HEADER TRANSCRIPTION/DNA 31-MAY-07 2Z33 TITLE SOLUTION STRUCTURE OF THE DNA COMPLEX OF PHOB DNA- TITLE 2 BINDING/TRANSACTIVATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY COMPND 3 PROTEIN PHOB; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 1-104; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'- COMPND 9 D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'- COMPND 14 D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: PHOB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7-CB; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS WINGED HELIX-TURN-HELIX, TRANSCRIPTION/DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.YAMANE,H.OKAMURA,M.IKEGUCHI,Y.NISHIMURA,A.KIDERA REVDAT 2 24-FEB-09 2Z33 1 VERSN REVDAT 1 22-APR-08 2Z33 0 JRNL AUTH T.YAMANE,H.OKAMURA,M.IKEGUCHI,Y.NISHIMURA,A.KIDERA JRNL TITL WATER-MEDIATED INTERACTIONS BETWEEN DNA AND PHOB JRNL TITL 2 DNA-BINDING/TRANSACTIVATION DOMAIN: NMR-RESTRAINED JRNL TITL 3 MOLECULAR DYNAMICS IN EXPLICIT WATER ENVIRONMENT. JRNL REF PROTEINS V. 71 1970 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18186481 JRNL DOI 10.1002/PROT.21874 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0, MARBLE 0.3.46 REMARK 3 AUTHORS : A.BRUNGER ET AL. (CNS), M.IKEGUCHI (MARBLE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 2508 RESTRAINTS, 2263 ARE NOE-DERIVED DISTANCE RESTRAINTS REMARK 3 229 ARE DIHEDRAL ANGLE RESTRAINTS AND 16 ARE RESTRAINTS OF DNA REMARK 3 BASE PLANALITY RESTRAINTS. STRUCTURE CALCULATIONS WERE REMARK 3 PERFORMED WITH CNS BY FOLLOWIN PROCEDURE. FIRST, ONLY THE REMARK 3 STRUCTURES OF PROTEIN WERE CALCULATED USING THE HYBRID REMARK 3 DISTANCE GEOMETRY-SIMULATED ANNEAING PROTOCOL WITH THE INTRA- REMARK 3 PROTEIN RESTRAINTS, 10 OUT OF 100 CALCULATED STRUCTURES WERE REMARK 3 SELECTED BY HAVING NO DISTANCE VIOLATION GREATER THAN 0.2 REMARK 3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATION GREATER THAN 2 REMARK 3 DEGREES AND A LOW TARGET ENERGY. SECOND, THE PROTEIN AND AN REMARK 3 IDEALIZED B-FORM OF 16-MER DUPLEX DNA WERE DOCKED BY A REMARK 3 SIMULATED ANNEALING PROTOCOL, FOR WHICH THE INTRA-DNA, INTER- REMARK 3 MOLECULAR AND INTRA-PROTEIN RESTRAINTS WERE EMPLOYED. AS AN REMARK 3 INITIAL STRUCTURE, EACH OF THE 10 PROTEIN STRUCTURES WAS REMARK 3 PLACED IN 15 DIFFERENT POSITIONS 50 ANGSTROMS AWAY FROM THE REMARK 3 DNA. NEXT, EACH OF THE 150 DOCKED COMPLEX STRUCTURES WAS REMARK 3 FURTHER REFINED BY A SIMULATED ANNEALING PROTOCOL. FINALLY, 20 REMARK 3 STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATION REMARK 3 GREATER THAN 0.2 ANGSTROME AND NO TORSION ANGLE VIOLATION THAN REMARK 3 2 DEGREES AND A LOW TARGET ENERGY. ADDITIONALLY, 10 CNS- REMARK 3 SELECTED STRUCTURES WERE REFINED IN REALISTIC SOLUTION SISTEM REMARK 3 BY USING MOLECULAR DYNAMICS SIMULATION PROGRAM, MARBLE WITH REMARK 3 RESTRAINT FUNCTIONS FOR NOE DISTANCE DIHEDRAL ANGLE AND REMARK 3 PLANARITY OF DNA BASE PAIR USED IN CNS. REMARK 4 REMARK 4 2Z33 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JUN-07. REMARK 100 THE RCSB ID CODE IS RCSB027459. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2MM PHOB-DNA U-15N, 13C; REMARK 210 10MM POTASSIUM PHOSPHATE REMARK 210 BUFFER; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D SEQUENTIAL ASSIGNMENT REMARK 210 PROTOCOL, 3D HNHA, 4D_13C- REMARK 210 SEPARATED_NOESY, 4D_13C/15N- REMARK 210 SEPARATED_NOESY, 3D_15N- REMARK 210 SEPARATED_NOESY, 3D_13C_ REMARK 210 SEPARATED_NOESY, 2D NOESY, 2D REMARK 210 TOCSY AND 2D COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, PIPP REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 MOLECLUAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 1 DT B 5 C4' DT B 5 C3' 0.130 REMARK 500 1 DT B 5 C3' DT B 5 C2' -0.276 REMARK 500 1 DT B 5 O3' DT B 5 C3' 0.094 REMARK 500 1 DT B 5 C1' DT B 5 N1 -0.166 REMARK 500 1 DT B 5 N1 DT B 5 C2 0.090 REMARK 500 1 DT B 5 C2 DT B 5 N3 0.152 REMARK 500 1 DT B 5 N3 DT B 5 C4 -0.066 REMARK 500 1 DT B 5 C5 DT B 5 C6 0.052 REMARK 500 1 DT B 5 C6 DT B 5 N1 0.043 REMARK 500 1 DT B 5 C2 DT B 5 O2 -0.272 REMARK 500 1 DT B 5 C5 DT B 5 C7 -0.051 REMARK 500 1 DA C 12 N3 DA C 12 C4 0.070 REMARK 500 1 DA C 12 C5 DA C 12 C6 0.064 REMARK 500 1 DA C 12 C6 DA C 12 N1 -0.068 REMARK 500 1 DA C 12 N9 DA C 12 C4 -0.086 REMARK 500 1 GLU A 66 CD GLU A 66 OE2 0.123 REMARK 500 1 GLU A 82 CD GLU A 82 OE2 0.116 REMARK 500 2 DT B 12 N1 DT B 12 C2 0.090 REMARK 500 2 DT B 12 C2 DT B 12 N3 0.114 REMARK 500 2 DT B 12 N3 DT B 12 C4 -0.055 REMARK 500 2 DT B 12 C6 DT B 12 N1 -0.047 REMARK 500 2 DT B 12 C2 DT B 12 O2 -0.246 REMARK 500 2 LEU A 54 CA LEU A 54 CB 0.255 REMARK 500 2 GLU A 66 CD GLU A 66 OE2 0.121 REMARK 500 2 GLU A 82 CD GLU A 82 OE2 0.117 REMARK 500 3 DT C 8 N1 DT C 8 C2 -0.065 REMARK 500 3 DT C 8 N3 DT C 8 C4 -0.069 REMARK 500 3 DT C 8 C6 DT C 8 N1 0.057 REMARK 500 3 DT C 8 C5 DT C 8 C7 0.042 REMARK 500 3 GLU A 66 CD GLU A 66 OE2 0.109 REMARK 500 3 GLU A 82 CD GLU A 82 OE2 0.116 REMARK 500 4 DT B 14 C2 DT B 14 N3 0.055 REMARK 500 4 DT B 14 N3 DT B 14 C4 0.053 REMARK 500 4 DT B 14 C5 DT B 14 C6 -0.054 REMARK 500 4 DT B 14 C2 DT B 14 O2 -0.146 REMARK 500 4 DT B 14 C4 DT B 14 O4 -0.097 REMARK 500 4 DT B 14 C5 DT B 14 C7 0.044 REMARK 500 4 GLU A 66 CD GLU A 66 OE2 0.123 REMARK 500 4 GLU A 82 CD GLU A 82 OE2 0.114 REMARK 500 5 GLU A 66 CD GLU A 66 OE2 0.119 REMARK 500 5 GLU A 82 CD GLU A 82 OE2 0.116 REMARK 500 6 GLU A 66 CD GLU A 66 OE2 0.118 REMARK 500 6 GLU A 82 CD GLU A 82 OE2 0.109 REMARK 500 7 DT B 12 N1 DT B 12 C2 -0.068 REMARK 500 7 DT B 12 C2 DT B 12 N3 0.053 REMARK 500 7 DT B 12 N3 DT B 12 C4 0.284 REMARK 500 7 DT B 12 C6 DT B 12 N1 0.123 REMARK 500 7 DT B 12 C2 DT B 12 O2 -0.072 REMARK 500 7 DT B 12 C4 DT B 12 O4 -0.312 REMARK 500 7 DT B 12 C5 DT B 12 C7 0.140 REMARK 500 REMARK 500 THIS ENTRY HAS 88 BOND DEVIATIONS. 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 1 DT B 5 O4' - C4' - C3' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DT B 5 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT B 5 C3' - C2' - C1' ANGL. DEV. = 12.9 DEGREES REMARK 500 1 DT B 5 O4' - C1' - C2' ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DT B 5 N1 - C1' - C2' ANGL. DEV. = 13.5 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 5 N1 - C2 - N3 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DT B 5 N3 - C4 - C5 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 5 N3 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DT B 5 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA C 12 N1 - C6 - N6 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DA C 12 C5 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT B 12 C6 - N1 - C2 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DT B 12 N1 - C2 - N3 ANGL. DEV. = -11.3 DEGREES REMARK 500 2 DT B 12 C2 - N3 - C4 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT B 12 N1 - C2 - O2 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DT B 12 N3 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 LEU A 54 CB - CA - C ANGL. DEV. = -14.8 DEGREES REMARK 500 2 LEU A 54 CA - C - O ANGL. DEV. = -14.4 DEGREES REMARK 500 2 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT C 8 C6 - N1 - C2 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT C 8 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DT C 8 C5 - C6 - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 3 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DT B 14 N1 - C2 - N3 ANGL. DEV. = -5.2 DEGREES REMARK 500 4 DT B 14 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 4 DT B 14 C4 - C5 - C6 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 DT B 14 C5 - C4 - O4 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 DT B 14 C4 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 4 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 5 DT B 12 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 5 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 5 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 94 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 107 ANGLE DEVIATIONS. 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 1 VAL A 6 137.83 -29.99 REMARK 500 1 THR A 96 -60.18 -139.93 REMARK 500 1 ARG A 103 -62.45 -153.45 REMARK 500 2 VAL A 58 -62.19 -105.78 REMARK 500 2 VAL A 65 168.28 -47.92 REMARK 500 3 VAL A 58 -60.54 -99.86 REMARK 500 4 ALA A 2 17.72 -144.21 REMARK 500 4 VAL A 6 133.64 -35.49 REMARK 500 4 THR A 61 -24.73 63.30 REMARK 500 4 THR A 96 -57.30 -127.21 REMARK 500 5 VAL A 58 -63.00 -99.07 REMARK 500 6 ALA A 2 27.02 -148.54 REMARK 500 6 VAL A 3 102.86 78.12 REMARK 500 6 HIS A 19 39.82 71.66 REMARK 500 6 THR A 96 -61.86 -134.95 REMARK 500 7 ALA A 2 -145.52 46.17 REMARK 500 7 GLU A 5 145.16 69.95 REMARK 500 7 GLU A 46 32.21 81.53 REMARK 500 7 VAL A 58 -72.49 -109.25 REMARK 500 7 THR A 96 -59.65 -135.09 REMARK 500 8 THR A 61 -47.76 79.52 REMARK 500 8 ASN A 62 34.65 -91.04 REMARK 500 8 VAL A 65 157.04 -41.18 REMARK 500 8 THR A 96 -63.77 -133.49 REMARK 500 10 GLU A 5 127.70 97.87 REMARK 500 10 THR A 96 -63.08 -139.70 REMARK 500 10 ARG A 103 -110.79 -143.80 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 VAL A 63 TYR A 64 8 -148.09 REMARK 500 VAL A 63 TYR A 64 10 -149.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG A 68 0.08 SIDE_CHAIN REMARK 500 3 ARG A 20 0.08 SIDE_CHAIN REMARK 500 3 ARG A 103 0.08 SIDE_CHAIN REMARK 500 4 ARG A 94 0.09 SIDE_CHAIN REMARK 500 5 ARG A 20 0.08 SIDE_CHAIN REMARK 500 5 ARG A 51 0.12 SIDE_CHAIN REMARK 500 5 ARG A 75 0.15 SIDE_CHAIN REMARK 500 6 ARG A 51 0.11 SIDE_CHAIN REMARK 500 6 ARG A 75 0.10 SIDE_CHAIN REMARK 500 6 ARG A 88 0.07 SIDE_CHAIN REMARK 500 7 ARG A 76 0.09 SIDE_CHAIN REMARK 500 9 ARG A 20 0.08 SIDE_CHAIN REMARK 500 9 ARG A 94 0.09 SIDE_CHAIN REMARK 500 10 ARG A 47 0.09 SIDE_CHAIN REMARK 500 10 ARG A 51 0.11 SIDE_CHAIN REMARK 500 10 ARG A 68 0.11 SIDE_CHAIN REMARK 500 10 ARG A 76 0.13 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 2 LEU A 54 -12.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QQI RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN ITS DNA-FREE FORM. DBREF 2Z33 A 1 104 UNP P0AFJ5 PHOB_ECOLI 126 229 DBREF 2Z33 B 1 16 PDB 2Z33 2Z33 1 16 DBREF 2Z33 C 1 16 PDB 2Z33 2Z33 1 16 SEQRES 1 A 104 MET ALA VAL GLU GLU VAL ILE GLU MET GLN GLY LEU SER SEQRES 2 A 104 LEU ASP PRO THR SER HIS ARG VAL MET ALA GLY GLU GLU SEQRES 3 A 104 PRO LEU GLU MET GLY PRO THR GLU PHE LYS LEU LEU HIS SEQRES 4 A 104 PHE PHE MET THR HIS PRO GLU ARG VAL TYR SER ARG GLU SEQRES 5 A 104 GLN LEU LEU ASN HIS VAL TRP GLY THR ASN VAL TYR VAL SEQRES 6 A 104 GLU ASP ARG THR VAL ASP VAL HIS ILE ARG ARG LEU ARG SEQRES 7 A 104 LYS ALA LEU GLU PRO GLY GLY HIS ASP ARG MET VAL GLN SEQRES 8 A 104 THR VAL ARG GLY THR GLY TYR ARG PHE SER THR ARG PHE SEQRES 1 B 16 DA DC DT DG DT DC DA DT DA DA DA DT DC SEQRES 2 B 16 DT DG DT SEQRES 1 C 16 DA DC DA DG DA DT DT DT DA DT DG DA DC SEQRES 2 C 16 DA DG DT HELIX 1 1 GLY A 31 HIS A 44 1 14 HELIX 2 2 ARG A 51 VAL A 58 1 8 HELIX 3 3 ASP A 67 GLU A 82 1 16 HELIX 4 4 HIS A 86 ARG A 88 5 3 SHEET 1 A 4 ILE A 7 MET A 9 0 SHEET 2 A 4 LEU A 12 ASP A 15 -1 O LEU A 14 N ILE A 7 SHEET 3 A 4 ARG A 20 ALA A 23 -1 O MET A 22 N SER A 13 SHEET 4 A 4 GLU A 26 LEU A 28 -1 O GLU A 26 N ALA A 23 SHEET 1 B 3 VAL A 48 SER A 50 0 SHEET 2 B 3 GLY A 97 PHE A 100 -1 O TYR A 98 N TYR A 49 SHEET 3 B 3 VAL A 90 VAL A 93 -1 N VAL A 93 O GLY A 97 CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 328 0 0 4 7 0 0 6 0 0 0 12 END