HEADER TRANSFERASE 27-AUG-15 5DFX TITLE STRUCTURE OF THE PARENTAL STATE OF GAF3 FROM SLR1393 OF SYNECHOCYSTIS TITLE 2 SP. PCC6803 (IN VIVO ASSEMBLED PROTEIN/CHROMOPHORE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 441-597; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KAZUSA); SOURCE 3 ORGANISM_TAXID: 1111708; SOURCE 4 GENE: SLR1393; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYANOBACTERIOCHROME, PHYCOCYANOBILIN CHROMOPHORE, PHOTOCHROMICITY, KEYWDS 2 BILIN-BINDING GAF DOMAIN, PHYTOCHROME-RELATED PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.-L.XU,K.-H.ZHAO,W.GAERTNER,A.HOEPPNER REVDAT 2 29-JAN-20 5DFX 1 JRNL REVDAT 1 14-SEP-16 5DFX 0 JRNL AUTH X.-L.XU,A.HOEPPNER,C.WIEBELER,K.-H.ZHAO,I.SCHAPIRO, JRNL AUTH 2 W.GAERTNER JRNL TITL STRUCTURAL ELEMENTS REGULATING THE PHOTOCHROMICITY IN A JRNL TITL 2 CYANOBACTERIOCHROME JRNL REF PROC.NATL.ACAD.SCI.USA 2020 JRNL REFN ESSN 1091-6490 JRNL DOI 10.1073/PNAS.1910208117 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21860 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1560 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1299 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.063 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1426 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1309 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1947 ; 2.428 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2978 ; 1.032 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 168 ; 6.711 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;32.319 ;23.659 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 218 ;12.336 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.042 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 198 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1678 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 389 ; 0.017 ; 0.020 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): 651 ; 3.050 ; 2.463 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 650 ; 3.037 ; 2.456 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 814 ; 4.163 ; 3.668 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 815 ; 4.170 ; 3.674 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 775 ; 3.907 ; 2.886 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 776 ; 3.905 ; 2.886 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1129 ; 5.776 ; 4.183 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1811 ; 7.580 ;21.958 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1812 ; 7.578 ;21.959 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 5DFX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000209636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.630 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.52 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.420 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M TRIS PH 7.0, 0.1 M SODIUM REMARK 280 CHLORIDE, 7.7 % (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K 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 59.41500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.56000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.70750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.56000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.12250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.56000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.56000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.70750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.56000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.56000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.12250 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 59.41500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 118.83000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 950 LIES ON A SPECIAL POSITION. 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 391 REMARK 465 HIS A 392 REMARK 465 HIS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 SER A 398 REMARK 465 SER A 399 REMARK 465 GLY A 400 REMARK 465 LEU A 401 REMARK 465 VAL A 402 REMARK 465 PRO A 403 REMARK 465 ARG A 404 REMARK 465 GLY A 405 REMARK 465 SER A 406 REMARK 465 GLY A 407 REMARK 465 MET A 408 REMARK 465 LYS A 409 REMARK 465 GLU A 410 REMARK 465 THR A 411 REMARK 465 ALA A 412 REMARK 465 ALA A 413 REMARK 465 ALA A 414 REMARK 465 LYS A 415 REMARK 465 PHE A 416 REMARK 465 GLU A 417 REMARK 465 ARG A 418 REMARK 465 GLN A 419 REMARK 465 HIS A 420 REMARK 465 MET A 421 REMARK 465 ASP A 422 REMARK 465 SER A 423 REMARK 465 PRO A 424 REMARK 465 ASP A 425 REMARK 465 LEU A 426 REMARK 465 GLY A 427 REMARK 465 THR A 428 REMARK 465 ASP A 429 REMARK 465 ASP A 430 REMARK 465 ASP A 431 REMARK 465 ASP A 432 REMARK 465 LYS A 433 REMARK 465 ALA A 434 REMARK 465 MET A 435 REMARK 465 ALA A 436 REMARK 465 ASP A 437 REMARK 465 ILE A 438 REMARK 465 GLU A 597 REMARK 465 LEU A 598 REMARK 465 GLU A 599 REMARK 465 HIS A 600 REMARK 465 HIS A 601 REMARK 465 HIS A 602 REMARK 465 HIS A 603 REMARK 465 HIS A 604 REMARK 465 HIS A 605 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 O SER A 457 NH2 ARG A 594 6455 2.01 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 A 451 CD GLU A 451 OE1 0.091 REMARK 500 GLU A 484 CD GLU A 484 OE1 -0.083 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 ASP A 450 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 469 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 535 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 594 C - N - CA ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG A 594 CA - C - O ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 594 CA - C - N ANGL. DEV. = -13.7 DEGREES 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 TRP A 470 SER A 471 148.88 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 ARG A 594 14.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYC A 701 DBREF 5DFX A 441 597 UNP P73184 P73184_SYNY3 441 597 SEQADV 5DFX MET A 391 UNP P73184 INITIATING METHIONINE SEQADV 5DFX HIS A 392 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 393 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 394 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 395 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 396 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 397 UNP P73184 EXPRESSION TAG SEQADV 5DFX SER A 398 UNP P73184 EXPRESSION TAG SEQADV 5DFX SER A 399 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLY A 400 UNP P73184 EXPRESSION TAG SEQADV 5DFX LEU A 401 UNP P73184 EXPRESSION TAG SEQADV 5DFX VAL A 402 UNP P73184 EXPRESSION TAG SEQADV 5DFX PRO A 403 UNP P73184 EXPRESSION TAG SEQADV 5DFX ARG A 404 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLY A 405 UNP P73184 EXPRESSION TAG SEQADV 5DFX SER A 406 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLY A 407 UNP P73184 EXPRESSION TAG SEQADV 5DFX MET A 408 UNP P73184 EXPRESSION TAG SEQADV 5DFX LYS A 409 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLU A 410 UNP P73184 EXPRESSION TAG SEQADV 5DFX THR A 411 UNP P73184 EXPRESSION TAG SEQADV 5DFX ALA A 412 UNP P73184 EXPRESSION TAG SEQADV 5DFX ALA A 413 UNP P73184 EXPRESSION TAG SEQADV 5DFX ALA A 414 UNP P73184 EXPRESSION TAG SEQADV 5DFX LYS A 415 UNP P73184 EXPRESSION TAG SEQADV 5DFX PHE A 416 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLU A 417 UNP P73184 EXPRESSION TAG SEQADV 5DFX ARG A 418 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLN A 419 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 420 UNP P73184 EXPRESSION TAG SEQADV 5DFX MET A 421 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 422 UNP P73184 EXPRESSION TAG SEQADV 5DFX SER A 423 UNP P73184 EXPRESSION TAG SEQADV 5DFX PRO A 424 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 425 UNP P73184 EXPRESSION TAG SEQADV 5DFX LEU A 426 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLY A 427 UNP P73184 EXPRESSION TAG SEQADV 5DFX THR A 428 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 429 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 430 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 431 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 432 UNP P73184 EXPRESSION TAG SEQADV 5DFX LYS A 433 UNP P73184 EXPRESSION TAG SEQADV 5DFX ALA A 434 UNP P73184 EXPRESSION TAG SEQADV 5DFX MET A 435 UNP P73184 EXPRESSION TAG SEQADV 5DFX ALA A 436 UNP P73184 EXPRESSION TAG SEQADV 5DFX ASP A 437 UNP P73184 EXPRESSION TAG SEQADV 5DFX ILE A 438 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLY A 439 UNP P73184 EXPRESSION TAG SEQADV 5DFX SER A 440 UNP P73184 EXPRESSION TAG SEQADV 5DFX LEU A 598 UNP P73184 EXPRESSION TAG SEQADV 5DFX GLU A 599 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 600 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 601 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 602 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 603 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 604 UNP P73184 EXPRESSION TAG SEQADV 5DFX HIS A 605 UNP P73184 EXPRESSION TAG SEQRES 1 A 215 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 215 ARG GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE SEQRES 3 A 215 GLU ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP SEQRES 4 A 215 ASP ASP ASP LYS ALA MET ALA ASP ILE GLY SER LEU GLN SEQRES 5 A 215 ASN ILE PHE ARG ALA THR SER ASP GLU VAL ARG HIS LEU SEQRES 6 A 215 LEU SER CYS ASP ARG VAL LEU VAL TYR ARG PHE ASN PRO SEQRES 7 A 215 ASP TRP SER GLY GLU PHE ILE HIS GLU SER VAL ALA GLN SEQRES 8 A 215 MET TRP GLU PRO LEU LYS ASP LEU GLN ASN ASN PHE PRO SEQRES 9 A 215 LEU TRP GLN ASP THR TYR LEU GLN GLU ASN GLU GLY GLY SEQRES 10 A 215 ARG TYR ARG ASN HIS GLU SER LEU ALA VAL GLY ASP VAL SEQRES 11 A 215 GLU THR ALA GLY PHE THR ASP CYS HIS LEU ASP ASN LEU SEQRES 12 A 215 ARG ARG PHE GLU ILE ARG ALA PHE LEU THR VAL PRO VAL SEQRES 13 A 215 PHE VAL GLY GLU GLN LEU TRP GLY LEU LEU GLY ALA TYR SEQRES 14 A 215 GLN ASN GLY ALA PRO ARG HIS TRP GLN ALA ARG GLU ILE SEQRES 15 A 215 HIS LEU LEU HIS GLN ILE ALA ASN GLN LEU GLY VAL ALA SEQRES 16 A 215 VAL TYR GLN ALA GLN LEU LEU ALA ARG PHE GLN GLU LEU SEQRES 17 A 215 GLU HIS HIS HIS HIS HIS HIS HET CYC A 701 43 HETNAM CYC PHYCOCYANOBILIN FORMUL 2 CYC C33 H40 N4 O6 FORMUL 3 HOH *168(H2 O) HELIX 1 AA1 GLY A 439 SER A 457 1 19 HELIX 2 AA2 ASP A 498 ASN A 504 1 7 HELIX 3 AA3 GLY A 506 HIS A 512 5 7 HELIX 4 AA4 ASP A 519 ALA A 523 5 5 HELIX 5 AA5 THR A 526 PHE A 536 1 11 HELIX 6 AA6 GLN A 568 ARG A 594 1 27 SHEET 1 AA1 5 GLY A 472 VAL A 479 0 SHEET 2 AA1 5 ARG A 460 PHE A 466 -1 N ARG A 465 O GLU A 473 SHEET 3 AA1 5 GLN A 551 GLN A 560 -1 O TYR A 559 N ARG A 460 SHEET 4 AA1 5 ALA A 540 VAL A 548 -1 N VAL A 546 O GLY A 554 SHEET 5 AA1 5 LEU A 515 VAL A 517 -1 N VAL A 517 O PHE A 541 LINK SG CYS A 528 CAC CYC A 701 1555 1555 1.63 SITE 1 AC1 20 TYR A 464 PHE A 474 TRP A 496 GLN A 497 SITE 2 AC1 20 ASP A 498 THR A 499 TYR A 500 ARG A 508 SITE 3 AC1 20 TYR A 509 LEU A 515 PHE A 525 THR A 526 SITE 4 AC1 20 CYS A 528 HIS A 529 ASN A 532 THR A 543 SITE 5 AC1 20 TYR A 559 HOH A 805 HOH A 820 HOH A 842 CRYST1 63.120 63.120 118.830 90.00 90.00 90.00 P 41 21 2 8 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 0.015843 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008415 0.00000