 122 THR GLU GLN GLU ARG LEU TYR GLY LEU LYS LEU LEU GLU SEQRES 4 A 122 VAL LEU ARG SER GLU PHE LYS GLU ILE GLY PHE LYS PRO SEQRES 5 A 122 ASN HIS THR GLU VAL TYR ARG SER LEU HIS GLU LEU LEU SEQRES 6 A 122 ASP ASP GLY ILE LEU LYS GLN ILE LYS VAL LYS LYS GLU SEQRES 7 A 122 GLY ALA LYS LEU GLN GLU VAL VAL LEU TYR GLN PHE LYS SEQRES 8 A 122 ASP TYR GLU ALA ALA LYS LEU TYR LYS LYS GLN LEU LYS SEQRES 9 A 122 VAL GLU LEU ASP ARG SER LYS LYS LEU ILE GLU LYS ALA SEQRES 10 A 122 LEU SER ASP ASN PHE SEQRES 1 B 122 MET LYS GLU GLU LYS ARG SER SER THR GLY PHE LEU VAL SEQRES 2 B 122 LYS GLN ARG ALA PHE LEU LYS LEU TYR MET ILE THR MET SEQRES 3 B 122 THR GLU GLN GLU ARG LEU TYR GLY LEU LYS LEU LEU GLU SEQRES 4 B 122 VAL LEU ARG SER GLU PHE LYS GLU ILE GLY PHE LYS PRO SEQRES 5 B 122 ASN HIS THR GLU VAL TYR ARG SER LEU HIS GLU LEU LEU SEQRES 6 B 122 ASP ASP GLY ILE LEU LYS GLN ILE LYS VAL LYS LYS GLU SEQRES 7 B 122 GLY ALA LYS LEU GLN GLU VAL VAL LEU TYR GLN PHE LYS SEQRES 8 B 122 ASP TYR GLU ALA ALA LYS LEU TYR LYS LYS GLN LEU LYS SEQRES 9 B 122 VAL GLU LEU ASP ARG SER LYS LYS LEU ILE GLU LYS ALA SEQRES 10 B 122 LEU SER ASP ASN PHE FORMUL 5 HOH *12(H2 O) HELIX 1 1 LYS A 14 GLU A 30 1 17 HELIX 2 2 TYR A 33 LYS A 46 1 14 HELIX 3 3 ASN A 53 ASP A 67 1 15 HELIX 4 4 ASP A 92 ASN A 121 1 30 HELIX 5 5 LYS B 14 GLU B 30 1 17 HELIX 6 6 TYR B 33 LYS B 46 1 14 HELIX 7 7 ASN B 53 ASP B 67 1 15 HELIX 8 8 ASP B 92 ASN B 121 1 30 SHEET 1 A 2 LEU A 70 ILE A 73 0 SHEET 2 A 2 LEU A 87 PHE A 90 -1 O GLN A 89 N LYS A 71 SHEET 1 B 2 LEU B 70 VAL B 75 0 SHEET 2 B 2 VAL B 85 PHE B 90 -1 O GLN B 89 N LYS B 71 CRYST1 117.006 117.006 165.553 90.00 90.00 120.00 P 64 2 2 24 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 0.008547 0.004934 0.000000 0.00000 SCALE2 0.000000 0.009869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006040 0.00000