PDB Short entry for 4BBU HEADER SIGNALING PROTEIN 27-SEP-12 4BBU TITLE THE PR2 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS PHOTORECEPTOR, LIGHT SENSOR, CHROMOPHORE, PHOTORECEPTOR PROTEIN, KEYWDS 2 RECEPTOR, SENSORY TRANSDUCTION, SIGNALING PROTEIN, PAS, LOV EXPDTA X-RAY DIFFRACTION AUTHOR F.SCHOTTE,H.S.CHO,V.R.I.KAILA,H.KAMIKUBO,N.DASHDORJ,E.R.HENRY, AUTHOR 2 T.J.GRABER,R.HENNING,M.WULFF,G.HUMMER,M.KATAOKA,P.A.ANFINRUD REVDAT 5 08-MAY-19 4BBU 1 REMARK LINK REVDAT 4 30-JAN-19 4BBU 1 REMARK REVDAT 3 25-JAN-17 4BBU 1 REMARK REVDAT 2 05-DEC-12 4BBU 1 JRNL REVDAT 1 14-NOV-12 4BBU 0 JRNL AUTH F.SCHOTTE,H.S.CHO,V.R.I.KAILA,H.KAMIKUBO,N.DASHDORJ, JRNL AUTH 2 E.R.HENRY,T.J.GRABER,R.HENNING,M.WULFF,G.HUMMER,M.KATAOKA, JRNL AUTH 3 P.A.ANFINRUD JRNL TITL WATCHING A SIGNALING PROTEIN FUNCTION IN REAL TIME VIA JRNL TITL 2 100-PS TIME-RESOLVED LAUE CRYSTALLOGRAPHY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 19256 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23132943 JRNL DOI 10.1073/PNAS.1210938109 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.7 REMARK 3 NUMBER OF REFLECTIONS : 10218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 13.2851 - 2.3051 0.82 3682 159 0.1288 0.1908 REMARK 3 2 2.3051 - 1.8312 0.82 3636 161 0.1942 0.2297 REMARK 3 3 1.8312 - 1.6001 0.57 2484 96 0.3203 0.3673 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.00 REMARK 3 SHRINKAGE RADIUS : 0.00 REMARK 3 K_SOL : 0.13 REMARK 3 B_SOL : 13.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34400 REMARK 3 B22 (A**2) : 0.34400 REMARK 3 B33 (A**2) : -0.68810 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1009 REMARK 3 ANGLE : 1.253 1359 REMARK 3 CHIRALITY : 0.076 140 REMARK 3 PLANARITY : 0.006 180 REMARK 3 DIHEDRAL : 15.284 367 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4BBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290054238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 0.96-1.30 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX SX-165MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 13.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 64.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 26.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.56 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, 1.0 M SODIUM REMARK 280 CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM REMARK 280 DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, REMARK 280 MICROSEEDING, TEMPERATURE 295 K, VAPOR DIFFUSION, HANGING DROP 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 20.47350 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 20.47350 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 20.47350 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 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 OH TYR A 98 O HOH A 2118 1.86 REMARK 500 OD2 ASP A 116 O HOH A 2131 2.12 REMARK 500 NE2 GLN A 32 O HOH A 2049 2.12 REMARK 500 O HOH A 2072 O HOH A 2119 2.14 REMARK 500 O HOH A 2016 O HOH A 2017 2.18 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 NZ LYS A 64 O HOH A 2070 5555 2.12 REMARK 500 O HOH A 2052 O HOH A 2052 3555 2.19 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 PHE A 75 -72.69 -127.78 REMARK 500 ASN A 89 91.15 -163.41 REMARK 500 ASP A 97 14.40 -141.52 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 A2011 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2042 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 5.92 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HC4 A 169 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: 1OT6 RELATED DB: PDB REMARK 900 CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OFPHOTOACTIVE REMARK 900 YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATIONAT 110K REMARK 900 RELATED ID: 1OT9 RELATED DB: PDB REMARK 900 CRYOTRAPPED STATE IN WILD TYPE PHOTOACTIVE YELLOW PROTEIN,INDUCED REMARK 900 WITH CONTINUOUS ILLUMINATION AT 110K REMARK 900 RELATED ID: 1OTA RELATED DB: PDB REMARK 900 E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K REMARK 900 RELATED ID: 1OTB RELATED DB: PDB REMARK 900 WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K REMARK 900 RELATED ID: 1OTD RELATED DB: PDB REMARK 900 STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN ANDTHEIR ROLE REMARK 900 IN ITS PHOTOCYCLE REMARK 900 RELATED ID: 1OTE RELATED DB: PDB REMARK 900 E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K REMARK 900 RELATED ID: 1OTI RELATED DB: PDB REMARK 900 E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 295K REMARK 900 RELATED ID: 1S1Y RELATED DB: PDB REMARK 900 PHOTOACTIVATED CHROMOPHORE CONFORMATION IN PHOTOACTIVEYELLOW REMARK 900 PROTEIN (E46Q MUTANT) FROM 10 MICROSECONDS TO 3MILLISECONDS REMARK 900 RELATED ID: 1S1Z RELATED DB: PDB REMARK 900 PHOTOACTIVATED CHROMOPHORE CONFORMATION IN PHOTOACTIVEYELLOW REMARK 900 PROTEIN (E46Q MUTANT) FROM 10 TO 500 NANOSECONDS REMARK 900 RELATED ID: 1S4R RELATED DB: PDB REMARK 900 STRUCTURE OF A REACTION INTERMEDIATE IN THE PHOTOCYCLE OFPYP REMARK 900 EXTRACTED BY A SVD-DRIVEN ANALYSIS REMARK 900 RELATED ID: 1S4S RELATED DB: PDB REMARK 900 REACTION INTERMEDIATE IN THE PHOTOCYCLE OF PYP, INTERMEDIATE REMARK 900 OCCUPIED BETWEEN 100 MICRO-SECONDS TO 5 MILLI-SECONDS REMARK 900 RELATED ID: 1T18 RELATED DB: PDB REMARK 900 EARLY INTERMEDIATE IE1 FROM TIME-RESOLVED CRYSTALLOGRAPHYOF THE REMARK 900 E46Q MUTANT OF PYP REMARK 900 RELATED ID: 1T19 RELATED DB: PDB REMARK 900 EARLY INTERMEDIATE IE2 FROM TIME-RESOLVED CRYSTALLOGRAPHYOF THE REMARK 900 E46Q MUTANT OF PYP REMARK 900 RELATED ID: 1T1A RELATED DB: PDB REMARK 900 LATE INTERMEDIATE IL1 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q REMARK 900 MUTANT OF PYP REMARK 900 RELATED ID: 1T1B RELATED DB: PDB REMARK 900 LATE INTERMEDIATE IL2 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q REMARK 900 MUTANT OF PYP REMARK 900 RELATED ID: 1T1C RELATED DB: PDB REMARK 900 LATE INTERMEDIATE IL3 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q REMARK 900 MUTANT OF PYP REMARK 900 RELATED ID: 1TS0 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PB1 INTERMEDIATE FROM TIME-RESOLVED REMARK 900 LAUECRYSTALLOGRAPHY REMARK 900 RELATED ID: 1TS6 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PB2 INTERMEDIATE FROM TIME-RESOLVED REMARK 900 LAUECRYSTALLOGRAPHY REMARK 900 RELATED ID: 1TS7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PR CIS WOBBLE AND PR E46Q INTERMEDIATESFROM TIME- REMARK 900 RESOLVED LAUE CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1TS8 RELATED DB: PDB REMARK 900 STRUCTURE OF THE PR CIS PLANAR INTERMEDIATE FROM TIME -RESOLVED REMARK 900 LAUE CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1UGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYP E46Q MUTANT REMARK 900 RELATED ID: 1UWN RELATED DB: PDB REMARK 900 THE INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN: REMARK 900 A COMMON MECHANISM ON LIGHT ACTIVATION IN PHOTORECEPTOR PROTEINS REMARK 900 RELATED ID: 1UWP RELATED DB: PDB REMARK 900 INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN REMARK 900 RELATED ID: 1XFN RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE GROUND STATE OF THE PHOTOACTIVE YELLOWPROTEIN REMARK 900 LACKING THE N-TERMINAL PART REMARK 900 RELATED ID: 1XFQ RELATED DB: PDB REMARK 900 STRUCTURE OF THE BLUE SHIFTED INTERMEDIATE STATE OF THEPHOTOACTIVE REMARK 900 YELLOW PROTEIN LACKING THE N-TERMINAL PART REMARK 900 RELATED ID: 2D01 RELATED DB: PDB REMARK 900 WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P65 FORM REMARK 900 RELATED ID: 2D02 RELATED DB: PDB REMARK 900 R52Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 FORM 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: 4B9O RELATED DB: PDB REMARK 900 THE PR0 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN REMARK 900 RELATED ID: 4BBT RELATED DB: PDB REMARK 900 THE PR1 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN REMARK 900 RELATED ID: 4BBV RELATED DB: PDB REMARK 900 THE PB0 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN DBREF 4BBU A 1 125 UNP P16113 PYP_HALHA 1 125 SEQRES 1 A 125 MET GLU HIS VAL ALA PHE GLY SER GLU ASP ILE GLU ASN SEQRES 2 A 125 THR LEU ALA LYS MET ASP ASP GLY GLN LEU ASP GLY LEU SEQRES 3 A 125 ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE SEQRES 4 A 125 LEU GLN TYR ASN ALA ALA GLU GLY ASP ILE THR GLY ARG SEQRES 5 A 125 ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS ASP SEQRES 6 A 125 VAL ALA PRO CYS THR ASP SER PRO GLU PHE TYR GLY LYS SEQRES 7 A 125 PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR MET SEQRES 8 A 125 PHE GLU TYR THR PHE ASP TYR GLN MET THR PRO THR LYS SEQRES 9 A 125 VAL LYS VAL HIS MET LYS LYS ALA LEU SER GLY ASP SER SEQRES 10 A 125 TYR TRP VAL PHE VAL LYS ARG VAL HET HC4 A 169 11 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 FORMUL 3 HOH *139(H2 O) HELIX 1 1 ASP A 10 ALA A 16 1 7 HELIX 2 2 ASP A 19 ASP A 24 1 6 HELIX 3 3 ASN A 43 GLY A 51 1 9 HELIX 4 4 ASP A 53 ILE A 58 1 6 HELIX 5 5 PHE A 62 VAL A 66 1 5 HELIX 6 6 ALA A 67 ASP A 71 5 5 HELIX 7 7 PHE A 75 GLY A 86 1 12 SHEET 1 AA 5 ILE A 39 TYR A 42 0 SHEET 2 AA 5 GLY A 29 ASP A 34 -1 O GLN A 32 N LEU A 40 SHEET 3 AA 5 SER A 117 ARG A 124 -1 O TYR A 118 N LEU A 33 SHEET 4 AA 5 THR A 103 LYS A 111 -1 O LYS A 106 N LYS A 123 SHEET 5 AA 5 ASN A 89 PHE A 96 -1 O THR A 90 N MET A 109 LINK C1 HC4 A 169 SG CYS A 69 1555 1555 1.75 SITE 1 AC1 8 TYR A 42 GLU A 46 THR A 50 ARG A 52 SITE 2 AC1 8 ALA A 67 CYS A 69 PHE A 96 TYR A 98 CRYST1 66.833 66.833 40.947 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 0.014963 0.008639 0.000000 0.00000 SCALE2 0.000000 0.017277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024422 0.00000