HEADER SIGNALING PROTEIN 14-JUL-12 3VV4 TITLE CRYSTAL STRUCTURE OF CYANOBACTERIOCHROME TEPIXJ GAF DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYL-ACCEPTING CHEMOTAXIS PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GAF DOMAIN, UNP RESIDUES 430-591; COMPND 5 SYNONYM: TEPIXJ; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS ELONGATUS; SOURCE 3 ORGANISM_TAXID: 197221; SOURCE 4 STRAIN: BP-1; SOURCE 5 GENE: TLL0569; SOURCE 6 EXPRESSION_SYSTEM: SYNECHOCYSTIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1148; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PCC6803 KEYWDS CYANOBACTERIOCHROME, PHYCOVIOLOBILIN BINDING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.ISHIZUKA,R.NARIKAWA,N.MURAKI,T.SHIBA,G.KURISU,M.IKEUCHI REVDAT 1 30-JAN-13 3VV4 0 JRNL AUTH R.NARIKAWA,T.ISHIZUKA,N.MURAKI,T.SHIBA,G.KURISU,M.IKEUCHI JRNL TITL STRUCTURES OF CYANOBACTERIOCHROMES FROM PHOTOTAXIS JRNL TITL 2 REGULATORS ANPIXJ AND TEPIXJ REVEAL GENERAL AND SPECIFIC JRNL TITL 3 PHOTOCONVERSION MECHANISM JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 918 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23256156 JRNL DOI 10.1073/PNAS.1212098110 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 32040 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1606 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2522 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : -0.06000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.994 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2680 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3650 ; 1.495 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 311 ; 7.173 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;40.290 ;23.942 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 438 ;18.522 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.623 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 400 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2060 ; 0.016 ; 0.021 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 201 3 REMARK 3 1 B 6 B 201 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 655 ; 0.140 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 623 ; 0.470 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 655 ; 3.290 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 623 ; 6.220 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 158 REMARK 3 RESIDUE RANGE : A 201 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2250 -20.7900 -15.4150 REMARK 3 T TENSOR REMARK 3 T11: 0.0796 T22: 0.0839 REMARK 3 T33: 0.0391 T12: -0.0635 REMARK 3 T13: 0.0111 T23: -0.0310 REMARK 3 L TENSOR REMARK 3 L11: 1.3597 L22: 0.9344 REMARK 3 L33: 2.4442 L12: -0.2149 REMARK 3 L13: -0.1438 L23: 0.0424 REMARK 3 S TENSOR REMARK 3 S11: -0.0655 S12: 0.0616 S13: -0.1102 REMARK 3 S21: -0.0774 S22: -0.0259 S23: 0.0020 REMARK 3 S31: 0.2378 S32: -0.2546 S33: 0.0914 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 : B -1 B 158 REMARK 3 RESIDUE RANGE : B 201 B 201 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2730 -44.2100 -41.2480 REMARK 3 T TENSOR REMARK 3 T11: 0.1235 T22: 0.0449 REMARK 3 T33: 0.0802 T12: -0.0587 REMARK 3 T13: -0.0177 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.2745 L22: 1.8400 REMARK 3 L33: 2.3896 L12: 0.1685 REMARK 3 L13: 0.4425 L23: 0.4805 REMARK 3 S TENSOR REMARK 3 S11: 0.0568 S12: -0.0365 S13: 0.0697 REMARK 3 S21: 0.3076 S22: -0.0975 S23: -0.0440 REMARK 3 S31: -0.2004 S32: 0.0316 S33: 0.0407 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3VV4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-12. REMARK 100 THE RCSB ID CODE IS RCSB095537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36534 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.15M AMMONIUM SULFATE, 100MM MES REMARK 280 BUFFER, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.11133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.55567 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.33350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.77783 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 138.88917 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 36.43400 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 -63.10554 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 55.55567 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -36.43400 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -63.10554 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -55.55567 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 -32 REMARK 465 GLY A -31 REMARK 465 GLY A -30 REMARK 465 SER A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 GLY A -22 REMARK 465 MET A -21 REMARK 465 ALA A -20 REMARK 465 SER A -19 REMARK 465 MET A -18 REMARK 465 THR A -17 REMARK 465 GLY A -16 REMARK 465 GLY A -15 REMARK 465 GLN A -14 REMARK 465 GLN A -13 REMARK 465 MET A -12 REMARK 465 GLY A -11 REMARK 465 ARG A -10 REMARK 465 ASP A -9 REMARK 465 LEU A -8 REMARK 465 TYR A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 LYS A -2 REMARK 465 ASP A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 VAL A 4 REMARK 465 GLN A 5 REMARK 465 GLU A 159 REMARK 465 GLN A 160 REMARK 465 THR A 161 REMARK 465 ILE A 162 REMARK 465 ALA A 163 REMARK 465 MET B -32 REMARK 465 GLY B -31 REMARK 465 GLY B -30 REMARK 465 SER B -29 REMARK 465 HIS B -28 REMARK 465 HIS B -27 REMARK 465 HIS B -26 REMARK 465 HIS B -25 REMARK 465 HIS B -24 REMARK 465 HIS B -23 REMARK 465 GLY B -22 REMARK 465 MET B -21 REMARK 465 ALA B -20 REMARK 465 SER B -19 REMARK 465 MET B -18 REMARK 465 THR B -17 REMARK 465 GLY B -16 REMARK 465 GLY B -15 REMARK 465 GLN B -14 REMARK 465 GLN B -13 REMARK 465 MET B -12 REMARK 465 GLY B -11 REMARK 465 ARG B -10 REMARK 465 ASP B -9 REMARK 465 LEU B -8 REMARK 465 TYR B -7 REMARK 465 ASP B -6 REMARK 465 ASP B -5 REMARK 465 ASP B -4 REMARK 465 ASP B -3 REMARK 465 LYS B -2 REMARK 465 GLU B 159 REMARK 465 GLN B 160 REMARK 465 THR B 161 REMARK 465 ILE B 162 REMARK 465 ALA B 163 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 374 O HOH A 377 1.82 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 CD1 ILE A 80 CE MET B 1 3545 2.19 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 31 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 31 NE - CZ - NH2 ANGL. DEV. = -4.2 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 ASP A 64 111.50 -161.27 REMARK 500 ASP B 64 109.70 -162.90 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 31 0.10 SIDE CHAIN REMARK 500 ARG B 31 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR B 18 24.9 L L OUTSIDE RANGE 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 PVG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PVG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W2Z RELATED DB: PDB DBREF 3VV4 A 2 163 UNP Q8DLC7 Q8DLC7_THEEB 430 591 DBREF 3VV4 B 2 163 UNP Q8DLC7 Q8DLC7_THEEB 430 591 SEQADV 3VV4 MET A -32 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -31 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -30 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 SER A -29 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -28 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -27 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -26 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -25 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -24 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A -23 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -22 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET A -21 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ALA A -20 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 SER A -19 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET A -18 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 THR A -17 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -16 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -15 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLN A -14 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLN A -13 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET A -12 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY A -11 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ARG A -10 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -9 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 LEU A -8 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 TYR A -7 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -6 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -5 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -4 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -3 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 LYS A -2 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP A -1 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS A 0 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET A 1 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET B -32 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -31 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -30 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 SER B -29 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -28 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -27 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -26 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -25 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -24 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B -23 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -22 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET B -21 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ALA B -20 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 SER B -19 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET B -18 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 THR B -17 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -16 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -15 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLN B -14 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLN B -13 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET B -12 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 GLY B -11 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ARG B -10 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -9 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 LEU B -8 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 TYR B -7 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -6 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -5 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -4 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -3 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 LYS B -2 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 ASP B -1 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 HIS B 0 UNP Q8DLC7 EXPRESSION TAG SEQADV 3VV4 MET B 1 UNP Q8DLC7 EXPRESSION TAG SEQRES 1 A 196 MET GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 196 SER MET THR GLY GLY GLN GLN MET GLY ARG ASP LEU TYR SEQRES 3 A 196 ASP ASP ASP ASP LYS ASP HIS MET ALA ALA VAL GLN LEU SEQRES 4 A 196 SER GLU LEU ARG ASP ARG GLN ALA ILE PHE GLU THR LEU SEQRES 5 A 196 VAL ALA LYS GLY ARG GLU LEU LEU ALA CYS ASP ARG VAL SEQRES 6 A 196 ILE VAL TYR ALA PHE ASP ASP ASN TYR VAL GLY THR VAL SEQRES 7 A 196 VAL ALA GLU SER VAL ALA GLU GLY TRP PRO GLN ALA ARG SEQRES 8 A 196 ASP GLN VAL ILE GLU ASP PRO CYS PHE ARG GLU HIS TRP SEQRES 9 A 196 VAL GLU ALA TYR ARG GLN GLY ARG ILE GLN ALA THR THR SEQRES 10 A 196 ASP ILE PHE LYS ALA GLY LEU THR GLU CYS HIS LEU ASN SEQRES 11 A 196 GLN LEU ARG PRO LEU LYS VAL ARG ALA ASN LEU VAL VAL SEQRES 12 A 196 PRO MET VAL ILE ASP ASP GLN LEU PHE GLY LEU LEU ILE SEQRES 13 A 196 ALA HIS GLN CYS SER GLU PRO ARG GLN TRP GLN GLU ILE SEQRES 14 A 196 GLU ILE ASP GLN PHE SER GLU LEU ALA SER THR GLY SER SEQRES 15 A 196 LEU VAL LEU GLU ARG LEU HIS PHE LEU GLU GLN THR ILE SEQRES 16 A 196 ALA SEQRES 1 B 196 MET GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 B 196 SER MET THR GLY GLY GLN GLN MET GLY ARG ASP LEU TYR SEQRES 3 B 196 ASP ASP ASP ASP LYS ASP HIS MET ALA ALA VAL GLN LEU SEQRES 4 B 196 SER GLU LEU ARG ASP ARG GLN ALA ILE PHE GLU THR LEU SEQRES 5 B 196 VAL ALA LYS GLY ARG GLU LEU LEU ALA CYS ASP ARG VAL SEQRES 6 B 196 ILE VAL TYR ALA PHE ASP ASP ASN TYR VAL GLY THR VAL SEQRES 7 B 196 VAL ALA GLU SER VAL ALA GLU GLY TRP PRO GLN ALA ARG SEQRES 8 B 196 ASP GLN VAL ILE GLU ASP PRO CYS PHE ARG GLU HIS TRP SEQRES 9 B 196 VAL GLU ALA TYR ARG GLN GLY ARG ILE GLN ALA THR THR SEQRES 10 B 196 ASP ILE PHE LYS ALA GLY LEU THR GLU CYS HIS LEU ASN SEQRES 11 B 196 GLN LEU ARG PRO LEU LYS VAL ARG ALA ASN LEU VAL VAL SEQRES 12 B 196 PRO MET VAL ILE ASP ASP GLN LEU PHE GLY LEU LEU ILE SEQRES 13 B 196 ALA HIS GLN CYS SER GLU PRO ARG GLN TRP GLN GLU ILE SEQRES 14 B 196 GLU ILE ASP GLN PHE SER GLU LEU ALA SER THR GLY SER SEQRES 15 B 196 LEU VAL LEU GLU ARG LEU HIS PHE LEU GLU GLN THR ILE SEQRES 16 B 196 ALA HET PVG A 201 43 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET PVG B 201 43 HET SO4 B 202 5 HETNAM PVG PHYCOVIOLOBILIN, GREEN LIGHT-ABSORBING FORM HETNAM SO4 SULFATE ION FORMUL 3 PVG 2(C33 H40 N4 O6) FORMUL 4 SO4 4(O4 S 2-) FORMUL 9 HOH *111(H2 O) HELIX 1 1 ASP A 11 ALA A 28 1 18 HELIX 2 2 GLN A 56 GLN A 60 5 5 HELIX 3 3 GLU A 69 GLN A 77 1 9 HELIX 4 4 ASP A 85 ALA A 89 5 5 HELIX 5 5 THR A 92 ARG A 100 1 9 HELIX 6 6 PRO A 101 LYS A 103 5 3 HELIX 7 7 GLN A 134 LEU A 158 1 25 HELIX 8 8 GLN B 5 LEU B 9 5 5 HELIX 9 9 ASP B 11 ALA B 28 1 18 HELIX 10 10 GLN B 56 GLN B 60 5 5 HELIX 11 11 HIS B 70 GLN B 77 1 8 HELIX 12 12 ASP B 85 ALA B 89 5 5 HELIX 13 13 THR B 92 ARG B 100 1 9 HELIX 14 14 PRO B 101 LYS B 103 5 3 HELIX 15 15 GLN B 134 LEU B 158 1 25 SHEET 1 A 5 GLY A 43 VAL A 50 0 SHEET 2 A 5 ARG A 31 PHE A 37 -1 N VAL A 32 O SER A 49 SHEET 3 A 5 GLN A 117 GLN A 126 -1 O HIS A 125 N ARG A 31 SHEET 4 A 5 ALA A 106 ILE A 114 -1 N VAL A 110 O LEU A 122 SHEET 5 A 5 GLN A 81 THR A 83 -1 N THR A 83 O ASN A 107 SHEET 1 B 5 GLY B 43 VAL B 50 0 SHEET 2 B 5 ARG B 31 PHE B 37 -1 N VAL B 32 O SER B 49 SHEET 3 B 5 GLN B 117 GLN B 126 -1 O ILE B 123 N ILE B 33 SHEET 4 B 5 ALA B 106 ILE B 114 -1 N MET B 112 O GLY B 120 SHEET 5 B 5 GLN B 81 THR B 83 -1 N THR B 83 O ASN B 107 SSBOND 1 CYS A 66 CYS B 66 1555 1555 2.05 LINK SG CYS A 94 C31 PVG A 201 1555 1555 2.03 LINK SG CYS B 94 C31 PVG B 201 1555 1555 2.16 SITE 1 AC1 19 TYR A 35 VAL A 45 GLU A 63 ASP A 64 SITE 2 AC1 19 PRO A 65 GLU A 69 TRP A 71 ARG A 79 SITE 3 AC1 19 GLN A 81 CYS A 94 HIS A 95 GLN A 98 SITE 4 AC1 19 ASN A 107 HOH A 311 HOH A 319 HOH A 321 SITE 5 AC1 19 HOH A 334 HOH A 351 HOH A 361 SITE 1 AC2 2 ARG A 24 GLU A 52 SITE 1 AC3 2 THR A 84 GLN A 132 SITE 1 AC4 1 ARG A 105 SITE 1 AC5 19 ILE B 33 TYR B 35 VAL B 45 ILE B 62 SITE 2 AC5 19 GLU B 63 ASP B 64 PRO B 65 GLU B 69 SITE 3 AC5 19 TRP B 71 ARG B 79 GLN B 81 CYS B 94 SITE 4 AC5 19 HIS B 95 GLN B 98 LEU B 102 ASN B 107 SITE 5 AC5 19 HOH B 307 HOH B 309 HOH B 316 SITE 1 AC6 3 ARG B 24 ALA B 51 GLU B 52 CRYST1 72.868 72.868 166.667 90.00 90.00 120.00 P 65 12 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 0.013723 0.007923 0.000000 0.00000 SCALE2 0.000000 0.015846 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006000 0.00000