HEADER SIGNALING PROTEIN 27-APR-10 2KX6 TITLE SIGNALING STATE 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_COMMON: ECTOTHIORHODOSPIRA HALOPHILA; SOURCE 4 ORGANISM_TAXID: 1053; SOURCE 5 STRAIN: BN9626; SOURCE 6 GENE: PYP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS SAXS, DEER, PYP INTERMEDIATE, SIGNALING STATE, PB, SIGNALING PROTEIN EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 14 AUTHOR P.L.RAMACHANDRAN,J.E.LOVETT,P.J.CARL,M.CAMMARATA,J.H.LEE,J.O.YANG, AUTHOR 2 H.IHEE,C.R.TIMMEL,J.VAN THOR REVDAT 4 18-JUL-12 2KX6 1 REMARK VERSN REVDAT 3 06-JUL-11 2KX6 1 REMARK REVDAT 2 29-JUN-11 2KX6 1 JRNL REVDAT 1 15-JUN-11 2KX6 0 JRNL AUTH P.L.RAMACHANDRAN,J.E.LOVETT,P.J.CARL,M.CAMMARATA,J.H.LEE, JRNL AUTH 2 Y.O.JUNG,H.IHEE,C.R.TIMMEL,J.J.VAN THOR JRNL TITL THE SHORT-LIVED SIGNALING STATE OF THE PHOTOACTIVE YELLOW JRNL TITL 2 PROTEIN PHOTORECEPTOR REVEALED BY COMBINED STRUCTURAL JRNL TITL 3 PROBES. JRNL REF J.AM.CHEM.SOC. V. 133 9395 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21627157 JRNL DOI 10.1021/JA200617T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-10. REMARK 100 THE RCSB ID CODE IS RCSB101684. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 50; 298 REMARK 210 PH : 5.75; 7.5; 7 REMARK 210 IONIC STRENGTH : 0; 0; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 75 UM PYP, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O; 75 UM REMARK 210 PYP, 50 MM TRIS, 10 % GLYCEROL, REMARK 210 50 MM TRIS; 4.4 MM PYP, 50-200 MM REMARK 210 SODIUM PHOSPHATE, 20 MM SODIUM REMARK 210 CHLORIDE, H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, DEERANALYSIS2006 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : ESRF REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : ID09B REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : CCD REMARK 265 DETECTOR MANUFACTURER DETAILS : MAR133: MAR RESEARCH REMARK 265 TEMPERATURE (KELVIN) : 293 REMARK 265 PH : 7 REMARK 265 NUMBER OF TIME FRAMES USED : NULL REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 64 REMARK 265 SAMPLE BUFFER : 20 MM NACL REMARK 265 DATA REDUCTION SOFTWARE : NULL REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 1.46 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : NULL REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : NULL REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 265 SOFTWARE USED : CNS (NIH SAXS VERSION) REMARK 265 SOFTWARE AUTHORS : GRISHAEV, WU, TREWHELLA, BAX, BRUNGER, ADAMS, REMARK 265 CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, REMARK 265 KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, REMARK 265 WARREN REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 15 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 265 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 265 RESTRAINT VIOLATIONS REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-14 REMARK 465 RES C SSSEQI REMARK 465 PHE A -4 REMARK 465 GLY A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 1 GLU A 2 -59.22 -168.24 REMARK 500 1 HIS A 3 42.00 -168.63 REMARK 500 1 PHE A 6 -144.76 -167.14 REMARK 500 1 SER A 8 -50.17 -171.41 REMARK 500 1 ASP A 10 50.85 -168.77 REMARK 500 1 ILE A 11 -110.97 -147.51 REMARK 500 1 GLU A 12 -20.39 -162.19 REMARK 500 1 ASN A 13 -89.43 -159.42 REMARK 500 1 THR A 14 -119.08 -166.30 REMARK 500 1 LYS A 17 -159.95 -150.30 REMARK 500 1 MET A 18 -98.83 -53.51 REMARK 500 1 ASP A 20 -10.69 -169.85 REMARK 500 1 GLN A 22 140.14 58.91 REMARK 500 1 LEU A 26 -120.18 -116.58 REMARK 500 1 ALA A 27 36.08 -165.41 REMARK 500 1 PHE A 28 -65.62 -159.22 REMARK 500 1 ALA A 30 145.67 159.29 REMARK 500 1 GLN A 32 146.05 58.83 REMARK 500 1 GLN A 41 83.79 -60.21 REMARK 500 1 TYR A 42 6.93 -171.16 REMARK 500 1 ASN A 43 80.77 -168.29 REMARK 500 1 ALA A 44 -43.40 -169.82 REMARK 500 1 ALA A 45 89.11 -172.73 REMARK 500 1 ASP A 48 93.12 -169.14 REMARK 500 1 ILE A 49 -39.05 -152.67 REMARK 500 1 THR A 50 87.18 50.39 REMARK 500 1 ARG A 52 -160.55 -166.41 REMARK 500 1 ASP A 53 155.37 -48.56 REMARK 500 1 LYS A 55 -101.00 -158.87 REMARK 500 1 GLN A 56 -22.01 -174.24 REMARK 500 1 LYS A 64 61.27 -167.07 REMARK 500 1 ASP A 65 19.18 -171.89 REMARK 500 1 VAL A 66 -46.10 -147.84 REMARK 500 1 CYS A 69 -42.71 -154.09 REMARK 500 1 THR A 70 94.99 -66.90 REMARK 500 1 ASP A 71 66.80 -114.35 REMARK 500 1 GLU A 74 -78.95 -169.77 REMARK 500 1 PHE A 75 -79.53 -99.97 REMARK 500 1 TYR A 76 25.34 -168.50 REMARK 500 1 PHE A 79 21.59 -159.07 REMARK 500 1 ASN A 87 56.54 -168.14 REMARK 500 1 ASN A 89 85.55 -169.42 REMARK 500 1 PHE A 92 -109.11 -165.94 REMARK 500 1 TYR A 94 -21.73 -174.51 REMARK 500 1 THR A 95 -164.30 51.83 REMARK 500 1 PHE A 96 -15.62 -166.93 REMARK 500 1 TYR A 98 38.36 -165.68 REMARK 500 1 GLN A 99 -31.80 -169.48 REMARK 500 1 MET A 100 -82.25 -89.03 REMARK 500 1 PRO A 102 174.83 -45.94 REMARK 500 REMARK 500 THIS ENTRY HAS 803 RAMACHANDRAN OUTLIERS. 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17269 RELATED DB: BMRB DBREF 2KX6 A 1 125 UNP P16113 PYP_HALHA 1 125 SEQADV 2KX6 PHE A -4 UNP P16113 EXPRESSION TAG SEQADV 2KX6 GLY A -3 UNP P16113 EXPRESSION TAG SEQADV 2KX6 LEU A -2 UNP P16113 EXPRESSION TAG SEQADV 2KX6 GLY A -1 UNP P16113 EXPRESSION TAG SEQADV 2KX6 SER A 0 UNP P16113 EXPRESSION TAG SEQRES 1 A 130 PHE GLY LEU GLY SER MET GLU HIS VAL ALA PHE GLY SER SEQRES 2 A 130 GLU ASP ILE GLU ASN THR LEU ALA LYS MET ASP ASP GLY SEQRES 3 A 130 GLN LEU ASP GLY LEU ALA PHE GLY ALA ILE GLN LEU ASP SEQRES 4 A 130 GLY ASP GLY ASN ILE LEU GLN TYR ASN ALA ALA GLU GLY SEQRES 5 A 130 ASP ILE THR GLY ARG ASP PRO LYS GLN VAL ILE GLY LYS SEQRES 6 A 130 ASN PHE PHE LYS ASP VAL ALA PRO CYS THR ASP SER PRO SEQRES 7 A 130 GLU PHE TYR GLY LYS PHE LYS GLU GLY VAL ALA SER GLY SEQRES 8 A 130 ASN LEU ASN THR MET PHE GLU TYR THR PHE ASP TYR GLN SEQRES 9 A 130 MET THR PRO THR LYS VAL LYS VAL HIS MET LYS LYS ALA SEQRES 10 A 130 LEU SER GLY ASP SER TYR TRP VAL PHE VAL LYS ARG VAL HET HC4 A 126 18 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 HELIX 1 1 GLU A 81 GLY A 86 1 6 SHEET 1 A 3 ASN A 89 MET A 91 0 SHEET 2 A 3 HIS A 108 LYS A 110 -1 O MET A 109 N THR A 90 SHEET 3 A 3 TRP A 119 VAL A 120 -1 O TRP A 119 N LYS A 110 LINK SG CYS A 69 C1 HC4 A 126 1555 1555 1.73 SITE 1 AC1 1 CYS A 69 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1