HEADER TRANSCRIPTION 29-MAY-12 4FE4 TITLE CRYSTAL STRUCTURE OF APO E. COLI XYLR COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE OPERON REGULATORY PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: XYLR, B3569, JW3541; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DAUIXIE, D-XYLOSE, XYLR, DNA LOOPING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER,L.NI REVDAT 4 28-FEB-24 4FE4 1 REMARK REVDAT 3 06-MAR-13 4FE4 1 JRNL REVDAT 2 02-JAN-13 4FE4 1 JRNL REVDAT 1 12-DEC-12 4FE4 0 JRNL AUTH L.NI,N.K.TONTHAT,N.CHINNAM,M.A.SCHUMACHER JRNL TITL STRUCTURES OF THE ESCHERICHIA COLI TRANSCRIPTION ACTIVATOR JRNL TITL 2 AND REGULATOR OF DIAUXIE, XYLR: AN ARAC DNA-BINDING FAMILY JRNL TITL 3 MEMBER WITH A LACI/GALR LIGAND-BINDING DOMAIN. JRNL REF NUCLEIC ACIDS RES. V. 41 1998 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23241389 JRNL DOI 10.1093/NAR/GKS1207 REMARK 2 REMARK 2 RESOLUTION. 3.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 107.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4722025.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 22149 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) : 0.289 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1222 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.56 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1869 REMARK 3 BIN R VALUE (WORKING SET) : 0.4660 REMARK 3 BIN FREE R VALUE : 0.4660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 134 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9189 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 117.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 22.51000 REMARK 3 B22 (A**2) : 22.51000 REMARK 3 B33 (A**2) : -45.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.63 REMARK 3 ESD FROM SIGMAA (A) : 1.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.74 REMARK 3 ESD FROM C-V SIGMAA (A) : 1.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.980 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) : 3.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.230 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.380 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.980 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 52.55 REMARK 3 REMARK 3 NCS MODEL : NONE 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4FE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22188 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 107.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 126.53333 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 63.26667 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 63.26667 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 126.53333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 215.64033 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.26667 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 ASP A 44 REMARK 465 ALA A 47 REMARK 465 ARG A 48 REMARK 465 ILE A 49 REMARK 465 ASP A 50 REMARK 465 LYS A 51 REMARK 465 ILE A 52 REMARK 465 LYS A 53 REMARK 465 ASP A 54 REMARK 465 VAL A 390 REMARK 465 MET A 391 REMARK 465 LEU A 392 REMARK 465 ASP B 44 REMARK 465 ALA B 47 REMARK 465 ARG B 48 REMARK 465 ILE B 49 REMARK 465 ASP B 50 REMARK 465 LYS B 51 REMARK 465 ILE B 52 REMARK 465 LYS B 53 REMARK 465 ASP B 54 REMARK 465 VAL B 390 REMARK 465 MET B 391 REMARK 465 LEU B 392 REMARK 465 ASP C 44 REMARK 465 ALA C 47 REMARK 465 ARG C 48 REMARK 465 ILE C 49 REMARK 465 ASP C 50 REMARK 465 LYS C 51 REMARK 465 ILE C 52 REMARK 465 LYS C 53 REMARK 465 ASP C 54 REMARK 465 VAL C 390 REMARK 465 MET C 391 REMARK 465 LEU C 392 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 LYS A 16 CG CD CE NZ REMARK 470 LYS B 16 CG CD CE NZ REMARK 470 LYS C 16 CG CD CE NZ 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 NH2 ARG B 225 O GLU B 389 1.94 REMARK 500 O LYS B 320 CE LYS B 323 2.01 REMARK 500 O GLU A 382 CG2 VAL A 386 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS C 320 NZ LYS C 320 6554 1.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU C 140 CG GLU C 140 CD -0.104 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 GLU A 325 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 VAL B 235 CB - CA - C ANGL. DEV. = -14.0 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 PHE A 2 84.49 -59.83 REMARK 500 THR A 3 19.70 -159.79 REMARK 500 LYS A 4 84.73 -66.11 REMARK 500 ARG A 7 84.21 -58.47 REMARK 500 ASN A 15 -71.35 -43.53 REMARK 500 LEU A 56 -83.98 -48.11 REMARK 500 ASP A 75 -36.31 -142.48 REMARK 500 PRO A 79 106.21 -52.70 REMARK 500 SER A 86 175.08 -53.14 REMARK 500 VAL A 96 152.74 159.29 REMARK 500 HIS A 97 107.59 -58.30 REMARK 500 ASN A 103 -72.34 -34.98 REMARK 500 VAL A 119 136.28 -2.81 REMARK 500 LEU A 127 145.82 -177.19 REMARK 500 GLU A 129 0.17 -64.99 REMARK 500 ALA A 148 4.61 -58.86 REMARK 500 GLU A 150 -160.09 -73.09 REMARK 500 LYS A 151 -60.82 -99.29 REMARK 500 ARG A 153 -165.24 -53.70 REMARK 500 GLU A 161 159.90 -46.00 REMARK 500 ALA A 163 79.65 -158.19 REMARK 500 PRO A 208 128.74 -29.48 REMARK 500 GLU A 211 -76.05 -40.47 REMARK 500 ILE A 216 133.77 -172.11 REMARK 500 ILE A 218 -74.63 -104.56 REMARK 500 ASP A 219 -32.43 -28.80 REMARK 500 ASN A 220 7.99 49.48 REMARK 500 GLU A 221 129.11 -39.39 REMARK 500 THR A 224 -77.98 -57.61 REMARK 500 ARG A 225 -18.33 -32.71 REMARK 500 SER A 228 163.40 167.86 REMARK 500 GLN A 237 174.85 -49.07 REMARK 500 LEU A 261 108.90 -28.34 REMARK 500 VAL A 269 -88.46 -51.83 REMARK 500 ARG A 270 -156.79 -122.65 REMARK 500 SER A 276 -12.28 -42.34 REMARK 500 ASP A 278 69.60 -50.94 REMARK 500 ARG A 280 39.11 -140.87 REMARK 500 SER A 281 42.60 32.34 REMARK 500 ILE A 288 -78.01 -57.95 REMARK 500 ALA A 298 -82.62 -36.20 REMARK 500 CYS A 299 14.37 -61.67 REMARK 500 ASP A 305 -54.69 -29.64 REMARK 500 LEU A 308 -79.09 -59.12 REMARK 500 SER A 314 170.42 -51.28 REMARK 500 GLU A 328 105.57 172.78 REMARK 500 THR A 329 171.85 -48.61 REMARK 500 LEU A 345 35.74 -73.48 REMARK 500 LEU A 346 -70.97 -145.44 REMARK 500 SER A 348 55.19 -116.24 REMARK 500 REMARK 500 THIS ENTRY HAS 156 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 4FE4 A 1 392 UNP P0ACI3 XYLR_ECOLI 1 392 DBREF 4FE4 B 1 392 UNP P0ACI3 XYLR_ECOLI 1 392 DBREF 4FE4 C 1 392 UNP P0ACI3 XYLR_ECOLI 1 392 SEQRES 1 A 392 MET PHE THR LYS ARG HIS ARG ILE THR LEU LEU PHE ASN SEQRES 2 A 392 ALA ASN LYS ALA TYR ASP ARG GLN VAL VAL GLU GLY VAL SEQRES 3 A 392 GLY GLU TYR LEU GLN ALA SER GLN SER GLU TRP ASP ILE SEQRES 4 A 392 PHE ILE GLU GLU ASP PHE ARG ALA ARG ILE ASP LYS ILE SEQRES 5 A 392 LYS ASP TRP LEU GLY ASP GLY VAL ILE ALA ASP PHE ASP SEQRES 6 A 392 ASP LYS GLN ILE GLU GLN ALA LEU ALA ASP VAL ASP VAL SEQRES 7 A 392 PRO ILE VAL GLY VAL GLY GLY SER TYR HIS LEU ALA GLU SEQRES 8 A 392 SER TYR PRO PRO VAL HIS TYR ILE ALA THR ASP ASN TYR SEQRES 9 A 392 ALA LEU VAL GLU SER ALA PHE LEU HIS LEU LYS GLU LYS SEQRES 10 A 392 GLY VAL ASN ARG PHE ALA PHE TYR GLY LEU PRO GLU SER SEQRES 11 A 392 SER GLY LYS ARG TRP ALA THR GLU ARG GLU TYR ALA PHE SEQRES 12 A 392 ARG GLN LEU VAL ALA GLU GLU LYS TYR ARG GLY VAL VAL SEQRES 13 A 392 TYR GLN GLY LEU GLU THR ALA PRO GLU ASN TRP GLN HIS SEQRES 14 A 392 ALA GLN ASN ARG LEU ALA ASP TRP LEU GLN THR LEU PRO SEQRES 15 A 392 PRO GLN THR GLY ILE ILE ALA VAL THR ASP ALA ARG ALA SEQRES 16 A 392 ARG HIS ILE LEU GLN VAL CYS GLU HIS LEU HIS ILE PRO SEQRES 17 A 392 VAL PRO GLU LYS LEU CYS VAL ILE GLY ILE ASP ASN GLU SEQRES 18 A 392 GLU LEU THR ARG TYR LEU SER ARG VAL ALA LEU SER SER SEQRES 19 A 392 VAL ALA GLN GLY ALA ARG GLN MET GLY TYR GLN ALA ALA SEQRES 20 A 392 LYS LEU LEU HIS ARG LEU LEU ASP LYS GLU GLU MET PRO SEQRES 21 A 392 LEU GLN ARG ILE LEU VAL PRO PRO VAL ARG VAL ILE GLU SEQRES 22 A 392 ARG ARG SER THR ASP TYR ARG SER LEU THR ASP PRO ALA SEQRES 23 A 392 VAL ILE GLN ALA MET HIS TYR ILE ARG ASN HIS ALA CYS SEQRES 24 A 392 LYS GLY ILE LYS VAL ASP GLN VAL LEU ASP ALA VAL GLY SEQRES 25 A 392 ILE SER ARG SER ASN LEU GLU LYS ARG PHE LYS GLU GLU SEQRES 26 A 392 VAL GLY GLU THR ILE HIS ALA MET ILE HIS ALA GLU LYS SEQRES 27 A 392 LEU GLU LYS ALA ARG SER LEU LEU ILE SER THR THR LEU SEQRES 28 A 392 SER ILE ASN GLU ILE SER GLN MET CYS GLY TYR PRO SER SEQRES 29 A 392 LEU GLN TYR PHE TYR SER VAL PHE LYS LYS ALA TYR ASP SEQRES 30 A 392 THR THR PRO LYS GLU TYR ARG ASP VAL ASN SER GLU VAL SEQRES 31 A 392 MET LEU SEQRES 1 B 392 MET PHE THR LYS ARG HIS ARG ILE THR LEU LEU PHE ASN SEQRES 2 B 392 ALA ASN LYS ALA TYR ASP ARG GLN VAL VAL GLU GLY VAL SEQRES 3 B 392 GLY GLU TYR LEU GLN ALA SER GLN SER GLU TRP ASP ILE SEQRES 4 B 392 PHE ILE GLU GLU ASP PHE ARG ALA ARG ILE ASP LYS ILE SEQRES 5 B 392 LYS ASP TRP LEU GLY ASP GLY VAL ILE ALA ASP PHE ASP SEQRES 6 B 392 ASP LYS GLN ILE GLU GLN ALA LEU ALA ASP VAL ASP VAL SEQRES 7 B 392 PRO ILE VAL GLY VAL GLY GLY SER TYR HIS LEU ALA GLU SEQRES 8 B 392 SER TYR PRO PRO VAL HIS TYR ILE ALA THR ASP ASN TYR SEQRES 9 B 392 ALA LEU VAL GLU SER ALA PHE LEU HIS LEU LYS GLU LYS SEQRES 10 B 392 GLY VAL ASN ARG PHE ALA PHE TYR GLY LEU PRO GLU SER SEQRES 11 B 392 SER GLY LYS ARG TRP ALA THR GLU ARG GLU TYR ALA PHE SEQRES 12 B 392 ARG GLN LEU VAL ALA GLU GLU LYS TYR ARG GLY VAL VAL SEQRES 13 B 392 TYR GLN GLY LEU GLU THR ALA PRO GLU ASN TRP GLN HIS SEQRES 14 B 392 ALA GLN ASN ARG LEU ALA ASP TRP LEU GLN THR LEU PRO SEQRES 15 B 392 PRO GLN THR GLY ILE ILE ALA VAL THR ASP ALA ARG ALA SEQRES 16 B 392 ARG HIS ILE LEU GLN VAL CYS GLU HIS LEU HIS ILE PRO SEQRES 17 B 392 VAL PRO GLU LYS LEU CYS VAL ILE GLY ILE ASP ASN GLU SEQRES 18 B 392 GLU LEU THR ARG TYR LEU SER ARG VAL ALA LEU SER SER SEQRES 19 B 392 VAL ALA GLN GLY ALA ARG GLN MET GLY TYR GLN ALA ALA SEQRES 20 B 392 LYS LEU LEU HIS ARG LEU LEU ASP LYS GLU GLU MET PRO SEQRES 21 B 392 LEU GLN ARG ILE LEU VAL PRO PRO VAL ARG VAL ILE GLU SEQRES 22 B 392 ARG ARG SER THR ASP TYR ARG SER LEU THR ASP PRO ALA SEQRES 23 B 392 VAL ILE GLN ALA MET HIS TYR ILE ARG ASN HIS ALA CYS SEQRES 24 B 392 LYS GLY ILE LYS VAL ASP GLN VAL LEU ASP ALA VAL GLY SEQRES 25 B 392 ILE SER ARG SER ASN LEU GLU LYS ARG PHE LYS GLU GLU SEQRES 26 B 392 VAL GLY GLU THR ILE HIS ALA MET ILE HIS ALA GLU LYS SEQRES 27 B 392 LEU GLU LYS ALA ARG SER LEU LEU ILE SER THR THR LEU SEQRES 28 B 392 SER ILE ASN GLU ILE SER GLN MET CYS GLY TYR PRO SER SEQRES 29 B 392 LEU GLN TYR PHE TYR SER VAL PHE LYS LYS ALA TYR ASP SEQRES 30 B 392 THR THR PRO LYS GLU TYR ARG ASP VAL ASN SER GLU VAL SEQRES 31 B 392 MET LEU SEQRES 1 C 392 MET PHE THR LYS ARG HIS ARG ILE THR LEU LEU PHE ASN SEQRES 2 C 392 ALA ASN LYS ALA TYR ASP ARG GLN VAL VAL GLU GLY VAL SEQRES 3 C 392 GLY GLU TYR LEU GLN ALA SER GLN SER GLU TRP ASP ILE SEQRES 4 C 392 PHE ILE GLU GLU ASP PHE ARG ALA ARG ILE ASP LYS ILE SEQRES 5 C 392 LYS ASP TRP LEU GLY ASP GLY VAL ILE ALA ASP PHE ASP SEQRES 6 C 392 ASP LYS GLN ILE GLU GLN ALA LEU ALA ASP VAL ASP VAL SEQRES 7 C 392 PRO ILE VAL GLY VAL GLY GLY SER TYR HIS LEU ALA GLU SEQRES 8 C 392 SER TYR PRO PRO VAL HIS TYR ILE ALA THR ASP ASN TYR SEQRES 9 C 392 ALA LEU VAL GLU SER ALA PHE LEU HIS LEU LYS GLU LYS SEQRES 10 C 392 GLY VAL ASN ARG PHE ALA PHE TYR GLY LEU PRO GLU SER SEQRES 11 C 392 SER GLY LYS ARG TRP ALA THR GLU ARG GLU TYR ALA PHE SEQRES 12 C 392 ARG GLN LEU VAL ALA GLU GLU LYS TYR ARG GLY VAL VAL SEQRES 13 C 392 TYR GLN GLY LEU GLU THR ALA PRO GLU ASN TRP GLN HIS SEQRES 14 C 392 ALA GLN ASN ARG LEU ALA ASP TRP LEU GLN THR LEU PRO SEQRES 15 C 392 PRO GLN THR GLY ILE ILE ALA VAL THR ASP ALA ARG ALA SEQRES 16 C 392 ARG HIS ILE LEU GLN VAL CYS GLU HIS LEU HIS ILE PRO SEQRES 17 C 392 VAL PRO GLU LYS LEU CYS VAL ILE GLY ILE ASP ASN GLU SEQRES 18 C 392 GLU LEU THR ARG TYR LEU SER ARG VAL ALA LEU SER SER SEQRES 19 C 392 VAL ALA GLN GLY ALA ARG GLN MET GLY TYR GLN ALA ALA SEQRES 20 C 392 LYS LEU LEU HIS ARG LEU LEU ASP LYS GLU GLU MET PRO SEQRES 21 C 392 LEU GLN ARG ILE LEU VAL PRO PRO VAL ARG VAL ILE GLU SEQRES 22 C 392 ARG ARG SER THR ASP TYR ARG SER LEU THR ASP PRO ALA SEQRES 23 C 392 VAL ILE GLN ALA MET HIS TYR ILE ARG ASN HIS ALA CYS SEQRES 24 C 392 LYS GLY ILE LYS VAL ASP GLN VAL LEU ASP ALA VAL GLY SEQRES 25 C 392 ILE SER ARG SER ASN LEU GLU LYS ARG PHE LYS GLU GLU SEQRES 26 C 392 VAL GLY GLU THR ILE HIS ALA MET ILE HIS ALA GLU LYS SEQRES 27 C 392 LEU GLU LYS ALA ARG SER LEU LEU ILE SER THR THR LEU SEQRES 28 C 392 SER ILE ASN GLU ILE SER GLN MET CYS GLY TYR PRO SER SEQRES 29 C 392 LEU GLN TYR PHE TYR SER VAL PHE LYS LYS ALA TYR ASP SEQRES 30 C 392 THR THR PRO LYS GLU TYR ARG ASP VAL ASN SER GLU VAL SEQRES 31 C 392 MET LEU HELIX 1 1 LYS A 16 GLN A 34 1 19 HELIX 2 2 ASP A 66 GLN A 71 1 6 HELIX 3 3 LEU A 89 TYR A 93 5 5 HELIX 4 4 ASP A 102 GLY A 118 1 17 HELIX 5 5 ARG A 134 ALA A 148 1 15 HELIX 6 6 ASN A 166 LEU A 181 1 16 HELIX 7 7 ALA A 193 LEU A 205 1 13 HELIX 8 8 GLY A 238 ASP A 255 1 18 HELIX 9 9 ARG A 274 ASP A 278 5 5 HELIX 10 10 ASP A 284 ALA A 298 1 15 HELIX 11 11 CYS A 299 GLY A 301 5 3 HELIX 12 12 LYS A 303 VAL A 311 1 9 HELIX 13 13 SER A 314 VAL A 326 1 13 HELIX 14 14 THR A 329 SER A 348 1 20 HELIX 15 15 ASN A 354 MET A 359 1 6 HELIX 16 16 LEU A 365 LYS A 374 1 10 HELIX 17 17 THR A 379 ASN A 387 1 9 HELIX 18 18 LYS B 16 SER B 33 1 18 HELIX 19 19 ASP B 66 LEU B 73 1 8 HELIX 20 20 ASP B 102 LYS B 115 1 14 HELIX 21 21 LYS B 133 ALA B 148 1 16 HELIX 22 22 ASN B 166 GLN B 179 1 14 HELIX 23 23 THR B 191 GLU B 203 1 13 HELIX 24 24 LEU B 223 LEU B 227 5 5 HELIX 25 25 GLY B 238 ASP B 255 1 18 HELIX 26 26 ALA B 286 ALA B 298 1 13 HELIX 27 27 CYS B 299 GLY B 301 5 3 HELIX 28 28 LYS B 303 ASP B 309 1 7 HELIX 29 29 SER B 314 VAL B 326 1 13 HELIX 30 30 MET B 333 SER B 348 1 16 HELIX 31 31 SER B 352 GLY B 361 1 10 HELIX 32 32 SER B 364 TYR B 376 1 13 HELIX 33 33 THR B 379 SER B 388 1 10 HELIX 34 34 LYS C 16 GLY C 27 1 12 HELIX 35 35 GLU C 28 GLN C 34 1 7 HELIX 36 36 ASP C 66 ALA C 74 1 9 HELIX 37 37 LEU C 89 TYR C 93 5 5 HELIX 38 38 ASP C 102 GLY C 118 1 17 HELIX 39 39 LYS C 133 ALA C 148 1 16 HELIX 40 40 ASN C 166 GLN C 179 1 14 HELIX 41 41 ALA C 193 CYS C 202 1 10 HELIX 42 42 GLU C 221 SER C 228 1 8 HELIX 43 43 GLY C 238 LEU C 254 1 17 HELIX 44 44 ARG C 274 ASP C 278 5 5 HELIX 45 45 ASP C 284 ARG C 295 1 12 HELIX 46 46 HIS C 297 GLY C 301 5 5 HELIX 47 47 LEU C 318 LYS C 320 5 3 HELIX 48 48 ARG C 321 VAL C 326 1 6 HELIX 49 49 LEU C 339 SER C 348 1 10 HELIX 50 50 ILE C 353 CYS C 360 1 8 HELIX 51 51 SER C 364 VAL C 371 1 8 HELIX 52 52 THR C 379 ASP C 385 1 7 SHEET 1 A 4 ILE A 8 LEU A 11 0 SHEET 2 A 4 GLY A 59 ASP A 63 1 O ILE A 61 N LEU A 11 SHEET 3 A 4 ILE A 80 VAL A 83 1 O VAL A 83 N ALA A 62 SHEET 4 A 4 HIS A 97 TYR A 98 1 O HIS A 97 N GLY A 82 SHEET 1 B 2 ALA A 100 THR A 101 0 SHEET 2 B 2 LEU A 265 VAL A 266 1 O VAL A 266 N ALA A 100 SHEET 1 C 4 GLY A 154 TYR A 157 0 SHEET 2 C 4 PHE A 122 TYR A 125 1 N PHE A 124 O VAL A 155 SHEET 3 C 4 THR A 185 ALA A 189 1 O ILE A 188 N TYR A 125 SHEET 4 C 4 LEU A 213 ILE A 216 1 O CYS A 214 N ILE A 187 SHEET 1 D 2 SER A 234 VAL A 235 0 SHEET 2 D 2 VAL A 271 ILE A 272 -1 O ILE A 272 N SER A 234 SHEET 1 E 3 TRP B 37 ILE B 41 0 SHEET 2 E 3 HIS B 6 LEU B 11 1 N ILE B 8 O PHE B 40 SHEET 3 E 3 GLY B 59 ALA B 62 1 O GLY B 59 N THR B 9 SHEET 1 F 4 TYR B 157 GLN B 158 0 SHEET 2 F 4 PHE B 122 GLY B 126 1 N GLY B 126 O TYR B 157 SHEET 3 F 4 THR B 185 ALA B 189 1 O ILE B 188 N TYR B 125 SHEET 4 F 4 LEU B 213 ILE B 216 1 O ILE B 216 N ILE B 187 SHEET 1 G 2 SER B 234 VAL B 235 0 SHEET 2 G 2 VAL B 271 ILE B 272 -1 O ILE B 272 N SER B 234 SHEET 1 H 6 TRP C 37 ILE C 41 0 SHEET 2 H 6 HIS C 6 LEU C 11 1 N HIS C 6 O ASP C 38 SHEET 3 H 6 VAL C 60 ASP C 63 1 O ILE C 61 N LEU C 11 SHEET 4 H 6 ILE C 80 GLY C 85 1 O VAL C 83 N ALA C 62 SHEET 5 H 6 HIS C 97 THR C 101 1 O THR C 101 N GLY C 84 SHEET 6 H 6 ARG C 263 VAL C 266 1 O ILE C 264 N ALA C 100 SHEET 1 I 4 TYR C 157 GLN C 158 0 SHEET 2 I 4 ARG C 121 GLY C 126 1 N GLY C 126 O TYR C 157 SHEET 3 I 4 THR C 185 ALA C 189 1 O GLY C 186 N ALA C 123 SHEET 4 I 4 CYS C 214 ILE C 216 1 O ILE C 216 N ALA C 189 CISPEP 1 VAL A 209 PRO A 210 0 -0.08 CISPEP 2 VAL B 209 PRO B 210 0 0.91 CISPEP 3 VAL C 209 PRO C 210 0 -0.57 CRYST1 124.500 124.500 189.800 90.00 90.00 120.00 P 32 2 1 18 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 0.008032 0.004637 0.000000 0.00000 SCALE2 0.000000 0.009275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005269 0.00000