HEADER TRANSCRIPTION 05-FEB-05 1YRX TITLE STRUCTURE OF A NOVEL PHOTORECEPTOR: THE BLUF DOMAIN OF APPA FROM TITLE 2 RHODOBACTER SPHAEROIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN RSPH03001874; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 17-133; COMPND 5 SYNONYM: APPA BLUF DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES 2.4.1; SOURCE 3 ORGANISM_TAXID: 272943; SOURCE 4 STRAIN: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FERREDOXIN-LIKE FOLD, FLAVIN BINDING, PHOTORECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.ANDERSON,V.DRAGNEA,S.MASUDA,J.YBE,K.MOFFAT,C.BAUER REVDAT 4 14-FEB-24 1YRX 1 REMARK SEQADV REVDAT 3 13-JUL-11 1YRX 1 VERSN REVDAT 2 24-FEB-09 1YRX 1 VERSN REVDAT 1 28-JUN-05 1YRX 0 JRNL AUTH S.ANDERSON,V.DRAGNEA,S.MASUDA,J.YBE,K.MOFFAT,C.BAUER JRNL TITL STRUCTURE OF A NOVEL PHOTORECEPTOR, THE BLUF DOMAIN OF APPA JRNL TITL 2 FROM RHODOBACTER SPHAEROIDES JRNL REF BIOCHEMISTRY V. 44 7998 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15924418 JRNL DOI 10.1021/BI0502691 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 25947 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1378 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 169 REMARK 3 SOLVENT ATOMS : 97 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000031861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9, 0.97939, 0.97962, 0.96113 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27558 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 24.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.06000 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, ETHYLENEGLYCOL, TRIS, DDMG, REMARK 280 PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.72650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.33550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.33550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.86325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.33550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.33550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 95.58975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.33550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.33550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.86325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.33550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.33550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 95.58975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.72650 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 300 REMARK: THE BIOLOGICAL UNIT IS A HOMODIMER, A+B CHAINS FORM ONE REMARK 300 HOMODIMER AND THE C CHAIN HALF OF A HOMODIMER 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 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.72650 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 -63.72650 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -63.72650 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 ARG A 131 REMARK 465 SER A 132 REMARK 465 LEU A 133 REMARK 465 ALA B 13 REMARK 465 GLY B 130 REMARK 465 ARG B 131 REMARK 465 SER B 132 REMARK 465 LEU B 133 REMARK 465 ALA C 13 REMARK 465 GLY C 14 REMARK 465 GLY C 130 REMARK 465 ARG C 131 REMARK 465 SER C 132 REMARK 465 LEU C 133 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 98 CG CD CE NZ REMARK 470 LYS B 98 CG CD CE NZ REMARK 470 HIS C 15 CG ND1 CD2 CE1 NE2 REMARK 470 ARG C 47 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 68 CG CD NE CZ NH1 NH2 REMARK 470 ILE C 96 CG1 CG2 CD1 REMARK 470 LYS C 98 CG CD CE NZ REMARK 470 ARG C 100 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 112 CG CD OE1 OE2 REMARK 470 ARG C 116 CG CD NE CZ NH1 NH2 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 OD1 ASP A 36 NH2 ARG C 32 7555 2.10 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 ALA B 97 C ALA B 97 O 0.171 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 GLN A 58 51.03 31.89 REMARK 500 ARG B 47 -43.34 150.72 REMARK 500 SER B 117 40.10 -99.79 REMARK 500 LEU B 118 -0.94 -150.07 REMARK 500 GLN C 49 31.55 76.47 REMARK 500 GLN C 58 80.12 50.68 REMARK 500 ALA C 92 103.13 -160.23 REMARK 500 ALA C 113 -37.78 177.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 D9G A 303 REMARK 610 D9G A 306 REMARK 610 D9G C 304 REMARK 610 D9G C 305 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D9G C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D9G A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D9G C 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D9G C 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D9G A 306 DBREF 1YRX A 17 133 UNP Q53119 Q53119_RHOSH 17 133 DBREF 1YRX B 17 133 UNP Q53119 Q53119_RHOSH 17 133 DBREF 1YRX C 17 133 UNP Q53119 Q53119_RHOSH 17 133 SEQADV 1YRX ALA A 13 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX GLY A 14 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX HIS A 15 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX MET A 16 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX ALA B 13 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX GLY B 14 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX HIS B 15 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX MET B 16 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX ALA C 13 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX GLY C 14 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX HIS C 15 UNP Q53119 CLONING ARTIFACT SEQADV 1YRX MET C 16 UNP Q53119 CLONING ARTIFACT SEQRES 1 A 121 ALA GLY HIS MET VAL SER CYS CYS TYR ARG SER LEU ALA SEQRES 2 A 121 ALA PRO ASP LEU THR LEU ARG ASP LEU LEU ASP ILE VAL SEQRES 3 A 121 GLU THR SER GLN ALA HIS ASN ALA ARG ALA GLN LEU THR SEQRES 4 A 121 GLY ALA LEU PHE TYR SER GLN GLY VAL PHE PHE GLN TRP SEQRES 5 A 121 LEU GLU GLY ARG PRO ALA ALA VAL ALA GLU VAL MET THR SEQRES 6 A 121 HIS ILE GLN ARG ASP ARG ARG HIS SER ASN VAL GLU ILE SEQRES 7 A 121 LEU ALA GLU GLU PRO ILE ALA LYS ARG ARG PHE ALA GLY SEQRES 8 A 121 TRP HIS MET GLN LEU SER CYS SER GLU ALA ASP MET ARG SEQRES 9 A 121 SER LEU GLY LEU ALA GLU SER ARG GLN ILE VAL THR VAL SEQRES 10 A 121 GLY ARG SER LEU SEQRES 1 B 121 ALA GLY HIS MET VAL SER CYS CYS TYR ARG SER LEU ALA SEQRES 2 B 121 ALA PRO ASP LEU THR LEU ARG ASP LEU LEU ASP ILE VAL SEQRES 3 B 121 GLU THR SER GLN ALA HIS ASN ALA ARG ALA GLN LEU THR SEQRES 4 B 121 GLY ALA LEU PHE TYR SER GLN GLY VAL PHE PHE GLN TRP SEQRES 5 B 121 LEU GLU GLY ARG PRO ALA ALA VAL ALA GLU VAL MET THR SEQRES 6 B 121 HIS ILE GLN ARG ASP ARG ARG HIS SER ASN VAL GLU ILE SEQRES 7 B 121 LEU ALA GLU GLU PRO ILE ALA LYS ARG ARG PHE ALA GLY SEQRES 8 B 121 TRP HIS MET GLN LEU SER CYS SER GLU ALA ASP MET ARG SEQRES 9 B 121 SER LEU GLY LEU ALA GLU SER ARG GLN ILE VAL THR VAL SEQRES 10 B 121 GLY ARG SER LEU SEQRES 1 C 121 ALA GLY HIS MET VAL SER CYS CYS TYR ARG SER LEU ALA SEQRES 2 C 121 ALA PRO ASP LEU THR LEU ARG ASP LEU LEU ASP ILE VAL SEQRES 3 C 121 GLU THR SER GLN ALA HIS ASN ALA ARG ALA GLN LEU THR SEQRES 4 C 121 GLY ALA LEU PHE TYR SER GLN GLY VAL PHE PHE GLN TRP SEQRES 5 C 121 LEU GLU GLY ARG PRO ALA ALA VAL ALA GLU VAL MET THR SEQRES 6 C 121 HIS ILE GLN ARG ASP ARG ARG HIS SER ASN VAL GLU ILE SEQRES 7 C 121 LEU ALA GLU GLU PRO ILE ALA LYS ARG ARG PHE ALA GLY SEQRES 8 C 121 TRP HIS MET GLN LEU SER CYS SER GLU ALA ASP MET ARG SEQRES 9 C 121 SER LEU GLY LEU ALA GLU SER ARG GLN ILE VAL THR VAL SEQRES 10 C 121 GLY ARG SER LEU HET FMN A 201 31 HET D9G A 302 19 HET D9G A 303 12 HET D9G A 306 6 HET FMN B 202 31 HET FMN C 203 31 HET D9G C 301 19 HET D9G C 304 10 HET D9G C 305 10 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM D9G N-DODECYL-N,N-DIMETHYLGLYCINATE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 4 FMN 3(C17 H21 N4 O9 P) FORMUL 5 D9G 6(C16 H33 N O2) FORMUL 13 HOH *97(H2 O) HELIX 1 1 THR A 30 GLN A 49 1 20 HELIX 2 2 ARG A 68 ARG A 81 1 14 HELIX 3 3 SER A 111 LEU A 118 1 8 HELIX 4 4 THR B 30 ALA B 46 1 17 HELIX 5 5 ARG B 68 ASP B 82 1 15 HELIX 6 6 SER B 111 SER B 117 1 7 HELIX 7 7 THR C 30 GLN C 49 1 20 HELIX 8 8 ARG C 68 ARG C 81 1 14 HELIX 9 9 ALA C 113 LEU C 118 1 6 SHEET 1 A 5 HIS A 85 ILE A 96 0 SHEET 2 A 5 MET A 16 ALA A 25 -1 N LEU A 24 O SER A 86 SHEET 3 A 5 VAL A 60 GLY A 67 -1 O LEU A 65 N CYS A 19 SHEET 4 A 5 THR A 51 SER A 57 -1 N SER A 57 O VAL A 60 SHEET 5 A 5 TRP A 104 LEU A 108 1 O GLN A 107 N LEU A 54 SHEET 1 B 5 HIS B 85 ILE B 96 0 SHEET 2 B 5 MET B 16 ALA B 25 -1 N ARG B 22 O GLU B 89 SHEET 3 B 5 VAL B 60 GLY B 67 -1 O LEU B 65 N CYS B 19 SHEET 4 B 5 THR B 51 SER B 57 -1 N PHE B 55 O PHE B 62 SHEET 5 B 5 TRP B 104 LEU B 108 1 O HIS B 105 N LEU B 54 SHEET 1 C 5 HIS C 85 ILE C 96 0 SHEET 2 C 5 MET C 16 ALA C 25 -1 N SER C 18 O GLU C 94 SHEET 3 C 5 VAL C 60 GLY C 67 -1 O GLN C 63 N TYR C 21 SHEET 4 C 5 THR C 51 SER C 57 -1 N PHE C 55 O PHE C 62 SHEET 5 C 5 TRP C 104 LEU C 108 1 O GLN C 107 N LEU C 54 SITE 1 AC1 17 TYR A 21 ILE A 37 THR A 40 SER A 41 SITE 2 AC1 17 HIS A 44 ASN A 45 ARG A 47 PHE A 61 SITE 3 AC1 17 GLN A 63 VAL A 75 HIS A 78 ILE A 79 SITE 4 AC1 17 ASP A 82 ARG A 84 HIS A 85 HOH A 343 SITE 5 AC1 17 HOH A 351 SITE 1 AC2 14 TYR B 21 THR B 40 SER B 41 HIS B 44 SITE 2 AC2 14 ASN B 45 PHE B 61 GLN B 63 VAL B 75 SITE 3 AC2 14 HIS B 78 ILE B 79 ASP B 82 ARG B 84 SITE 4 AC2 14 HIS B 85 HOH B 222 SITE 1 AC3 18 ARG B 68 ALA B 70 TYR C 21 ILE C 37 SITE 2 AC3 18 THR C 40 SER C 41 HIS C 44 ASN C 45 SITE 3 AC3 18 PHE C 61 GLN C 63 VAL C 75 HIS C 78 SITE 4 AC3 18 ILE C 79 ARG C 81 ASP C 82 ARG C 84 SITE 5 AC3 18 HIS C 85 HOH C 324 SITE 1 AC4 9 LEU A 35 GLU A 39 LEU A 108 MET A 115 SITE 2 AC4 9 THR C 30 LEU C 31 ARG C 32 LEU C 118 SITE 3 AC4 9 D9G C 305 SITE 1 AC5 3 GLU A 122 ARG B 124 ARG C 124 SITE 1 AC6 2 GLN C 58 PHE C 62 SITE 1 AC7 6 LEU A 34 TYR A 56 CYS A 110 ASP A 114 SITE 2 AC7 6 LEU A 118 D9G C 301 SITE 1 AC8 2 PHE A 62 PHE B 55 CRYST1 98.671 98.671 127.453 90.00 90.00 90.00 P 41 21 2 24 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 0.010135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010135 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007846 0.00000