HEADER FLUORESCENT PROTEIN 17-FEB-14 4CQH TITLE STRUCTURE OF INFRARED FLUORESCENT PROTEIN IFP2.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOPHYTOCHROME; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-317; COMPND 5 SYNONYM: PHYTOCHROME-LIKE PROTEIN, INFRARED FLUORESCENT PROTEIN COMPND 6 VERSION 2.0; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBAD KEYWDS FLUORESCENT PROTEIN, INFRARED FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.LAFAYE,D.YU,M.NOIRCLERC-SAVOYE,X.SHU,A.ROYANT REVDAT 2 20-DEC-23 4CQH 1 COMPND REMARK HETNAM LINK REVDAT 1 28-MAY-14 4CQH 0 JRNL AUTH D.YU,W.C.GUSTAFSON,C.HAN,C.LAFAYE,M.NOIRCLERC-SAVOYE,W.GE, JRNL AUTH 2 D.A.THAYER,H.HUANG,T.B.KORNBERG,A.ROYANT,L.Y.JAN,Y.N.JAN, JRNL AUTH 3 W.A.WEISS,X.SHU JRNL TITL AN IMPROVED MONOMERIC INFRARED FLUORESCENT PROTEIN FOR JRNL TITL 2 NEURONAL AND TUMOUR BRAIN IMAGING. JRNL REF NAT.COMMUN. V. 5 3626 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24832154 JRNL DOI 10.1038/NCOMMS4626 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.SHU,A.ROYANT,M.Z.LIN,T.A.AGUILERA,V.LEV-RAM,P.A.STEINBACH, REMARK 1 AUTH 2 R.Y.TSIEN REMARK 1 TITL MAMMALIAN EXPRESSION OF INFRARED FLUORESCENT PROTEINS REMARK 1 TITL 2 ENGINEERED FROM A BACTERIAL PHYTOCHROME. REMARK 1 REF SCIENCE V. 324 804 2009 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 19423828 REMARK 1 DOI 10.1126/SCIENCE.1168683 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 114179 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) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6054 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) : 1.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 481 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.029 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.892 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2635 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2588 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3653 ; 1.963 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5958 ; 0.950 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 6.260 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;35.716 ;22.617 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 414 ;12.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.054 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 423 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3046 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 606 ; 0.002 ; 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): 1296 ; 1.751 ; 1.189 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1295 ; 1.733 ; 1.186 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1636 ; 2.292 ; 1.796 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1637 ; 2.307 ; 1.799 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1339 ; 2.591 ; 1.436 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1340 ; 2.590 ; 1.436 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1993 ; 3.113 ; 2.074 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3132 ; 4.275 ;11.333 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2961 ; 3.632 ;10.573 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5223 ; 3.144 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 69 ;26.425 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5354 ; 9.863 ; 5.000 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4CQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1290059749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 46.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 2O9C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 100 MM SODIUM ACETATE PH REMARK 280 4.6 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 47.84600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.45600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.84600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.45600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A2018 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 1 REMARK 465 ALA A 2 REMARK 465 ARG A 3 REMARK 465 ASP A 4 REMARK 465 PRO A 5 REMARK 465 GLN A 6 REMARK 465 GLU A 130 REMARK 465 ALA A 131 REMARK 465 TRP A 132 REMARK 465 ASP A 133 REMARK 465 SER A 134 REMARK 465 ILE A 135 REMARK 465 GLY A 136 REMARK 465 PRO A 137 REMARK 465 ALA A 321 REMARK 465 GLU A 322 REMARK 465 PHE A 323 REMARK 465 HIS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 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 22 CD OE1 OE2 REMARK 470 GLN A 94 CG CD OE1 NE2 REMARK 470 ASP A 95 CG OD1 OD2 REMARK 470 ARG A 100 CD NE CZ NH1 NH2 REMARK 470 HIS A 138 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 148 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 O HOH A 2217 O HOH A 2277 2.12 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 OG SER A 149 O HOH A 2243 3445 2.18 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 189 CB GLU A 189 CG -0.132 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 ARG A 192 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 254 CG - CD - NE ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 302 NE - CZ - NH2 ANGL. DEV. = -6.1 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 ASN A 23 37.94 -148.64 REMARK 500 ALA A 119 -117.94 55.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 191 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2074 DISTANCE = 5.96 ANGSTROMS 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 A1322 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2225 O REMARK 620 2 HOH A2254 O 93.1 REMARK 620 3 HOH A2293 O 107.4 115.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LBV A 1321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1322 REMARK 999 REMARK 999 SEQUENCE REMARK 999 IFP2.0 HAS BEEN ENGINEERED FROM A FRAGMENT OF THE REMARK 999 BACTERIOPHYTOCHROME FROM DEINOCOCCUS RADIODURANS DBREF 4CQH A 1 317 UNP Q9RZA4 BPHY_DEIRA 1 317 SEQADV 4CQH ALA A 2 UNP Q9RZA4 SER 2 ENGINEERED MUTATION SEQADV 4CQH GLN A 6 UNP Q9RZA4 LEU 6 ENGINEERED MUTATION SEQADV 4CQH VAL A 54 UNP Q9RZA4 MET 54 ENGINEERED MUTATION SEQADV 4CQH ASP A 80 UNP Q9RZA4 GLU 80 ENGINEERED MUTATION SEQADV 4CQH THR A 87 UNP Q9RZA4 ALA 87 ENGINEERED MUTATION SEQADV 4CQH GLN A 94 UNP Q9RZA4 PRO 94 ENGINEERED MUTATION SEQADV 4CQH ALA A 119 UNP Q9RZA4 GLY 119 ENGINEERED MUTATION SEQADV 4CQH ILE A 135 UNP Q9RZA4 THR 135 ENGINEERED MUTATION SEQADV 4CQH SER A 168 UNP Q9RZA4 THR 168 ENGINEERED MUTATION SEQADV 4CQH MET A 195 UNP Q9RZA4 LEU 195 ENGINEERED MUTATION SEQADV 4CQH GLN A 196 UNP Q9RZA4 HIS 196 ENGINEERED MUTATION SEQADV 4CQH TYR A 198 UNP Q9RZA4 PHE 198 ENGINEERED MUTATION SEQADV 4CQH THR A 207 UNP Q9RZA4 ASP 207 ENGINEERED MUTATION SEQADV 4CQH THR A 208 UNP Q9RZA4 ILE 208 ENGINEERED MUTATION SEQADV 4CQH VAL A 288 UNP Q9RZA4 ALA 288 ENGINEERED MUTATION SEQADV 4CQH ARG A 318 UNP Q9RZA4 VAL 318 ENGINEERED MUTATION SEQADV 4CQH LYS A 319 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH GLU A 320 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH ALA A 321 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH GLU A 322 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH PHE A 323 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 324 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 325 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 326 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 327 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 328 UNP Q9RZA4 EXPRESSION TAG SEQADV 4CQH HIS A 329 UNP Q9RZA4 EXPRESSION TAG SEQRES 1 A 329 MET ALA ARG ASP PRO GLN PRO PHE PHE PRO PRO LEU TYR SEQRES 2 A 329 LEU GLY GLY PRO GLU ILE THR THR GLU ASN CYS GLU ARG SEQRES 3 A 329 GLU PRO ILE HIS ILE PRO GLY SER ILE GLN PRO HIS GLY SEQRES 4 A 329 ALA LEU LEU THR ALA ASP GLY HIS SER GLY GLU VAL LEU SEQRES 5 A 329 GLN VAL SER LEU ASN ALA ALA THR PHE LEU GLY GLN GLU SEQRES 6 A 329 PRO THR VAL LEU ARG GLY GLN THR LEU ALA ALA LEU LEU SEQRES 7 A 329 PRO ASP GLN TRP PRO ALA LEU GLN THR ALA LEU PRO PRO SEQRES 8 A 329 GLY CYS GLN ASP ALA LEU GLN TYR ARG ALA THR LEU ASP SEQRES 9 A 329 TRP PRO ALA ALA GLY HIS LEU SER LEU THR VAL HIS ARG SEQRES 10 A 329 VAL ALA GLU LEU LEU ILE LEU GLU PHE GLU PRO THR GLU SEQRES 11 A 329 ALA TRP ASP SER ILE GLY PRO HIS ALA LEU ARG ASN ALA SEQRES 12 A 329 MET PHE ALA LEU GLU SER ALA PRO ASN LEU ARG ALA LEU SEQRES 13 A 329 ALA GLU VAL ALA THR GLN THR VAL ARG GLU LEU SER GLY SEQRES 14 A 329 PHE ASP ARG VAL MET LEU TYR LYS PHE ALA PRO ASP ALA SEQRES 15 A 329 THR GLY GLU VAL ILE ALA GLU ALA ARG ARG GLU GLY MET SEQRES 16 A 329 GLN ALA TYR LEU GLY HIS ARG PHE PRO ALA SER THR THR SEQRES 17 A 329 PRO ALA GLN ALA ARG ALA LEU TYR THR ARG HIS LEU LEU SEQRES 18 A 329 ARG LEU THR ALA ASP THR ARG ALA ALA ALA VAL PRO LEU SEQRES 19 A 329 ASP PRO VAL LEU ASN PRO GLN THR ASN ALA PRO THR PRO SEQRES 20 A 329 LEU GLY GLY ALA VAL LEU ARG ALA THR SER PRO MET HIS SEQRES 21 A 329 MET GLN TYR LEU ARG ASN MET GLY VAL GLY SER SER LEU SEQRES 22 A 329 SER VAL SER VAL VAL VAL GLY GLY GLN LEU TRP GLY LEU SEQRES 23 A 329 ILE VAL CYS HIS HIS GLN THR PRO TYR VAL LEU PRO PRO SEQRES 24 A 329 ASP LEU ARG THR THR LEU GLU TYR LEU GLY ARG LEU LEU SEQRES 25 A 329 SER LEU GLN VAL GLN ARG LYS GLU ALA GLU PHE HIS HIS SEQRES 26 A 329 HIS HIS HIS HIS HET LBV A1321 43 HET NA A1322 1 HETNAM LBV 3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3- HETNAM 2 LBV METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4- HETNAM 3 LBV METHYL-PYRROL-1-IUM -2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3- HETNAM 4 LBV ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2- HETNAM 5 LBV YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3- YL]PROPANOIC HETNAM 6 LBV ACID HETNAM NA SODIUM ION HETSYN LBV 2(R),3(E)- PHYTOCHROMOBILIN FORMUL 2 LBV C33 H37 N4 O6 1+ FORMUL 3 NA NA 1+ FORMUL 4 HOH *291(H2 O) HELIX 1 1 PRO A 11 GLY A 15 5 5 HELIX 2 2 ASN A 23 GLU A 27 5 5 HELIX 3 3 ASN A 57 GLY A 63 1 7 HELIX 4 4 GLU A 65 ARG A 70 1 6 HELIX 5 5 THR A 73 LEU A 78 1 6 HELIX 6 6 GLN A 81 LEU A 89 1 9 HELIX 7 7 HIS A 138 ALA A 150 1 13 HELIX 8 8 ASN A 152 GLY A 169 1 18 HELIX 9 9 PRO A 204 THR A 208 5 5 HELIX 10 10 PRO A 209 TYR A 216 1 8 HELIX 11 11 SER A 257 MET A 267 1 11 HELIX 12 12 PRO A 298 GLU A 320 1 23 SHEET 1 AA 7 SER A 34 ILE A 35 0 SHEET 2 AA 7 VAL A 232 ASP A 235 -1 O VAL A 232 N ILE A 35 SHEET 3 AA 7 VAL A 51 SER A 55 -1 O VAL A 54 N ASP A 235 SHEET 4 AA 7 ALA A 40 ASP A 45 -1 O LEU A 41 N SER A 55 SHEET 5 AA 7 LEU A 121 THR A 129 -1 O LEU A 122 N ALA A 44 SHEET 6 AA 7 HIS A 110 VAL A 118 -1 O HIS A 110 N THR A 129 SHEET 7 AA 7 TYR A 99 LEU A 103 -1 O TYR A 99 N VAL A 115 SHEET 1 AB 6 ARG A 202 PHE A 203 0 SHEET 2 AB 6 GLY A 184 ARG A 191 -1 O GLY A 184 N PHE A 203 SHEET 3 AB 6 ARG A 172 PHE A 178 -1 O VAL A 173 N ALA A 190 SHEET 4 AB 6 GLN A 282 HIS A 291 -1 O TRP A 284 N PHE A 178 SHEET 5 AB 6 SER A 271 VAL A 279 -1 O SER A 271 N HIS A 291 SHEET 6 AB 6 LEU A 221 THR A 224 -1 O ARG A 222 N SER A 274 LINK SG CYS A 24 CBA LBV A1321 1555 1555 1.74 LINK NA NA A1322 O HOH A2225 1555 1555 2.62 LINK NA NA A1322 O HOH A2254 1555 1555 3.12 LINK NA NA A1322 O HOH A2293 1555 1555 2.98 CISPEP 1 ASP A 235 PRO A 236 0 -5.70 SITE 1 AC1 26 THR A 20 CYS A 24 MET A 174 TYR A 176 SITE 2 AC1 26 PHE A 203 SER A 206 THR A 207 THR A 208 SITE 3 AC1 26 PRO A 209 TYR A 216 ARG A 254 THR A 256 SITE 4 AC1 26 SER A 257 HIS A 260 TYR A 263 SER A 272 SITE 5 AC1 26 SER A 274 VAL A 288 HIS A 290 HOH A2211 SITE 6 AC1 26 HOH A2212 HOH A2230 HOH A2258 HOH A2272 SITE 7 AC1 26 HOH A2274 HOH A2292 SITE 1 AC2 5 PRO A 247 LEU A 248 GLY A 249 HOH A2225 SITE 2 AC2 5 HOH A2293 CRYST1 95.692 52.912 66.316 90.00 91.37 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 0.010450 0.000000 0.000250 0.00000 SCALE2 0.000000 0.018899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015084 0.00000