HEADER PHOTOSYNTHESIS 09-JAN-02 1GSW TITLE CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW TITLE 2 PROTEIN G51S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ECTOTHIORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHISP KEYWDS PHOTOSYNTHESIS, PHOTORECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR D.M.F.VAN AALTEN,W.CRIELAARD,K.J.HELLINGWERF,L.JOSHUA-TOR REVDAT 4 13-DEC-23 1GSW 1 REMARK LINK REVDAT 3 24-FEB-09 1GSW 1 VERSN REVDAT 2 03-MAY-05 1GSW 1 JRNL REMARK REVDAT 1 14-FEB-02 1GSW 0 JRNL AUTH D.M.F.VAN AALTEN,A.HAKER,J.HENDRIKS,K.J.HELLINGWERF, JRNL AUTH 2 L.JOSHUA-TOR,W.CRIELAARD JRNL TITL ENGINEERING PHOTOCYCLE DYNAMICS: CRYSTAL STRUCTURES AND JRNL TITL 2 KINETICS OF THREE PHOTOACTIVE YELLOW PROTEIN HINGE-BENDING JRNL TITL 3 MUTANTS JRNL REF J.BIOL.CHEM. V. 227 6438 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11714713 JRNL DOI 10.1074/JBC.M109313200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 8430 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 606 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 951 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.520 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) : 2.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.200 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GSW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1290009241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25707 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1D7E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2K, MES., PH 6.50 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 86.79333 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 43.39667 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 65.09500 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 21.69833 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 108.49167 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: 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. (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 1 REMARK 465 GLU A 2 REMARK 465 HIS A 3 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 9 OE1 OE2 REMARK 480 ASP A 19 CB CG OD1 OD2 REMARK 480 ASP A 20 CB CG OD1 OD2 REMARK 480 LYS A 55 CD CE NZ REMARK 480 LYS A 64 NZ REMARK 480 LYS A 106 NZ 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 20 -62.91 -28.36 REMARK 500 TYR A 42 107.92 -161.35 REMARK 500 PHE A 75 -78.52 -112.79 REMARK 500 ASN A 89 76.56 -175.39 REMARK 500 ASP A 116 -8.11 -148.09 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 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: 1GSV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW REMARK 900 PROTEIN G47S 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: 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: 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 DBREF 1GSW A 1 125 UNP P16113 PYP_ECTHA 1 125 SEQADV 1GSW SER A 51 UNP P16113 GLY 51 ENGINEERED MUTATION 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 SER 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 *57(H2 O) HELIX 1 1 ASP A 10 LYS A 17 1 8 HELIX 2 2 GLN A 22 LEU A 26 5 5 HELIX 3 3 ASN A 43 SER A 51 1 9 HELIX 4 4 ASP A 53 ILE A 58 1 6 HELIX 5 5 VAL A 4 VAL A 66 1 63 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 SG CYS A 69 C1 HC4 A 169 1555 1555 1.79 SITE 1 AC1 9 TYR A 42 GLU A 46 THR A 50 ARG A 52 SITE 2 AC1 9 VAL A 66 ALA A 67 CYS A 69 PHE A 96 SITE 3 AC1 9 TYR A 98 CRYST1 36.730 36.730 130.190 90.00 90.00 120.00 P 65 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 0.027226 0.015719 0.000000 0.00000 SCALE2 0.000000 0.031437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007681 0.00000