HEADER PHOTORECEPTOR 03-FEB-97 2PYP TITLE PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, TITLE 2 50% BLEACHED COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 STRAIN: BN9626 KEYWDS PHOTORECEPTOR, CHROMOPHORE, LIGHT SENSOR FOR PHOTOTAXIS EXPDTA X-RAY DIFFRACTION AUTHOR U.K.GENICK,G.E.O.BORGSTAHL,K.NG,Z.REN,C.PRADERVAND,P.BURKE,V.SRAJER, AUTHOR 2 T.TENG,W.SCHILDKAMP,D.E.MCREE,K.MOFFAT,E.D.GETZOFF REVDAT 4 29-NOV-17 2PYP 1 REMARK HELIX REVDAT 3 24-FEB-09 2PYP 1 VERSN REVDAT 2 01-APR-03 2PYP 1 JRNL REVDAT 1 29-APR-98 2PYP 0 JRNL AUTH U.K.GENICK,G.E.BORGSTAHL,K.NG,Z.REN,C.PRADERVAND,P.M.BURKE, JRNL AUTH 2 V.SRAJER,T.Y.TENG,W.SCHILDKAMP,D.E.MCREE,K.MOFFAT, JRNL AUTH 3 E.D.GETZOFF JRNL TITL STRUCTURE OF A PROTEIN PHOTOCYCLE INTERMEDIATE BY JRNL TITL 2 MILLISECOND TIME-RESOLVED CRYSTALLOGRAPHY. JRNL REF SCIENCE V. 275 1471 1997 JRNL REFN ISSN 0036-8075 JRNL PMID 9045611 JRNL DOI 10.1126/SCIENCE.275.5305.1471 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 7392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.34 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 765 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 976 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.605 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PYP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-93 REMARK 200 TEMPERATURE (KELVIN) : 261 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : ALUMINUM FOIL 150 MICRON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : LAUEVIEW REMARK 200 DATA SCALING SOFTWARE : LAUEVIEW REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 5.500 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE MODEL OF THE GROUND STATE STRUCTURE WAS USED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.8 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 20.40000 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 20.40000 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 20.40000 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 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: 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 -74.27 -130.59 REMARK 500 ASN A 89 94.56 -163.00 REMARK 500 ASP A 97 18.54 -141.79 REMARK 500 ASP A 116 58.81 -107.86 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 HC4 A 126 DBREF 2PYP A 1 125 UNP P16113 PYP_ECTHA 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 126 22 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 FORMUL 3 HOH *56(H2 O) HELIX 1 A-1 ILE A 11 LEU A 15 1 5 HELIX 2 A-2 ASP A 19 LEU A 23 1 5 HELIX 3 A-3 ASN A 43 THR A 50 1 8 HELIX 4 A-4 ASP A 53 VAL A 57 1 5 HELIX 5 PI ASN A 61 ALA A 67 3 7 HELIX 6 A-5 PHE A 75 GLY A 86 1 12 SHEET 1 B-1 6 LYS A 60 PHE A 62 0 SHEET 2 B-1 6 GLY A 37 GLN A 41 -1 O GLY A 37 N PHE A 62 SHEET 3 B-1 6 GLY A 29 ASP A 34 -1 O GLN A 32 N LEU A 40 SHEET 4 B-1 6 SER A 117 VAL A 125 -1 O VAL A 120 N ILE A 31 SHEET 5 B-1 6 THR A 103 ALA A 112 -1 O HIS A 108 N PHE A 121 SHEET 6 B-1 6 LEU A 88 PHE A 96 -1 O THR A 90 N MET A 109 SHEET 1 B-2 6 LYS A 60 PHE A 62 0 SHEET 2 B-2 6 GLY A 37 GLN A 41 -1 O GLY A 37 N PHE A 62 SHEET 3 B-2 6 GLY A 29 ASP A 34 -1 O GLN A 32 N LEU A 40 SHEET 4 B-2 6 SER A 117 VAL A 125 -1 O VAL A 120 N ILE A 31 SHEET 5 B-2 6 THR A 103 ALA A 112 -1 O HIS A 108 N PHE A 121 SHEET 6 B-2 6 LEU A 88 PHE A 96 -1 O THR A 90 N MET A 109 LINK C1 AHC4 A 126 SG ACYS A 69 1555 1555 1.75 LINK C1 AHC4 A 126 SG BCYS A 69 1555 1555 2.02 LINK C1 BHC4 A 126 SG ACYS A 69 1555 1555 1.48 LINK C1 BHC4 A 126 SG BCYS A 69 1555 1555 1.74 LINK C3'BHC4 A 126 NH2AARG A 52 1555 1555 1.67 LINK C4'BHC4 A 126 NE AARG A 52 1555 1555 2.03 LINK C4'BHC4 A 126 CZ AARG A 52 1555 1555 1.46 LINK C4'BHC4 A 126 NH2AARG A 52 1555 1555 1.57 LINK O4'BHC4 A 126 NE AARG A 52 1555 1555 1.03 LINK O4'BHC4 A 126 CZ AARG A 52 1555 1555 0.78 LINK O4'BHC4 A 126 NH1AARG A 52 1555 1555 2.06 LINK O4'BHC4 A 126 NH2AARG A 52 1555 1555 1.33 SITE 1 AC1 12 TYR A 42 GLU A 46 THR A 50 ARG A 52 SITE 2 AC1 12 VAL A 66 ALA A 67 PRO A 68 CYS A 69 SITE 3 AC1 12 THR A 70 PHE A 96 TYR A 98 MET A 100 CRYST1 66.900 66.900 40.800 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 0.014948 0.008630 0.000000 0.00000 SCALE2 0.000000 0.017260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024510 0.00000