HEADER TRANSFERASE 07-JUN-11 3ZQ5 TITLE STRUCTURE OF THE Y263F MUTANT OF THE CYANOBACTERIAL PHYTOCHROME CPH1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYTOCHROME-LIKE PROTEIN CPH1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SENSORY MODULE, RESIDUES 1-514; COMPND 5 SYNONYM: LIGHT-REGULATED HISTIDINE KINASE 1, BACTERIOPHYTOCHROME COMPND 6 CPH1; COMPND 7 EC: 2.7.13.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: P45.2; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PQE12 KEYWDS ARGININE FINGER, TANDEM GAF DOMAIN, RECEPTOR, PAS DOMAIN, KEYWDS 2 CHROMOPHORE, SENSORY TRANSDUCTION, PHOTORECEPTOR PROTEIN, BILIN-LIKE KEYWDS 3 CHROMOPHORE, PHYTOCHROME, TRANSFERASE, PHOTORECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR J.MAILLIET,G.PSAKIS,V.SINESHCHEKOV,L.-O.ESSEN,J.HUGHES REVDAT 3 20-DEC-23 3ZQ5 1 REMARK LINK REVDAT 2 07-FEB-18 3ZQ5 1 SOURCE REVDAT 1 30-NOV-11 3ZQ5 0 JRNL AUTH J.MAILLIET,G.PSAKIS,K.FEILKE,V.SINESHCHEKOV,L.-O.ESSEN, JRNL AUTH 2 J.HUGHES JRNL TITL SPECTROSCOPY AND A HIGH-RESOLUTION CRYSTAL STRUCTURE OF JRNL TITL 2 TYR263 MUTANTS OF CYANOBACTERIAL PHYTOCHROME CPH1. JRNL REF J.MOL.BIOL. V. 413 115 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21888915 JRNL DOI 10.1016/J.JMB.2011.08.023 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 50593 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2662 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3472 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : 1.32000 REMARK 3 B33 (A**2) : -1.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.72000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.129 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.676 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4324 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2870 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5892 ; 1.388 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6994 ; 0.891 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 7.343 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;38.952 ;23.942 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 704 ;17.685 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;13.626 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 657 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4837 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 881 ; 0.004 ; 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): 2620 ; 1.296 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1045 ; 0.356 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4240 ; 2.341 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1704 ; 3.305 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1643 ; 5.252 ; 4.500 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 18 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1116 -19.0885 9.6030 REMARK 3 T TENSOR REMARK 3 T11: 0.5507 T22: 0.1846 REMARK 3 T33: 0.5080 T12: -0.0361 REMARK 3 T13: -0.0951 T23: -0.1215 REMARK 3 L TENSOR REMARK 3 L11: 4.8933 L22: 4.5508 REMARK 3 L33: 12.5850 L12: -1.8730 REMARK 3 L13: 1.5777 L23: -6.5355 REMARK 3 S TENSOR REMARK 3 S11: 0.2129 S12: 0.3878 S13: -0.6106 REMARK 3 S21: -0.9417 S22: 0.0969 S23: 0.2222 REMARK 3 S31: 1.6251 S32: -0.5744 S33: -0.3098 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 19 A 125 REMARK 3 RESIDUE RANGE : A 230 A 252 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3167 -13.6798 38.4475 REMARK 3 T TENSOR REMARK 3 T11: 0.1245 T22: 0.1168 REMARK 3 T33: 0.1205 T12: 0.0924 REMARK 3 T13: 0.0112 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 2.2550 L22: 2.6244 REMARK 3 L33: 2.1744 L12: -0.6117 REMARK 3 L13: 1.8099 L23: -0.2945 REMARK 3 S TENSOR REMARK 3 S11: -0.1054 S12: -0.3382 S13: 0.0221 REMARK 3 S21: 0.2649 S22: 0.0915 S23: -0.1775 REMARK 3 S31: -0.0075 S32: -0.2018 S33: 0.0139 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 132 A 229 REMARK 3 RESIDUE RANGE : A 253 A 321 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9967 3.9361 24.5912 REMARK 3 T TENSOR REMARK 3 T11: 0.0296 T22: 0.0058 REMARK 3 T33: 0.0213 T12: 0.0056 REMARK 3 T13: -0.0015 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 1.2535 L22: 1.4492 REMARK 3 L33: 1.5668 L12: -0.2185 REMARK 3 L13: -0.2212 L23: 0.2795 REMARK 3 S TENSOR REMARK 3 S11: -0.0358 S12: 0.0497 S13: 0.0462 REMARK 3 S21: -0.1337 S22: -0.0222 S23: -0.0523 REMARK 3 S31: 0.0210 S32: 0.0403 S33: 0.0580 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 322 A 442 REMARK 3 RESIDUE RANGE : A 485 A 514 REMARK 3 ORIGIN FOR THE GROUP (A): -31.4861 7.4468 14.1661 REMARK 3 T TENSOR REMARK 3 T11: 0.0770 T22: 0.0954 REMARK 3 T33: 0.1088 T12: 0.0146 REMARK 3 T13: 0.0074 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.9817 L22: 1.0375 REMARK 3 L33: 2.9178 L12: -0.0368 REMARK 3 L13: -0.1996 L23: 0.1508 REMARK 3 S TENSOR REMARK 3 S11: -0.1345 S12: 0.1982 S13: -0.2007 REMARK 3 S21: -0.0571 S22: 0.0095 S23: 0.2135 REMARK 3 S31: 0.2570 S32: -0.2027 S33: 0.1250 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 444 A 484 REMARK 3 ORIGIN FOR THE GROUP (A): 4.4526 -5.1223 5.0647 REMARK 3 T TENSOR REMARK 3 T11: 0.1797 T22: 0.1811 REMARK 3 T33: 0.0702 T12: 0.0307 REMARK 3 T13: -0.0031 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 4.0751 L22: 3.2832 REMARK 3 L33: 1.1215 L12: -3.1793 REMARK 3 L13: 1.2511 L23: -1.2109 REMARK 3 S TENSOR REMARK 3 S11: 0.1287 S12: 0.1331 S13: -0.1527 REMARK 3 S21: -0.0908 S22: -0.1321 S23: -0.0779 REMARK 3 S31: 0.3445 S32: -0.0015 S33: 0.0034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES, RESIDUAL ONLY REMARK 4 REMARK 4 3ZQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53522 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 33.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.370 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2VEA REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG / ML PROTEIN, 1.9 M SODIUM REMARK 280 ACETATE, 0.4 M MES PH 7.2. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.78500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.78500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.57500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.7 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 -1.000000 0.000000 0.000000 -12.35947 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 72.53454 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 263 TO PHE 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 519 REMARK 465 HIS A 520 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 GLN A 401 CG CD OE1 NE2 REMARK 470 GLU A 463 CG CD OE1 OE2 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 SG CYS A 259 CBC CYC A 1521 2.12 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 MET A 99 -72.58 34.87 REMARK 500 ASP A 101 44.72 -99.17 REMARK 500 THR A 127 -97.01 18.65 REMARK 500 ASN A 130 -10.74 -170.73 REMARK 500 GLN A 401 -172.28 -69.03 REMARK 500 VAL A 403 141.79 -170.26 REMARK 500 ALA A 423 58.65 -149.22 REMARK 500 ARG A 433 -73.23 66.16 REMARK 500 HIS A 456 58.57 -152.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PHYCOCYANOBILIN (CYC): CHROMOPHORE REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1530 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 66 O REMARK 620 2 PHE A 69 O 72.4 REMARK 620 3 ASP A 70 OD1 159.6 87.4 REMARK 620 4 HOH A2042 O 91.4 96.8 88.5 REMARK 620 5 HOH A2043 O 79.4 70.7 96.6 166.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1522 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 447 O REMARK 620 2 ASN A 449 OD1 90.4 REMARK 620 3 HOH A2143 O 160.9 84.1 REMARK 620 4 HOH A2144 O 100.4 95.9 98.4 REMARK 620 5 HOH A2290 O 70.1 88.7 91.5 169.5 REMARK 620 6 HOH A2291 O 82.7 169.2 99.7 93.6 81.1 REMARK 620 N 1 2 3 4 5 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 1521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1522 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1524 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1528 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1529 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1530 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VEA RELATED DB: PDB REMARK 900 THE COMPLETE SENSORY MODULE OF THE CYANOBACTERIAL PHYTOCHROME CPH1 REMARK 900 IN THE PR-STATE DBREF 3ZQ5 A 1 514 UNP Q55168 PHY1_SYNY3 1 514 SEQADV 3ZQ5 HIS A 515 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 HIS A 516 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 HIS A 517 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 HIS A 518 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 HIS A 519 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 HIS A 520 UNP Q55168 EXPRESSION TAG SEQADV 3ZQ5 PHE A 263 UNP Q55168 TYR 263 ENGINEERED MUTATION SEQRES 1 A 520 MET ALA THR THR VAL GLN LEU SER ASP GLN SER LEU ARG SEQRES 2 A 520 GLN LEU GLU THR LEU ALA ILE HIS THR ALA HIS LEU ILE SEQRES 3 A 520 GLN PRO HIS GLY LEU VAL VAL VAL LEU GLN GLU PRO ASP SEQRES 4 A 520 LEU THR ILE SER GLN ILE SER ALA ASN CYS THR GLY ILE SEQRES 5 A 520 LEU GLY ARG SER PRO GLU ASP LEU LEU GLY ARG THR LEU SEQRES 6 A 520 GLY GLU VAL PHE ASP SER PHE GLN ILE ASP PRO ILE GLN SEQRES 7 A 520 SER ARG LEU THR ALA GLY GLN ILE SER SER LEU ASN PRO SEQRES 8 A 520 SER LYS LEU TRP ALA ARG VAL MET GLY ASP ASP PHE VAL SEQRES 9 A 520 ILE PHE ASP GLY VAL PHE HIS ARG ASN SER ASP GLY LEU SEQRES 10 A 520 LEU VAL CYS GLU LEU GLU PRO ALA TYR THR SER ASP ASN SEQRES 11 A 520 LEU PRO PHE LEU GLY PHE TYR HIS MET ALA ASN ALA ALA SEQRES 12 A 520 LEU ASN ARG LEU ARG GLN GLN ALA ASN LEU ARG ASP PHE SEQRES 13 A 520 TYR ASP VAL ILE VAL GLU GLU VAL ARG ARG MET THR GLY SEQRES 14 A 520 PHE ASP ARG VAL MET LEU TYR ARG PHE ASP GLU ASN ASN SEQRES 15 A 520 HIS GLY ASP VAL ILE ALA GLU ASP LYS ARG ASP ASP MET SEQRES 16 A 520 GLU PRO TYR LEU GLY LEU HIS TYR PRO GLU SER ASP ILE SEQRES 17 A 520 PRO GLN PRO ALA ARG ARG LEU PHE ILE HIS ASN PRO ILE SEQRES 18 A 520 ARG VAL ILE PRO ASP VAL TYR GLY VAL ALA VAL PRO LEU SEQRES 19 A 520 THR PRO ALA VAL ASN PRO SER THR ASN ARG ALA VAL ASP SEQRES 20 A 520 LEU THR GLU SER ILE LEU ARG SER ALA TYR HIS CYS HIS SEQRES 21 A 520 LEU THR PHE LEU LYS ASN MET GLY VAL GLY ALA SER LEU SEQRES 22 A 520 THR ILE SER LEU ILE LYS ASP GLY HIS LEU TRP GLY LEU SEQRES 23 A 520 ILE ALA CYS HIS HIS GLN THR PRO LYS VAL ILE PRO PHE SEQRES 24 A 520 GLU LEU ARG LYS ALA CYS GLU PHE PHE GLY ARG VAL VAL SEQRES 25 A 520 PHE SER ASN ILE SER ALA GLN GLU ASP THR GLU THR PHE SEQRES 26 A 520 ASP TYR ARG VAL GLN LEU ALA GLU HIS GLU ALA VAL LEU SEQRES 27 A 520 LEU ASP LYS MET THR THR ALA ALA ASP PHE VAL GLU GLY SEQRES 28 A 520 LEU THR ASN HIS PRO ASP ARG LEU LEU GLY LEU THR GLY SEQRES 29 A 520 SER GLN GLY ALA ALA ILE CYS PHE GLY GLU LYS LEU ILE SEQRES 30 A 520 LEU VAL GLY GLU THR PRO ASP GLU LYS ALA VAL GLN TYR SEQRES 31 A 520 LEU LEU GLN TRP LEU GLU ASN ARG GLU VAL GLN ASP VAL SEQRES 32 A 520 PHE PHE THR SER SER LEU SER GLN ILE TYR PRO ASP ALA SEQRES 33 A 520 VAL ASN PHE LYS SER VAL ALA SER GLY LEU LEU ALA ILE SEQRES 34 A 520 PRO ILE ALA ARG HIS ASN PHE LEU LEU TRP PHE ARG PRO SEQRES 35 A 520 GLU VAL LEU GLN THR VAL ASN TRP GLY GLY ASP PRO ASN SEQRES 36 A 520 HIS ALA TYR GLU ALA THR GLN GLU ASP GLY LYS ILE GLU SEQRES 37 A 520 LEU HIS PRO ARG GLN SER PHE ASP LEU TRP LYS GLU ILE SEQRES 38 A 520 VAL ARG LEU GLN SER LEU PRO TRP GLN SER VAL GLU ILE SEQRES 39 A 520 GLN SER ALA LEU ALA LEU LYS LYS ALA ILE VAL ASN LEU SEQRES 40 A 520 ILE LEU ARG GLN ALA GLU GLU HIS HIS HIS HIS HIS HIS HET CYC A1521 43 HET NA A1522 1 HET PO4 A1523 5 HET ACT A1524 4 HET ACT A1525 4 HET ACT A1526 4 HET ACT A1527 4 HET GOL A1528 6 HET GOL A1529 6 HET NA A1530 1 HETNAM CYC PHYCOCYANOBILIN HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CYC C33 H40 N4 O6 FORMUL 3 NA 2(NA 1+) FORMUL 4 PO4 O4 P 3- FORMUL 5 ACT 4(C2 H3 O2 1-) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 12 HOH *328(H2 O) HELIX 1 1 SER A 8 THR A 17 1 10 HELIX 2 2 ALA A 19 ALA A 23 5 5 HELIX 3 3 ASN A 48 GLY A 54 1 7 HELIX 4 4 SER A 56 LEU A 61 1 6 HELIX 5 5 THR A 64 PHE A 69 1 6 HELIX 6 6 THR A 82 LEU A 89 1 8 HELIX 7 7 GLY A 135 GLN A 150 1 16 HELIX 8 8 ASN A 152 GLY A 169 1 18 HELIX 9 9 PRO A 204 ILE A 208 5 5 HELIX 10 10 PRO A 209 ASN A 219 1 11 HELIX 11 11 TYR A 257 MET A 267 1 11 HELIX 12 12 PRO A 298 ALA A 345 1 48 HELIX 13 13 ASP A 347 ASN A 354 1 8 HELIX 14 14 HIS A 355 LEU A 362 1 8 HELIX 15 15 ASP A 384 ARG A 398 1 15 HELIX 16 16 SER A 408 ILE A 412 5 5 HELIX 17 17 TYR A 413 ASN A 418 5 6 HELIX 18 18 PHE A 419 SER A 424 1 6 HELIX 19 19 ASP A 453 ALA A 457 5 5 HELIX 20 20 GLN A 490 HIS A 518 1 29 SHEET 1 AA 3 THR A 4 VAL A 5 0 SHEET 2 AA 3 GLU A 459 GLU A 463 -1 O ALA A 460 N VAL A 5 SHEET 3 AA 3 LYS A 466 HIS A 470 -1 O LYS A 466 N GLU A 463 SHEET 1 AB 8 LEU A 25 ILE A 26 0 SHEET 2 AB 8 VAL A 232 THR A 235 -1 O VAL A 232 N ILE A 26 SHEET 3 AB 8 THR A 41 SER A 46 -1 O ILE A 45 N THR A 235 SHEET 4 AB 8 LEU A 31 GLN A 36 -1 O VAL A 32 N SER A 46 SHEET 5 AB 8 LEU A 118 PRO A 124 -1 O LEU A 118 N LEU A 35 SHEET 6 AB 8 ASP A 102 ARG A 112 -1 O ASP A 107 N GLU A 123 SHEET 7 AB 8 SER A 92 VAL A 98 -1 O SER A 92 N GLY A 108 SHEET 8 AB 8 ASP A 70 SER A 71 -1 O ASP A 70 N TRP A 95 SHEET 1 AC 8 ILE A 221 ILE A 224 0 SHEET 2 AC 8 ALA A 271 LYS A 279 -1 O SER A 272 N ILE A 224 SHEET 3 AC 8 HIS A 282 HIS A 291 -1 O HIS A 282 N LYS A 279 SHEET 4 AC 8 ARG A 172 PHE A 178 -1 O ARG A 172 N HIS A 290 SHEET 5 AC 8 GLY A 184 LYS A 191 -1 O ASP A 185 N ARG A 177 SHEET 6 AC 8 LEU A 201 TYR A 203 -1 O LEU A 201 N VAL A 186 SHEET 7 AC 8 GLN A 446 TRP A 450 1 O ASN A 449 N HIS A 202 SHEET 8 AC 8 TRP A 478 VAL A 482 -1 O TRP A 478 N TRP A 450 SHEET 1 AD 5 LYS A 375 GLY A 380 0 SHEET 2 AD 5 GLY A 367 PHE A 372 -1 O ALA A 368 N VAL A 379 SHEET 3 AD 5 ASN A 435 ARG A 441 -1 O PHE A 436 N CYS A 371 SHEET 4 AD 5 GLY A 425 ILE A 431 -1 O GLY A 425 N ARG A 441 SHEET 5 AD 5 PHE A 404 THR A 406 -1 O PHE A 404 N ALA A 428 LINK SG ACYS A 259 CAC CYC A1521 1555 1555 1.61 LINK SG BCYS A 259 CAC CYC A1521 1555 1555 1.63 LINK O GLY A 66 NA NA A1530 1555 1555 2.36 LINK O PHE A 69 NA NA A1530 1555 1555 3.11 LINK OD1 ASP A 70 NA NA A1530 1555 1555 2.49 LINK O THR A 447 NA NA A1522 1555 1555 2.62 LINK OD1 ASN A 449 NA NA A1522 1555 1555 2.60 LINK NA NA A1522 O HOH A2143 1555 1555 2.11 LINK NA NA A1522 O HOH A2144 1555 1555 2.29 LINK NA NA A1522 O HOH A2290 1555 1555 2.26 LINK NA NA A1522 O HOH A2291 1555 1555 2.40 LINK NA NA A1530 O HOH A2042 1555 1555 2.60 LINK NA NA A1530 O HOH A2043 1555 1555 2.27 CISPEP 1 GLU A 37 PRO A 38 0 1.76 CISPEP 2 ASN A 90 PRO A 91 0 -10.96 CISPEP 3 THR A 235 PRO A 236 0 -13.72 SITE 1 AC1 26 LEU A 15 MET A 174 VAL A 186 TYR A 203 SITE 2 AC1 26 SER A 206 ASP A 207 ILE A 208 PRO A 209 SITE 3 AC1 26 ALA A 212 PHE A 216 ARG A 254 ALA A 256 SITE 4 AC1 26 TYR A 257 CYS A 259 HIS A 260 PHE A 263 SITE 5 AC1 26 THR A 274 HIS A 290 TYR A 458 LEU A 469 SITE 6 AC1 26 HOH A2150 HOH A2160 HOH A2161 HOH A2192 SITE 7 AC1 26 HOH A2212 HOH A2306 SITE 1 AC2 6 THR A 447 ASN A 449 HOH A2143 HOH A2144 SITE 2 AC2 6 HOH A2290 HOH A2291 SITE 1 AC3 5 ARG A 172 MET A 195 GLU A 196 GLN A 292 SITE 2 AC3 5 HOH A2199 SITE 1 AC4 5 HIS A 24 VAL A 337 ARG A 358 HOH A2325 SITE 2 AC4 5 HOH A2326 SITE 1 AC5 7 GLU A 196 TYR A 198 TYR A 203 GLY A 451 SITE 2 AC5 7 LEU A 477 ARG A 483 HOH A2296 SITE 1 AC6 3 ARG A 213 LEU A 283 HOH A2128 SITE 1 AC7 4 SER A 407 PRO A 488 TRP A 489 HOH A2272 SITE 1 AC8 8 HIS A 24 PRO A 233 LEU A 234 ALA A 237 SITE 2 AC8 8 GLU A 333 ARG A 358 HOH A2179 HOH A2327 SITE 1 AC9 4 GLU A 162 ARG A 166 ASP A 190 HOH A2328 SITE 1 BC1 5 GLY A 66 PHE A 69 ASP A 70 HOH A2042 SITE 2 BC1 5 HOH A2043 CRYST1 107.570 95.150 73.580 90.00 99.67 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009296 0.000000 0.001584 0.00000 SCALE2 0.000000 0.010510 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013787 0.00000