PDB Short entry for 1BDF HEADER NUCLEOTIDYLTRANSFERASE 08-MAY-98 1BDF TITLE STRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE ALPHA SUBUNIT N-TERMINAL TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE ALPHA SUBUNIT; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN RESIDUES 1-235; COMPND 5 EC: 2.7.7.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELL_LINE: BL-21; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: BL-21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15-B KEYWDS NUCLEOTIDYLTRANSFERASE, RNAP, ALPHA, ASSEMBLE EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHANG,S.A.DARST REVDAT 4 07-FEB-24 1BDF 1 REMARK REVDAT 3 03-NOV-21 1BDF 1 SEQADV REVDAT 2 24-FEB-09 1BDF 1 VERSN REVDAT 1 11-MAY-99 1BDF 0 JRNL AUTH G.ZHANG,S.A.DARST JRNL TITL STRUCTURE OF THE ESCHERICHIA COLI RNA POLYMERASE ALPHA JRNL TITL 2 SUBUNIT AMINO-TERMINAL DOMAIN. JRNL REF SCIENCE V. 281 262 1998 JRNL REFN ISSN 0036-8075 JRNL PMID 9657722 JRNL DOI 10.1126/SCIENCE.281.5374.262 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.4 REMARK 3 NUMBER OF REFLECTIONS : 23574 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 SET) : 0.225 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1178 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1314 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 70 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.740 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.500 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; 2.000 REMARK 3 REMARK 3 NCS MODEL : RESTRAINTS REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.75 REMARK 200 NUMBER OF CRYSTALS USED : 20 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27865 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.05700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 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 (%) : 52.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : 0.19000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: PHASES, X-PLOR 3.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.75 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 58.60000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.83273 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 116.80000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 58.60000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 33.83273 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 116.80000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 58.60000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 33.83273 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 116.80000 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 58.60000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 33.83273 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 116.80000 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 58.60000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 33.83273 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 116.80000 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 58.60000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 33.83273 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 116.80000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 67.66545 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 233.60000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 67.66545 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 233.60000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 67.66545 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 233.60000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 67.66545 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 233.60000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 67.66545 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 233.60000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 67.66545 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 233.60000 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: TETRAMERIC 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 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 HIS A 160 REMARK 465 SER A 161 REMARK 465 GLU A 162 REMARK 465 GLU A 163 REMARK 465 ASP A 164 REMARK 465 ASP A 233 REMARK 465 LEU A 234 REMARK 465 ARG A 235 REMARK 465 SER B 161 REMARK 465 GLU B 162 REMARK 465 GLU B 163 REMARK 465 SER C 161 REMARK 465 GLU C 162 REMARK 465 GLU C 163 REMARK 465 ASP C 164 REMARK 465 GLU C 165 REMARK 465 ARG C 166 REMARK 465 PRO C 167 REMARK 465 SER D 161 REMARK 465 GLU D 162 REMARK 465 GLU D 163 REMARK 465 ASP D 164 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 GLN A 2 CG CD OE1 NE2 REMARK 470 THR A 157 OG1 CG2 REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 159 CG1 CG2 CD1 REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 ARG A 166 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 167 CG CD REMARK 470 HIS B 66 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 67 CG CD OE1 OE2 REMARK 470 ILE B 159 CG1 CG2 CD1 REMARK 470 HIS B 160 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 164 CG OD1 OD2 REMARK 470 ILE B 168 CG1 CG2 CD1 REMARK 470 ARG B 170 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 2 CG CD OE1 NE2 REMARK 470 THR C 157 OG1 CG2 REMARK 470 ARG C 158 CG CD NE CZ NH1 NH2 REMARK 470 ILE C 159 CG1 CG2 CD1 REMARK 470 HIS C 160 CG ND1 CD2 CE1 NE2 REMARK 470 ILE C 168 CG1 CG2 CD1 REMARK 470 ARG C 170 CG CD NE CZ NH1 NH2 REMARK 470 VAL C 192 CG1 CG2 REMARK 470 GLN C 194 CG CD OE1 NE2 REMARK 470 GLN D 2 CG CD OE1 NE2 REMARK 470 THR D 157 OG1 CG2 REMARK 470 ARG D 158 CG CD NE CZ NH1 NH2 REMARK 470 ILE D 159 CG1 CG2 CD1 REMARK 470 HIS D 160 CG ND1 CD2 CE1 NE2 REMARK 470 GLU D 165 CG CD OE1 OE2 REMARK 470 ARG D 166 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 191 CG CD NE CZ NH1 NH2 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 VAL A 5 REMARK 475 ARG C 158 REMARK 475 ILE C 159 REMARK 475 HIS C 160 REMARK 475 ILE D 159 REMARK 475 HIS D 160 REMARK 475 ARG D 191 REMARK 475 VAL D 192 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR C 157 O REMARK 480 GLU D 193 C O 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 CYS D 131 CB CYS D 131 SG -0.105 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 PRO A 154 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 219 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 219 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 219 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 219 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG C 219 CD - NE - CZ ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG C 219 NE - CZ - NH1 ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG C 219 NE - CZ - NH2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG D 219 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG D 219 NE - CZ - NH2 ANGL. DEV. = -3.4 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 SER A 4 176.74 59.47 REMARK 500 VAL A 5 97.64 94.74 REMARK 500 THR A 6 106.15 47.92 REMARK 500 GLU A 7 -25.24 -152.32 REMARK 500 SER A 20 -168.23 -165.77 REMARK 500 GLU A 29 -73.63 -99.06 REMARK 500 PRO A 30 100.37 -53.05 REMARK 500 SER A 49 -19.59 -163.29 REMARK 500 PRO A 52 -108.41 -63.91 REMARK 500 GLN A 93 -94.13 -41.40 REMARK 500 GLU A 97 124.63 -173.47 REMARK 500 HIS A 117 104.74 -54.33 REMARK 500 PRO A 154 162.47 -47.82 REMARK 500 ARG A 158 -30.35 -139.41 REMARK 500 ARG A 166 -82.67 -96.59 REMARK 500 ILE A 168 -139.73 -84.67 REMARK 500 LEU A 171 139.17 17.42 REMARK 500 CYS A 176 75.00 -112.44 REMARK 500 GLU A 188 130.82 31.10 REMARK 500 GLU A 193 45.20 -74.28 REMARK 500 GLN A 194 -68.55 -127.05 REMARK 500 ARG A 195 -150.50 -119.13 REMARK 500 THR A 196 -23.97 -142.74 REMARK 500 SER B 4 112.19 71.48 REMARK 500 THR B 6 -87.72 -64.19 REMARK 500 SER B 20 -168.52 -164.71 REMARK 500 GLU B 29 -75.08 -99.16 REMARK 500 PRO B 30 102.29 -52.31 REMARK 500 SER B 49 -19.91 -164.19 REMARK 500 PRO B 52 -112.11 -64.30 REMARK 500 GLN B 93 -88.76 -41.45 REMARK 500 LYS B 95 131.65 179.26 REMARK 500 GLU B 97 123.97 -173.34 REMARK 500 HIS B 117 103.39 -54.02 REMARK 500 THR B 157 34.53 -82.44 REMARK 500 ARG B 158 12.54 -143.10 REMARK 500 GLU B 165 -79.70 -152.27 REMARK 500 ARG B 170 102.80 -52.88 REMARK 500 CYS B 176 73.07 -109.54 REMARK 500 GLU B 188 134.67 32.08 REMARK 500 ARG B 191 63.59 -60.33 REMARK 500 GLN B 194 -57.35 -120.99 REMARK 500 ARG B 195 175.95 -52.72 REMARK 500 THR B 196 -1.33 -152.82 REMARK 500 ASP B 233 -99.51 -157.50 REMARK 500 LEU B 234 75.16 47.06 REMARK 500 SER C 4 -40.34 -160.42 REMARK 500 GLU C 7 28.65 -158.47 REMARK 500 PHE C 8 -120.83 -121.99 REMARK 500 LEU C 9 65.75 67.04 REMARK 500 REMARK 500 THIS ENTRY HAS 99 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1BDF A 1 235 UNP P0A7Z4 RPOA_ECOLI 1 235 DBREF 1BDF B 1 235 UNP P0A7Z4 RPOA_ECOLI 1 235 DBREF 1BDF C 1 235 UNP P0A7Z4 RPOA_ECOLI 1 235 DBREF 1BDF D 1 235 UNP P0A7Z4 RPOA_ECOLI 1 235 SEQADV 1BDF ALA A 45 UNP P0A7Z4 ARG 45 ENGINEERED MUTATION SEQADV 1BDF ALA B 45 UNP P0A7Z4 ARG 45 ENGINEERED MUTATION SEQADV 1BDF ALA C 45 UNP P0A7Z4 ARG 45 ENGINEERED MUTATION SEQADV 1BDF ALA D 45 UNP P0A7Z4 ARG 45 ENGINEERED MUTATION SEQRES 1 A 235 MET GLN GLY SER VAL THR GLU PHE LEU LYS PRO ARG LEU SEQRES 2 A 235 VAL ASP ILE GLU GLN VAL SER SER THR HIS ALA LYS VAL SEQRES 3 A 235 THR LEU GLU PRO LEU GLU ARG GLY PHE GLY HIS THR LEU SEQRES 4 A 235 GLY ASN ALA LEU ARG ALA ILE LEU LEU SER SER MET PRO SEQRES 5 A 235 GLY CYS ALA VAL THR GLU VAL GLU ILE ASP GLY VAL LEU SEQRES 6 A 235 HIS GLU TYR SER THR LYS GLU GLY VAL GLN GLU ASP ILE SEQRES 7 A 235 LEU GLU ILE LEU LEU ASN LEU LYS GLY LEU ALA VAL ARG SEQRES 8 A 235 VAL GLN GLY LYS ASP GLU VAL ILE LEU THR LEU ASN LYS SEQRES 9 A 235 SER GLY ILE GLY PRO VAL THR ALA ALA ASP ILE THR HIS SEQRES 10 A 235 ASP GLY ASP VAL GLU ILE VAL LYS PRO GLN HIS VAL ILE SEQRES 11 A 235 CYS HIS LEU THR ASP GLU ASN ALA SER ILE SER MET ARG SEQRES 12 A 235 ILE LYS VAL GLN ARG GLY ARG GLY TYR VAL PRO ALA SER SEQRES 13 A 235 THR ARG ILE HIS SER GLU GLU ASP GLU ARG PRO ILE GLY SEQRES 14 A 235 ARG LEU LEU VAL ASP ALA CYS TYR SER PRO VAL GLU ARG SEQRES 15 A 235 ILE ALA TYR ASN VAL GLU ALA ALA ARG VAL GLU GLN ARG SEQRES 16 A 235 THR ASP LEU ASP LYS LEU VAL ILE GLU MET GLU THR ASN SEQRES 17 A 235 GLY THR ILE ASP PRO GLU GLU ALA ILE ARG ARG ALA ALA SEQRES 18 A 235 THR ILE LEU ALA GLU GLN LEU GLU ALA PHE VAL ASP LEU SEQRES 19 A 235 ARG SEQRES 1 B 235 MET GLN GLY SER VAL THR GLU PHE LEU LYS PRO ARG LEU SEQRES 2 B 235 VAL ASP ILE GLU GLN VAL SER SER THR HIS ALA LYS VAL SEQRES 3 B 235 THR LEU GLU PRO LEU GLU ARG GLY PHE GLY HIS THR LEU SEQRES 4 B 235 GLY ASN ALA LEU ARG ALA ILE LEU LEU SER SER MET PRO SEQRES 5 B 235 GLY CYS ALA VAL THR GLU VAL GLU ILE ASP GLY VAL LEU SEQRES 6 B 235 HIS GLU TYR SER THR LYS GLU GLY VAL GLN GLU ASP ILE SEQRES 7 B 235 LEU GLU ILE LEU LEU ASN LEU LYS GLY LEU ALA VAL ARG SEQRES 8 B 235 VAL GLN GLY LYS ASP GLU VAL ILE LEU THR LEU ASN LYS SEQRES 9 B 235 SER GLY ILE GLY PRO VAL THR ALA ALA ASP ILE THR HIS SEQRES 10 B 235 ASP GLY ASP VAL GLU ILE VAL LYS PRO GLN HIS VAL ILE SEQRES 11 B 235 CYS HIS LEU THR ASP GLU ASN ALA SER ILE SER MET ARG SEQRES 12 B 235 ILE LYS VAL GLN ARG GLY ARG GLY TYR VAL PRO ALA SER SEQRES 13 B 235 THR ARG ILE HIS SER GLU GLU ASP GLU ARG PRO ILE GLY SEQRES 14 B 235 ARG LEU LEU VAL ASP ALA CYS TYR SER PRO VAL GLU ARG SEQRES 15 B 235 ILE ALA TYR ASN VAL GLU ALA ALA ARG VAL GLU GLN ARG SEQRES 16 B 235 THR ASP LEU ASP LYS LEU VAL ILE GLU MET GLU THR ASN SEQRES 17 B 235 GLY THR ILE ASP PRO GLU GLU ALA ILE ARG ARG ALA ALA SEQRES 18 B 235 THR ILE LEU ALA GLU GLN LEU GLU ALA PHE VAL ASP LEU SEQRES 19 B 235 ARG SEQRES 1 C 235 MET GLN GLY SER VAL THR GLU PHE LEU LYS PRO ARG LEU SEQRES 2 C 235 VAL ASP ILE GLU GLN VAL SER SER THR HIS ALA LYS VAL SEQRES 3 C 235 THR LEU GLU PRO LEU GLU ARG GLY PHE GLY HIS THR LEU SEQRES 4 C 235 GLY ASN ALA LEU ARG ALA ILE LEU LEU SER SER MET PRO SEQRES 5 C 235 GLY CYS ALA VAL THR GLU VAL GLU ILE ASP GLY VAL LEU SEQRES 6 C 235 HIS GLU TYR SER THR LYS GLU GLY VAL GLN GLU ASP ILE SEQRES 7 C 235 LEU GLU ILE LEU LEU ASN LEU LYS GLY LEU ALA VAL ARG SEQRES 8 C 235 VAL GLN GLY LYS ASP GLU VAL ILE LEU THR LEU ASN LYS SEQRES 9 C 235 SER GLY ILE GLY PRO VAL THR ALA ALA ASP ILE THR HIS SEQRES 10 C 235 ASP GLY ASP VAL GLU ILE VAL LYS PRO GLN HIS VAL ILE SEQRES 11 C 235 CYS HIS LEU THR ASP GLU ASN ALA SER ILE SER MET ARG SEQRES 12 C 235 ILE LYS VAL GLN ARG GLY ARG GLY TYR VAL PRO ALA SER SEQRES 13 C 235 THR ARG ILE HIS SER GLU GLU ASP GLU ARG PRO ILE GLY SEQRES 14 C 235 ARG LEU LEU VAL ASP ALA CYS TYR SER PRO VAL GLU ARG SEQRES 15 C 235 ILE ALA TYR ASN VAL GLU ALA ALA ARG VAL GLU GLN ARG SEQRES 16 C 235 THR ASP LEU ASP LYS LEU VAL ILE GLU MET GLU THR ASN SEQRES 17 C 235 GLY THR ILE ASP PRO GLU GLU ALA ILE ARG ARG ALA ALA SEQRES 18 C 235 THR ILE LEU ALA GLU GLN LEU GLU ALA PHE VAL ASP LEU SEQRES 19 C 235 ARG SEQRES 1 D 235 MET GLN GLY SER VAL THR GLU PHE LEU LYS PRO ARG LEU SEQRES 2 D 235 VAL ASP ILE GLU GLN VAL SER SER THR HIS ALA LYS VAL SEQRES 3 D 235 THR LEU GLU PRO LEU GLU ARG GLY PHE GLY HIS THR LEU SEQRES 4 D 235 GLY ASN ALA LEU ARG ALA ILE LEU LEU SER SER MET PRO SEQRES 5 D 235 GLY CYS ALA VAL THR GLU VAL GLU ILE ASP GLY VAL LEU SEQRES 6 D 235 HIS GLU TYR SER THR LYS GLU GLY VAL GLN GLU ASP ILE SEQRES 7 D 235 LEU GLU ILE LEU LEU ASN LEU LYS GLY LEU ALA VAL ARG SEQRES 8 D 235 VAL GLN GLY LYS ASP GLU VAL ILE LEU THR LEU ASN LYS SEQRES 9 D 235 SER GLY ILE GLY PRO VAL THR ALA ALA ASP ILE THR HIS SEQRES 10 D 235 ASP GLY ASP VAL GLU ILE VAL LYS PRO GLN HIS VAL ILE SEQRES 11 D 235 CYS HIS LEU THR ASP GLU ASN ALA SER ILE SER MET ARG SEQRES 12 D 235 ILE LYS VAL GLN ARG GLY ARG GLY TYR VAL PRO ALA SER SEQRES 13 D 235 THR ARG ILE HIS SER GLU GLU ASP GLU ARG PRO ILE GLY SEQRES 14 D 235 ARG LEU LEU VAL ASP ALA CYS TYR SER PRO VAL GLU ARG SEQRES 15 D 235 ILE ALA TYR ASN VAL GLU ALA ALA ARG VAL GLU GLN ARG SEQRES 16 D 235 THR ASP LEU ASP LYS LEU VAL ILE GLU MET GLU THR ASN SEQRES 17 D 235 GLY THR ILE ASP PRO GLU GLU ALA ILE ARG ARG ALA ALA SEQRES 18 D 235 THR ILE LEU ALA GLU GLN LEU GLU ALA PHE VAL ASP LEU SEQRES 19 D 235 ARG FORMUL 5 HOH *239(H2 O) HELIX 1 1 PHE A 35 LEU A 47 1 13 HELIX 2 2 ILE A 78 LYS A 86 1 9 HELIX 3 3 ALA A 112 ASP A 114 5 3 HELIX 4 4 ALA A 155 THR A 157 5 3 HELIX 5 5 PRO A 213 ALA A 230 1 18 HELIX 6 6 PHE B 35 LEU B 47 1 13 HELIX 7 7 ILE B 78 LYS B 86 1 9 HELIX 8 8 ALA B 112 ASP B 114 5 3 HELIX 9 9 SER B 156 ARG B 158 5 3 HELIX 10 10 PRO B 213 VAL B 232 1 20 HELIX 11 11 PHE C 35 LEU C 47 1 13 HELIX 12 12 ILE C 78 LYS C 86 1 9 HELIX 13 13 ALA C 112 ASP C 114 5 3 HELIX 14 14 PRO C 213 PHE C 231 1 19 HELIX 15 15 PHE D 35 LEU D 47 1 13 HELIX 16 16 ILE D 78 LYS D 86 1 9 HELIX 17 17 ALA D 112 ASP D 114 5 3 HELIX 18 18 PRO D 213 PHE D 231 1 19 SHEET 1 A 4 LEU A 13 GLN A 18 0 SHEET 2 A 4 HIS A 23 LEU A 28 -1 N THR A 27 O VAL A 14 SHEET 3 A 4 LEU A 201 THR A 207 -1 N MET A 205 O ALA A 24 SHEET 4 A 4 VAL A 180 ASN A 186 -1 N ASN A 186 O VAL A 202 SHEET 1 B 3 GLU A 97 SER A 105 0 SHEET 2 B 3 SER A 139 ARG A 148 -1 N VAL A 146 O VAL A 98 SHEET 3 B 3 CYS A 54 ILE A 61 -1 N GLU A 60 O ARG A 143 SHEET 1 C 2 GLY A 108 THR A 111 0 SHEET 2 C 2 VAL A 129 LEU A 133 -1 N LEU A 133 O GLY A 108 SHEET 1 D 4 LEU B 13 GLN B 18 0 SHEET 2 D 4 HIS B 23 LEU B 28 -1 N THR B 27 O VAL B 14 SHEET 3 D 4 LEU B 201 THR B 207 -1 N MET B 205 O ALA B 24 SHEET 4 D 4 VAL B 180 ASN B 186 -1 N ASN B 186 O VAL B 202 SHEET 1 E 2 VAL B 90 VAL B 92 0 SHEET 2 E 2 VAL B 121 ILE B 123 -1 N GLU B 122 O ARG B 91 SHEET 1 F 3 GLU B 97 GLY B 106 0 SHEET 2 F 3 ALA B 138 ARG B 148 -1 N VAL B 146 O VAL B 98 SHEET 3 F 3 CYS B 54 ILE B 61 -1 N GLU B 60 O ARG B 143 SHEET 1 G 2 GLY B 108 THR B 111 0 SHEET 2 G 2 VAL B 129 LEU B 133 -1 N LEU B 133 O GLY B 108 SHEET 1 H 4 LEU C 13 GLN C 18 0 SHEET 2 H 4 HIS C 23 LEU C 28 -1 N THR C 27 O VAL C 14 SHEET 3 H 4 LEU C 201 THR C 207 -1 N MET C 205 O ALA C 24 SHEET 4 H 4 VAL C 180 ASN C 186 -1 N ASN C 186 O VAL C 202 SHEET 1 I 2 VAL C 90 VAL C 92 0 SHEET 2 I 2 VAL C 121 ILE C 123 -1 N GLU C 122 O ARG C 91 SHEET 1 J 3 GLU C 97 SER C 105 0 SHEET 2 J 3 SER C 139 ARG C 148 -1 N VAL C 146 O VAL C 98 SHEET 3 J 3 CYS C 54 ILE C 61 -1 N GLU C 60 O ARG C 143 SHEET 1 K 2 GLY C 108 THR C 111 0 SHEET 2 K 2 VAL C 129 LEU C 133 -1 N LEU C 133 O GLY C 108 SHEET 1 L 4 LEU D 13 GLN D 18 0 SHEET 2 L 4 HIS D 23 LEU D 28 -1 N THR D 27 O VAL D 14 SHEET 3 L 4 LEU D 201 THR D 207 -1 N MET D 205 O ALA D 24 SHEET 4 L 4 VAL D 180 ASN D 186 -1 N ASN D 186 O VAL D 202 SHEET 1 M 2 VAL D 90 VAL D 92 0 SHEET 2 M 2 VAL D 121 ILE D 123 -1 N GLU D 122 O ARG D 91 SHEET 1 N 3 GLU D 97 SER D 105 0 SHEET 2 N 3 SER D 139 ARG D 148 -1 N VAL D 146 O VAL D 98 SHEET 3 N 3 CYS D 54 ILE D 61 -1 N GLU D 60 O ARG D 143 SHEET 1 O 2 GLY D 108 THR D 111 0 SHEET 2 O 2 VAL D 129 LEU D 133 -1 N LEU D 133 O GLY D 108 CRYST1 117.200 117.200 350.400 90.00 90.00 120.00 H 3 2 72 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 0.008532 0.004926 0.000000 0.00000 SCALE2 0.000000 0.009852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002854 0.00000