HEADER SIGNALING PROTEIN 10-FEB-04 1UWN TITLE THE INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN: A TITLE 2 COMMON MECHANISM ON LIGHT ACTIVATION IN PHOTORECEPTOR PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: PYP; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DARK STATE, GROUND STATE (PG) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 STRAIN: BN9626; SOURCE 5 CELL: BACTERIUM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15/ PREP4 PHISP; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE30; SOURCE 10 OTHER_DETAILS: HALORHODOSPIRA HALOPHILA WAS PREVIOUSLY KNOWN AS SOURCE 11 ECTOTHIORHODOSPIRA HALOPHILA KEYWDS SIGNALING PROTEIN, PAS, LOV, PHOTOCYCLE, PHOTORECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR R.KORT,K.J.HELLINGWERF,R.B.G.RAVELLI REVDAT 6 27-FEB-19 1UWN 1 JRNL REMARK LINK REVDAT 5 30-JAN-19 1UWN 1 REMARK LINK REVDAT 4 13-JUL-11 1UWN 1 VERSN REVDAT 3 24-FEB-09 1UWN 1 VERSN REVDAT 2 03-MAY-05 1UWN 1 JRNL REMARK REVDAT 1 25-MAR-04 1UWN 0 JRNL AUTH R.KORT,K.J.HELLINGWERF,R.B.RAVELLI JRNL TITL INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW JRNL TITL 2 PROTEIN. JRNL REF J. BIOL. CHEM. V. 279 26417 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15026418 JRNL DOI 10.1074/JBC.M311961200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.KORT,R.B.G.RAVELLI,F.SCHOTTE,D.BOURGEOIS,W.CRIELAARD, REMARK 1 AUTH 2 K.J.HELLINGWERF,M.WULFF REMARK 1 TITL CHARACTERIZATION OF PHOTOCYCLE INTERMEDIATES IN CRYSTALLINE REMARK 1 TITL 2 PHOTOACTIVE YELLOW PROTEIN REMARK 1 REF PHOTOCHEM.PHOTOBIOL. V. 78 131 2003 REMARK 1 REFN ISSN 0031-8655 REMARK 1 PMID 12945580 REMARK 1 DOI 10.1562/0031-8655(2003)078<0131:COPIIC>2.0.CO;2 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 29290 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1559 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2026 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1460 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.1620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 970 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.24000 REMARK 3 B12 (A**2) : -0.08000 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): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.466 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1127 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 967 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1522 ; 1.830 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2302 ; 1.660 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 139 ; 5.508 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 155 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1273 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 227 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 474 ; 0.279 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1243 ; 0.264 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1099 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 105 ; 0.163 ; 0.200 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): 59 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 90 ; 0.281 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.266 ; 0.200 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): 668 ; 1.469 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1087 ; 2.234 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 459 ; 2.932 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 433 ; 4.288 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS 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. THE EXPERIMENTAL DENSITY SHOWS MAIN-CHAIN DISORDER REMARK 3 FOR RESIDUES 16-18 AND 115-117. THE FIRST 3 RESIDUES (MSE1-HIS3) REMARK 3 ARE DISORDERED AS WELL. REMARK 4 REMARK 4 1UWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1290014537. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 85.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393, 0.9796 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: STATISTICS ARE GIVEN FOR REMOTE DATA SET (2 SWEEPS) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE REMARK 280 PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 0.00000 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 0.00000 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 20.29200 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 20.29200 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 20.29200 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 S SO4 X1128 LIES ON A SPECIAL POSITION. REMARK 375 HOH X2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH X2017 LIES ON A SPECIAL POSITION. 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 X 2089 O HOH X 2090 1.98 REMARK 500 OE1 GLN X 99 O HOH X 2103 2.16 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 X 53 CB - CG - OD2 ANGL. DEV. = 6.3 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 LYS X 17 15.43 56.26 REMARK 500 PHE X 75 -74.39 -131.46 REMARK 500 ASN X 89 98.97 -160.61 REMARK 500 ASP X 97 14.14 -142.42 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 X2016 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH X2017 DISTANCE = 6.03 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 1127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 1128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HC4 X 1126 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D7E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVEYELLOW REMARK 900 PROTEIN REMARK 900 RELATED ID: 1F98 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTT50V REMARK 900 RELATED ID: 1F9I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTY42F REMARK 900 RELATED ID: 1GSV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW REMARK 900 PROTEIN REMARK 900 RELATED ID: 1GSW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW REMARK 900 PROTEIN G51S MUTANT REMARK 900 RELATED ID: 1GSX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW REMARK 900 PROTEIN G47S/G51S MUTANT REMARK 900 RELATED ID: 1KOU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEINRECONSTITUTED REMARK 900 WITH CAFFEIC ACID AT 1. 16 A RESOLUTION REMARK 900 RELATED ID: 1NWZ RELATED DB: PDB REMARK 900 PYP ULTRA-HIGH RESOLUTION STRUCTURE OF A BACTERIALPHOTORECEPTOR REMARK 900 RELATED ID: 1ODV RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN 1-25 DELETION MUTANT REMARK 900 RELATED ID: 2PHY RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) 2PHY 3 REMARK 900 RELATED ID: 2PYP RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50%GROUND STATE, REMARK 900 50% BLEACHED REMARK 900 RELATED ID: 2PYR RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K) REMARK 900 RELATED ID: 3PHY RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED),SOLUTION REMARK 900 STRUCTURE, NMR, 26 STRUCTURES REMARK 900 RELATED ID: 3PYP RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT REMARK 900 CYCLEINTERMEDIATE REMARK 900 RELATED ID: 1UWP RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, INITIAL EVENTS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MET-RESIDUES WERE SUBSTITUTED BY SEMET DBREF 1UWN X 1 125 UNP P16113 PYP_HALHA 1 125 SEQRES 1 X 125 MSE GLU HIS VAL ALA PHE GLY SER GLU ASP ILE GLU ASN SEQRES 2 X 125 THR LEU ALA LYS MSE ASP ASP GLY GLN LEU ASP GLY LEU SEQRES 3 X 125 ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE SEQRES 4 X 125 LEU GLN TYR ASN ALA ALA GLU GLY ASP ILE THR GLY ARG SEQRES 5 X 125 ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS ASP SEQRES 6 X 125 VAL ALA PRO CYS THR ASP SER PRO GLU PHE TYR GLY LYS SEQRES 7 X 125 PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR MSE SEQRES 8 X 125 PHE GLU TYR THR PHE ASP TYR GLN MSE THR PRO THR LYS SEQRES 9 X 125 VAL LYS VAL HIS MSE LYS LYS ALA LEU SER GLY ASP SER SEQRES 10 X 125 TYR TRP VAL PHE VAL LYS ARG VAL MODRES 1UWN MSE X 1 MET SELENOMETHIONINE MODRES 1UWN MSE X 18 MET SELENOMETHIONINE MODRES 1UWN MSE X 91 MET SELENOMETHIONINE MODRES 1UWN MSE X 100 MET SELENOMETHIONINE MODRES 1UWN MSE X 109 MET SELENOMETHIONINE HET MSE X 1 2 HET MSE X 18 16 HET MSE X 91 16 HET MSE X 100 16 HET MSE X 109 24 HET HC4 X1126 11 HET SO4 X1127 5 HET SO4 X1128 5 HETNAM MSE SELENOMETHIONINE HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETNAM SO4 SULFATE ION HETSYN HC4 PARA-COUMARIC ACID FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HC4 C9 H8 O3 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *138(H2 O) HELIX 1 1 ASP X 10 ALA X 16 1 7 HELIX 2 2 ASP X 19 ASP X 24 1 6 HELIX 3 3 ASN X 43 GLY X 51 1 9 HELIX 4 4 ASP X 53 ILE X 58 1 6 HELIX 5 5 MSE X 1 VAL X 66 1 66 HELIX 6 6 ALA X 67 ASP X 71 5 5 HELIX 7 7 PHE X 75 GLY X 86 1 12 SHEET 1 XA 5 ILE X 39 TYR X 42 0 SHEET 2 XA 5 GLY X 29 ASP X 34 -1 O GLN X 32 N LEU X 40 SHEET 3 XA 5 SER X 117 ARG X 124 -1 O TYR X 118 N LEU X 33 SHEET 4 XA 5 THR X 103 LYS X 111 -1 O LYS X 106 N LYS X 123 SHEET 5 XA 5 ASN X 89 PHE X 96 -1 O THR X 90 N MSE X 109 LINK C ALYS X 17 N AMSE X 18 1555 1555 1.35 LINK C BLYS X 17 N BMSE X 18 1555 1555 1.34 LINK C AMSE X 18 N ASP X 19 1555 1555 1.33 LINK C BMSE X 18 N ASP X 19 1555 1555 1.34 LINK SG CYS X 69 C1 HC4 X1126 1555 1555 1.79 LINK C THR X 90 N AMSE X 91 1555 1555 1.32 LINK C THR X 90 N BMSE X 91 1555 1555 1.33 LINK C BMSE X 91 N PHE X 92 1555 1555 1.33 LINK C AMSE X 91 N PHE X 92 1555 1555 1.32 LINK C GLN X 99 N BMSE X 100 1555 1555 1.33 LINK C GLN X 99 N AMSE X 100 1555 1555 1.33 LINK C BMSE X 100 N THR X 101 1555 1555 1.32 LINK C AMSE X 100 N THR X 101 1555 1555 1.34 LINK C HIS X 108 N BMSE X 109 1555 1555 1.34 LINK C HIS X 108 N AMSE X 109 1555 1555 1.33 LINK C HIS X 108 N CMSE X 109 1555 1555 1.33 LINK C CMSE X 109 N LYS X 110 1555 1555 1.32 LINK C BMSE X 109 N LYS X 110 1555 1555 1.34 LINK C AMSE X 109 N LYS X 110 1555 1555 1.33 LINK C MSE X 1 N GLU X 2 1555 1555 1.33 SITE 1 AC1 3 ASP X 19 ASP X 20 GLY X 21 SITE 1 AC2 3 LYS X 104 HOH X2137 HOH X2138 SITE 1 AC3 11 ILE X 31 TYR X 42 GLU X 46 THR X 50 SITE 2 AC3 11 ARG X 52 PHE X 62 ALA X 67 PRO X 68 SITE 3 AC3 11 CYS X 69 PHE X 96 TYR X 98 CRYST1 65.922 65.922 40.584 90.00 90.00 120.00 P 63 6 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 0.015169 0.008758 0.000000 0.00000 SCALE2 0.000000 0.017516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024640 0.00000 HETATM 1 C MSE X 1 1.522 29.407 -9.596 0.40 21.75 C ANISOU 1 C MSE X 1 2815 2747 2702 26 -50 144 C HETATM 2 O MSE X 1 1.399 30.030 -10.651 0.40 21.37 O ANISOU 2 O MSE X 1 2773 2765 2581 13 -91 171 O