HEADER TRANSCRIPTION 16-JUL-15 5CLV TITLE CRYSTAL STRUCTURE OF KORA-OPERATOR DNA COMPLEX (KORA-OA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KORA; COMPND 5 SYNONYM: REGULATORY PROTEIN KORA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP* COMPND 9 GP*GP*)-3'; COMPND 10 CHAIN: C, D, G, H, K, L, O, P; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN; COMPND 14 CHAIN: E, F, I, J, M, N; COMPND 15 SYNONYM: REGULATORY PROTEIN KORA; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: TRFB, KORA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 15 ORGANISM_TAXID: 562; SOURCE 16 GENE: TRFB, KORA; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HELIX-TURN-HELIX, COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.A.WHITE,E.I.HYDE,K.V.RAJASEKAR REVDAT 4 10-JAN-24 5CLV 1 REMARK REVDAT 3 11-SEP-19 5CLV 1 REMARK REVDAT 2 15-JUN-16 5CLV 1 JRNL REVDAT 1 06-APR-16 5CLV 0 JRNL AUTH K.V.RAJASEKAR,A.L.LOVERING,F.DANCEA,D.J.SCOTT,S.A.HARRIS, JRNL AUTH 2 L.E.BINGLE,M.ROESSLE,C.M.THOMAS,E.I.HYDE,S.A.WHITE JRNL TITL FLEXIBILITY OF KORA, A PLASMID-ENCODED, GLOBAL TRANSCRIPTION JRNL TITL 2 REGULATOR, IN THE PRESENCE AND THE ABSENCE OF ITS OPERATOR. JRNL REF NUCLEIC ACIDS RES. V. 44 4947 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27016739 JRNL DOI 10.1093/NAR/GKW191 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.E.BINGLE,K.V.RAJASEKAR,S.T.MUNTAHA,V.NADELLA,E.I.HYDE, REMARK 1 AUTH 2 C.M.THOMAS REMARK 1 TITL A SINGLE AROMATIC RESIDUE IN TRANSCRIPTIONAL REPRESSOR REMARK 1 TITL 2 PROTEIN KORA IS CRITICAL FOR COOPERATIVITY WITH ITS REMARK 1 TITL 3 CO-REGULATOR KORB. REMARK 1 REF MOL. MICROBIOL. V. 70 1502 2008 REMARK 1 REFN ESSN 1365-2958 REMARK 1 PMID 19019158 REMARK 1 DOI 10.1111/J.1365-2958.2008.06498.X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 85480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.280 REMARK 3 R VALUE (WORKING SET) : 0.279 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 4619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.0483 - 7.6949 0.90 2825 177 0.2191 0.2441 REMARK 3 2 7.6949 - 6.1372 0.96 3009 180 0.2031 0.1939 REMARK 3 3 6.1372 - 5.3701 0.96 3025 138 0.2169 0.2274 REMARK 3 4 5.3701 - 4.8831 0.96 3086 148 0.2181 0.2429 REMARK 3 5 4.8831 - 4.5353 0.96 2952 196 0.2300 0.2421 REMARK 3 6 4.5353 - 4.2693 0.96 2977 215 0.2096 0.2466 REMARK 3 7 4.2693 - 4.0564 0.96 2979 215 0.2278 0.2300 REMARK 3 8 4.0564 - 3.8805 0.79 2590 4 0.2896 0.2504 REMARK 3 9 3.8805 - 3.7316 0.82 2447 253 0.2668 0.3045 REMARK 3 10 3.7316 - 3.6033 0.68 2273 0 0.3438 0.0000 REMARK 3 11 3.6033 - 3.4909 0.90 2648 337 0.2978 0.3281 REMARK 3 12 3.4909 - 3.3913 0.68 2243 0 0.3696 0.0000 REMARK 3 13 3.3913 - 3.3023 0.89 2639 325 0.2818 0.2904 REMARK 3 14 3.3023 - 3.2219 0.94 3116 0 0.2772 0.0000 REMARK 3 15 3.2219 - 3.1488 0.95 2767 406 0.2855 0.3564 REMARK 3 16 3.1488 - 3.0819 0.95 3083 0 0.3167 0.0000 REMARK 3 17 3.0819 - 3.0203 0.95 3159 0 0.3231 0.0000 REMARK 3 18 3.0203 - 2.9634 0.94 2710 430 0.3384 0.3809 REMARK 3 19 2.9634 - 2.9106 0.95 3113 0 0.3274 0.0000 REMARK 3 20 2.9106 - 2.8613 0.95 2684 471 0.3366 0.3971 REMARK 3 21 2.8613 - 2.8152 0.94 3089 0 0.3504 0.0000 REMARK 3 22 2.8152 - 2.7720 0.95 3140 0 0.3655 0.0000 REMARK 3 23 2.7720 - 2.7313 0.94 2895 282 0.3757 0.4801 REMARK 3 24 2.7313 - 2.6928 0.33 799 287 0.5436 0.4283 REMARK 3 25 2.6928 - 2.6565 0.67 2221 0 0.5051 0.0000 REMARK 3 26 2.6565 - 2.6220 0.17 565 0 0.5374 0.0000 REMARK 3 27 2.6220 - 2.5893 0.94 2501 553 0.3515 0.3768 REMARK 3 28 2.5893 - 2.5581 0.93 3134 0 0.3505 0.0000 REMARK 3 29 2.5581 - 2.5284 0.94 3086 0 0.3350 0.0000 REMARK 3 30 2.5284 - 2.5000 0.94 3106 2 0.3445 0.7552 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.46 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 7971 REMARK 3 ANGLE : 0.797 11419 REMARK 3 CHIRALITY : 0.042 1298 REMARK 3 PLANARITY : 0.005 942 REMARK 3 DIHEDRAL : 24.428 3155 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CLV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-06 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 : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49516 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5CKT, THEORETICAL DNA MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, ETHYLENE REMARK 280 GLYCOL, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 57.01500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, J, K, L 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: M, N, O, P 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 GLN A 97 REMARK 465 ASN F 66 REMARK 465 LYS I 2 REMARK 465 LYS I 3 REMARK 465 ASN I 66 REMARK 465 LYS J 2 REMARK 465 ASN J 66 REMARK 465 LYS M 65 REMARK 465 ASN M 66 REMARK 465 ASN N 66 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 DG C 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG C 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG C 20 C2 N2 N3 C4 REMARK 470 DG D 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG D 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG D 20 C2 N2 N3 C4 REMARK 470 DG G 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG G 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG G 20 C2 N2 N3 C4 REMARK 470 DG H 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG H 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG H 20 C2 N2 N3 C4 REMARK 470 DG K 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG K 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG K 20 C2 N2 N3 C4 REMARK 470 DG L 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG L 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG L 20 C2 N2 N3 C4 REMARK 470 DG O 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG O 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG O 20 C2 N2 N3 C4 REMARK 470 DG P 20 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DG P 20 N9 C8 N7 C5 C6 O6 N1 REMARK 470 DG P 20 C2 N2 N3 C4 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 C 7 O HOH C 101 2.19 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 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA D 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA G 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC G 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA G 14 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG H 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC H 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA H 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT K 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC K 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA K 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC K 16 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT L 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC L 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA L 14 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DA L 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC L 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG O 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA O 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG P 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA P 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC P 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT P 17 O4' - C1' - N1 ANGL. DEV. = 2.1 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 18 95.36 -69.42 REMARK 500 LYS A 65 -155.10 -97.57 REMARK 500 LYS A 94 31.91 -86.18 REMARK 500 ASN B 66 -115.92 43.97 REMARK 500 LEU B 67 69.23 -119.58 REMARK 500 PRO B 68 16.08 -145.36 REMARK 500 GLU B 69 45.80 -24.67 REMARK 500 LYS F 3 80.77 69.13 REMARK 500 GLU I 18 69.12 -64.78 REMARK 500 LYS M 3 93.18 55.05 REMARK 500 LYS N 3 107.62 65.47 REMARK 500 THR N 6 -163.78 -76.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CKT RELATED DB: PDB REMARK 900 5CKT CONTAINS THE SAME PROTEIN IN THE ABSENCE OF DNA DBREF 5CLV A 2 97 UNP P03052 KORA2_ECOLX 2 97 DBREF 5CLV B 2 97 UNP P03052 KORA2_ECOLX 2 97 DBREF 5CLV C 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV D 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV E 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV F 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV G 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV H 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV I 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV J 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV K 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV L 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV M 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV N 2 66 UNP P03052 KORA2_ECOLX 2 66 DBREF 5CLV O 1 20 PDB 5CLV 5CLV 1 20 DBREF 5CLV P 1 20 PDB 5CLV 5CLV 1 20 SEQRES 1 A 96 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 A 96 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 A 96 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 A 96 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 A 96 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 6 A 96 LEU PRO GLU GLY TYR ALA ARG VAL THR ALA VAL LEU PRO SEQRES 7 A 96 GLU HIS GLN ALA TYR ILE VAL ARG LYS TRP GLU ALA ASP SEQRES 8 A 96 ALA LYS LYS LYS GLN SEQRES 1 B 96 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 B 96 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 B 96 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 B 96 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 B 96 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 6 B 96 LEU PRO GLU GLY TYR ALA ARG VAL THR ALA VAL LEU PRO SEQRES 7 B 96 GLU HIS GLN ALA TYR ILE VAL ARG LYS TRP GLU ALA ASP SEQRES 8 B 96 ALA LYS LYS LYS GLN SEQRES 1 C 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 C 20 DA DA DC DT DT DG DG SEQRES 1 D 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 D 20 DA DA DC DT DT DG DG SEQRES 1 E 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 E 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 E 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 E 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 E 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 F 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 F 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 F 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 F 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 F 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 G 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 G 20 DA DA DC DT DT DG DG SEQRES 1 H 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 H 20 DA DA DC DT DT DG DG SEQRES 1 I 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 I 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 I 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 I 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 I 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 J 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 J 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 J 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 J 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 J 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 K 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 K 20 DA DA DC DT DT DG DG SEQRES 1 L 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 L 20 DA DA DC DT DT DG DG SEQRES 1 M 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 M 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 M 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 M 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 M 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 N 65 LYS LYS ARG LEU THR GLU SER GLN PHE GLN GLU ALA ILE SEQRES 2 N 65 GLN GLY LEU GLU VAL GLY GLN GLN THR ILE GLU ILE ALA SEQRES 3 N 65 ARG GLY VAL LEU VAL ASP GLY LYS PRO GLN ALA THR PHE SEQRES 4 N 65 ALA THR SER LEU GLY LEU THR ARG GLY ALA VAL SER GLN SEQRES 5 N 65 ALA VAL HIS ARG VAL TRP ALA ALA PHE GLU ASP LYS ASN SEQRES 1 O 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 O 20 DA DA DC DT DT DG DG SEQRES 1 P 20 DC DC DA DA DG DT DT DT DA DG DC DT DA SEQRES 2 P 20 DA DA DC DT DT DG DG FORMUL 17 HOH *164(H2 O) HELIX 1 AA1 THR A 6 ILE A 14 1 9 HELIX 2 AA2 GLY A 20 VAL A 32 1 13 HELIX 3 AA3 PRO A 36 GLY A 45 1 10 HELIX 4 AA4 THR A 47 LYS A 65 1 19 HELIX 5 AA5 PRO A 79 LYS A 94 1 16 HELIX 6 AA6 THR B 6 ILE B 14 1 9 HELIX 7 AA7 GLY B 20 VAL B 32 1 13 HELIX 8 AA8 PRO B 36 GLY B 45 1 10 HELIX 9 AA9 THR B 47 ASP B 64 1 18 HELIX 10 AB1 GLU B 80 GLN B 97 1 18 HELIX 11 AB2 THR E 6 ILE E 14 1 9 HELIX 12 AB3 GLY E 20 VAL E 32 1 13 HELIX 13 AB4 PRO E 36 GLY E 45 1 10 HELIX 14 AB5 THR E 47 LYS E 65 1 19 HELIX 15 AB6 THR F 6 ILE F 14 1 9 HELIX 16 AB7 GLY F 20 VAL F 32 1 13 HELIX 17 AB8 PRO F 36 GLY F 45 1 10 HELIX 18 AB9 THR F 47 ASP F 64 1 18 HELIX 19 AC1 THR I 6 GLN I 15 1 10 HELIX 20 AC2 GLY I 20 VAL I 32 1 13 HELIX 21 AC3 PRO I 36 LEU I 44 1 9 HELIX 22 AC4 THR I 47 GLU I 63 1 17 HELIX 23 AC5 THR J 6 ILE J 14 1 9 HELIX 24 AC6 GLY J 20 VAL J 32 1 13 HELIX 25 AC7 GLN J 37 GLY J 45 1 9 HELIX 26 AC8 THR J 47 ASP J 64 1 18 HELIX 27 AC9 THR M 6 ILE M 14 1 9 HELIX 28 AD1 GLY M 20 VAL M 32 1 13 HELIX 29 AD2 PRO M 36 GLY M 45 1 10 HELIX 30 AD3 THR M 47 ASP M 64 1 18 HELIX 31 AD4 THR N 6 ILE N 14 1 9 HELIX 32 AD5 GLY N 20 VAL N 32 1 13 HELIX 33 AD6 PRO N 36 LEU N 44 1 9 HELIX 34 AD7 THR N 47 ASP N 64 1 18 SHEET 1 AA1 2 TYR A 71 LEU A 78 0 SHEET 2 AA1 2 ALA B 72 PRO B 79 -1 O VAL B 74 N ALA A 76 CISPEP 1 ASN B 66 LEU B 67 0 -3.89 CRYST1 80.460 114.030 82.070 90.00 99.59 90.00 P 1 21 1 16 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 0.012429 0.000000 0.002100 0.00000 SCALE2 0.000000 0.008770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012357 0.00000