PDB Short entry for 1RIO HEADER TRANSCRIPTION/DNA 17-NOV-03 1RIO TITLE STRUCTURE OF BACTERIOPHAGE LAMBDA CI-NTD IN COMPLEX WITH SIGMA-REGION4 TITLE 2 OF THERMUS AQUATICUS BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 27-MER; COMPND 3 CHAIN: U; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 27-MER; COMPND 8 CHAIN: T; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SIGMA FACTOR SIGA; COMPND 13 CHAIN: H; COMPND 14 FRAGMENT: SIGMA REGION 4; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: REPRESSOR PROTEIN CI; COMPND 18 CHAIN: A, B; COMPND 19 FRAGMENT: CI-N-TERMINUS DOMAIN; COMPND 20 ENGINEERED: 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: THERMUS AQUATICUS; SOURCE 7 ORGANISM_TAXID: 271; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PAO6; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 15 ORGANISM_TAXID: 10710; SOURCE 16 GENE: CI; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS HELIX-TURN-HELIX, TRANSCRIPTION ACTIVATION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.JAIN,B.E.NICKELS,L.SUN,A.HOCHSCHILD,S.A.DARST REVDAT 3 13-JUL-11 1RIO 1 VERSN REVDAT 2 24-FEB-09 1RIO 1 VERSN REVDAT 1 27-JAN-04 1RIO 0 JRNL AUTH D.JAIN,B.E.NICKELS,L.SUN,A.HOCHSCHILD,S.A.DARST JRNL TITL STRUCTURE OF A TERNARY TRANSCRIPTION ACTIVATION COMPLEX. JRNL REF MOL.CELL V. 13 45 2004 JRNL REFN ISSN 1097-2765 JRNL PMID 14731393 JRNL DOI 10.1016/S1097-2765(03)00483-0 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21761 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1605 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2000 REMARK 3 NUCLEIC ACID ATOMS : 1101 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.38 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.884 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3256 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2386 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4605 ; 2.353 ; 2.394 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5664 ; 1.143 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 4.745 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;17.587 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2774 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 387 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 753 ; 0.258 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2579 ; 0.250 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 191 ; 0.209 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 9 ; 0.062 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.224 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.281 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.254 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.063 ; 0.500 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): 1243 ; 1.002 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1969 ; 1.875 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2013 ; 2.481 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2636 ; 3.585 ; 4.500 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : T 1 T 10 REMARK 3 RESIDUE RANGE : U 18 U 27 REMARK 3 RESIDUE RANGE : H 366 H 426 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2370 3.5190 49.3970 REMARK 3 T TENSOR REMARK 3 T11: 0.3294 T22: 0.0569 REMARK 3 T33: 0.1890 T12: -0.0975 REMARK 3 T13: -0.1132 T23: 0.0383 REMARK 3 L TENSOR REMARK 3 L11: 2.8087 L22: 2.2748 REMARK 3 L33: 5.5721 L12: 1.0799 REMARK 3 L13: -2.9196 L23: -1.6821 REMARK 3 S TENSOR REMARK 3 S11: 0.1547 S12: 0.0688 S13: 0.1900 REMARK 3 S21: 0.5090 S22: -0.2417 S23: -0.0109 REMARK 3 S31: -0.6450 S32: 0.0434 S33: 0.0869 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : T 11 T 16 REMARK 3 RESIDUE RANGE : U 12 U 17 REMARK 3 RESIDUE RANGE : B 2 B 96 REMARK 3 ORIGIN FOR THE GROUP (A): 13.0170 12.8500 24.9360 REMARK 3 T TENSOR REMARK 3 T11: 0.0643 T22: 0.0864 REMARK 3 T33: 0.2095 T12: -0.0640 REMARK 3 T13: 0.0240 T23: 0.0439 REMARK 3 L TENSOR REMARK 3 L11: 1.5328 L22: 2.7038 REMARK 3 L33: 2.5977 L12: -0.0885 REMARK 3 L13: 0.5964 L23: -1.0360 REMARK 3 S TENSOR REMARK 3 S11: -0.0827 S12: 0.0909 S13: -0.0096 REMARK 3 S21: 0.2496 S22: -0.1785 S23: -0.5632 REMARK 3 S31: -0.0900 S32: 0.2171 S33: 0.2612 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : T 17 T 27 REMARK 3 RESIDUE RANGE : U 1 U 11 REMARK 3 RESIDUE RANGE : A 2 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): -8.9170 1.3420 1.9560 REMARK 3 T TENSOR REMARK 3 T11: 0.3130 T22: 0.3487 REMARK 3 T33: 0.1690 T12: -0.2330 REMARK 3 T13: -0.0278 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 3.9934 L22: 3.1282 REMARK 3 L33: 7.9750 L12: -1.4193 REMARK 3 L13: 3.7875 L23: -2.4403 REMARK 3 S TENSOR REMARK 3 S11: 0.2120 S12: 0.4873 S13: -0.6712 REMARK 3 S21: -0.6234 S22: 0.3412 S23: 0.5680 REMARK 3 S31: 0.7405 S32: -0.7041 S33: -0.5533 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 : 1.40 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 1RIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB020776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22889 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM ACETATE, CALCIUM CHLORIDE, REMARK 280 PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K, PH 4.60 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 35.63450 REMARK 290 SMTRY3 2 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: U, T, H, 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 GLU H 427 REMARK 465 SER H 428 REMARK 465 ARG H 429 REMARK 465 THR H 430 REMARK 465 ARG H 431 REMARK 465 LYS H 432 REMARK 465 LEU H 433 REMARK 465 ARG H 434 REMARK 465 ASP H 435 REMARK 465 PHE H 436 REMARK 465 LEU H 437 REMARK 465 GLU H 438 REMARK 465 MET A 1 REMARK 465 MET B 1 REMARK 465 HIS B 98 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 GLU H 367 CG CD OE1 OE2 REMARK 470 GLU H 368 CG CD OE1 OE2 REMARK 470 GLU H 370 CG CD OE1 OE2 REMARK 470 LYS H 371 CG CD CE NZ REMARK 470 LYS H 375 CG CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 SER H 366 REMARK 475 GLU H 367 REMARK 475 GLU H 368 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 DT U 4 O3' DT U 4 C3' -0.057 REMARK 500 DC U 12 O3' DC U 12 C3' -0.052 REMARK 500 DA U 14 N3 DA U 14 C4 -0.044 REMARK 500 DT U 19 O3' DT U 19 C3' -0.040 REMARK 500 DA T 8 O3' DA T 8 C3' -0.077 REMARK 500 DA T 12 N7 DA T 12 C8 -0.048 REMARK 500 DA T 22 C5 DA T 22 N7 -0.042 REMARK 500 MSE B 43 SE MSE B 43 CE -0.367 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 U 1 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG U 3 P - O5' - C5' ANGL. DEV. = -10.1 DEGREES REMARK 500 DG U 3 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 DG U 3 C5' - C4' - C3' ANGL. DEV. = -13.1 DEGREES REMARK 500 DG U 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG U 3 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT U 4 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA U 5 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 DT U 6 O4' - C1' - N1 ANGL. DEV. = 8.6 DEGREES REMARK 500 DC U 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA U 8 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA U 8 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA U 8 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA U 8 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA U 8 O4' - C1' - N9 ANGL. DEV. = 10.9 DEGREES REMARK 500 DC U 9 O4' - C1' - N1 ANGL. DEV. = 8.7 DEGREES REMARK 500 DA U 8 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 DC U 10 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG U 11 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DG U 11 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DG U 11 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC U 13 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC U 13 N1 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG U 15 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT U 16 N3 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT U 16 C5 - C4 - O4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT U 16 C4 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG U 17 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC U 18 O5' - P - OP1 ANGL. DEV. = -8.4 DEGREES REMARK 500 DC U 18 C5' - C4' - O4' ANGL. DEV. = -16.6 DEGREES REMARK 500 DC U 18 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT U 19 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG U 21 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 DG U 21 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG U 21 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG U 21 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA U 22 P - O5' - C5' ANGL. DEV. = -14.7 DEGREES REMARK 500 DC U 23 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT U 25 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG U 27 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DC T 1 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC T 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC T 2 N1 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA T 3 C1' - O4' - C4' ANGL. DEV. = 6.1 DEGREES REMARK 500 DT T 4 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT T 4 N3 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT T 6 C5' - C4' - O4' ANGL. DEV. = -14.4 DEGREES REMARK 500 DT T 6 N3 - C4 - O4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT T 6 C5 - C4 - O4 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC T 7 O5' - P - OP1 ANGL. DEV. = -5.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 81 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 LYS H 375 -13.46 -178.17 REMARK 500 THR B 3 74.70 31.20 REMARK 500 HIS B 95 -167.41 -126.36 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 GLU H 368 LEU H 369 144.02 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 ANGLE, 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 GLU H 368 13.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU H 369 11.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 306 O REMARK 620 2 HOH A 311 O 116.8 REMARK 620 3 HOH T 44 O 142.2 50.7 REMARK 620 4 HOH T 45 O 68.2 100.5 79.0 REMARK 620 5 GLY A 42 O 63.2 53.6 94.0 80.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KU7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS AQUATICS RNA POLYMERASE SIGMAA REMARK 900 SUBUNIT REGION 4 BOUND TO-35 ELEMENT DNA REMARK 900 RELATED ID: 1LMB RELATED DB: PDB REMARK 900 REFINED 1.8 A CRYSTAL STRUCTURE OF THE REPRESSOR-OPERATOR REMARK 900 COMPLEX DBREF 1RIO H 366 438 UNP Q9EZJ8 Q9EZJ8_THEAQ 366 438 DBREF 1RIO A 1 92 UNP P03034 RPC1_LAMBD 1 91 DBREF 1RIO B 1 92 UNP P03034 RPC1_LAMBD 1 91 DBREF 1RIO U 1 27 PDB 1RIO 1RIO 1 27 DBREF 1RIO T 1 27 PDB 1RIO 1RIO 1 27 SEQADV 1RIO MSE A 41 UNP P03034 MET 40 MODIFIED RESIDUE SEQADV 1RIO MSE A 43 UNP P03034 MET 42 MODIFIED RESIDUE SEQADV 1RIO MSE A 88 UNP P03034 MET 87 MODIFIED RESIDUE SEQADV 1RIO HIS A 93 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS A 94 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS A 95 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS A 96 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS A 97 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS A 98 UNP P03034 EXPRESSION TAG SEQADV 1RIO MSE B 41 UNP P03034 MET 40 MODIFIED RESIDUE SEQADV 1RIO MSE B 43 UNP P03034 MET 42 MODIFIED RESIDUE SEQADV 1RIO MSE B 88 UNP P03034 MET 87 MODIFIED RESIDUE SEQADV 1RIO HIS B 93 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS B 94 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS B 95 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS B 96 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS B 97 UNP P03034 EXPRESSION TAG SEQADV 1RIO HIS B 98 UNP P03034 EXPRESSION TAG SEQRES 1 U 27 DC DG DG DT DA DT DC DA DC DC DG DC DC SEQRES 2 U 27 DA DG DT DG DC DT DT DG DA DC DA DT DG SEQRES 3 U 27 DG SEQRES 1 T 27 DC DC DA DT DG DT DC DA DA DG DC DA DC SEQRES 2 T 27 DT DG DG DC DG DG DT DG DA DT DA DC DC SEQRES 3 T 27 DG SEQRES 1 H 73 SER GLU GLU LEU GLU LYS ALA LEU SER LYS LEU SER GLU SEQRES 2 H 73 ARG GLU ALA MET VAL LEU LYS LEU ARG LYS GLY LEU ILE SEQRES 3 H 73 ASP GLY ARG GLU HIS THR LEU GLU GLU VAL GLY ALA TYR SEQRES 4 H 73 PHE GLY VAL THR ARG GLU ARG ILE ARG GLN ILE GLU ASN SEQRES 5 H 73 LYS ALA LEU ARG LYS LEU LYS TYR HIS GLU SER ARG THR SEQRES 6 H 73 ARG LYS LEU ARG ASP PHE LEU GLU SEQRES 1 A 98 MET SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU SEQRES 2 A 98 GLU ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS SEQRES 3 A 98 LYS ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP SEQRES 4 A 98 LYS MSE GLY MSE GLY GLN SER GLY VAL GLY ALA LEU PHE SEQRES 5 A 98 ASN GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU SEQRES 6 A 98 LEU ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER SEQRES 7 A 98 PRO SER ILE ALA ARG GLU ILE TYR GLU MSE TYR GLU ALA SEQRES 8 A 98 VAL HIS HIS HIS HIS HIS HIS SEQRES 1 B 98 MET SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU SEQRES 2 B 98 GLU ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS SEQRES 3 B 98 LYS ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP SEQRES 4 B 98 LYS MSE GLY MSE GLY GLN SER GLY VAL GLY ALA LEU PHE SEQRES 5 B 98 ASN GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU SEQRES 6 B 98 LEU ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER SEQRES 7 B 98 PRO SER ILE ALA ARG GLU ILE TYR GLU MSE TYR GLU ALA SEQRES 8 B 98 VAL HIS HIS HIS HIS HIS HIS MODRES 1RIO MSE A 41 MET SELENOMETHIONINE MODRES 1RIO MSE A 43 MET SELENOMETHIONINE MODRES 1RIO MSE A 88 MET SELENOMETHIONINE MODRES 1RIO MSE B 41 MET SELENOMETHIONINE MODRES 1RIO MSE B 43 MET SELENOMETHIONINE MODRES 1RIO MSE B 88 MET SELENOMETHIONINE HET MSE A 41 8 HET MSE A 43 8 HET MSE A 88 8 HET MSE B 41 8 HET MSE B 43 8 HET MSE B 88 8 HET CA A 301 1 HET MPD A 201 8 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 4 MSE 6(C5 H11 N O2 SE) FORMUL 6 CA CA 2+ FORMUL 7 MPD C6 H14 O2 FORMUL 8 HOH *176(H2 O) HELIX 1 1 SER H 366 LYS H 371 1 6 HELIX 2 2 SER H 377 LYS H 388 1 12 HELIX 3 3 THR H 397 GLY H 406 1 10 HELIX 4 4 THR H 408 LYS H 424 1 17 HELIX 5 5 THR A 9 GLY A 31 1 23 HELIX 6 6 SER A 33 GLY A 42 1 10 HELIX 7 7 GLY A 44 ASN A 53 1 10 HELIX 8 8 ASN A 59 LYS A 71 1 13 HELIX 9 9 SER A 73 PHE A 77 5 5 HELIX 10 10 SER A 78 HIS A 94 1 17 HELIX 11 11 THR B 9 GLY B 31 1 23 HELIX 12 12 SER B 33 MSE B 41 1 9 HELIX 13 13 GLY B 44 ASN B 53 1 10 HELIX 14 14 ASN B 59 LYS B 71 1 13 HELIX 15 15 SER B 73 PHE B 77 5 5 HELIX 16 16 SER B 78 ALA B 91 1 14 LINK C LYS A 40 N MSE A 41 1555 1555 1.34 LINK C MSE A 41 N GLY A 42 1555 1555 1.33 LINK C GLY A 42 N MSE A 43 1555 1555 1.33 LINK C MSE A 43 N GLY A 44 1555 1555 1.32 LINK C GLU A 87 N MSE A 88 1555 1555 1.31 LINK C MSE A 88 N TYR A 89 1555 1555 1.33 LINK CA CA A 301 O HOH A 306 1555 1555 2.89 LINK CA CA A 301 O HOH A 311 1555 1555 3.39 LINK CA CA A 301 O HOH T 44 1555 1555 2.57 LINK CA CA A 301 O HOH T 45 1555 1555 2.79 LINK CA CA A 301 O GLY A 42 1555 1555 2.20 LINK C LYS B 40 N MSE B 41 1555 1555 1.33 LINK C MSE B 41 N GLY B 42 1555 1555 1.31 LINK C GLY B 42 N MSE B 43 1555 1555 1.33 LINK C MSE B 43 N GLY B 44 1555 1555 1.33 LINK C GLU B 87 N MSE B 88 1555 1555 1.31 LINK C MSE B 88 N TYR B 89 1555 1555 1.33 SITE 1 AC1 4 GLY A 42 HOH A 306 HOH T 44 HOH T 45 SITE 1 AC2 3 GLU A 75 ALA A 82 HOH A 326 CRYST1 47.256 71.269 77.199 90.00 91.34 90.00 P 1 21 1 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 0.021161 0.000000 0.000495 0.00000 SCALE2 0.000000 0.014031 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012957 0.00000