HEADER PHOTORECEPTOR 15-APR-04 1T18 TITLE EARLY INTERMEDIATE IE1 FROM TIME-RESOLVED CRYSTALLOGRAPHY OF THE E46Q TITLE 2 MUTANT OF PYP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 GENE: PYP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOTOACTIVE YELLOW PROTEIN, PAS DOMAIN, PHOTORECEPTOR EXPDTA X-RAY DIFFRACTION NUMMDL 2 AUTHOR S.RAJAGOPAL,S.ANDERSON,V.SRAJER,M.SCHMIDT,R.PAHL,K.MOFFAT REVDAT 5 27-OCT-21 1T18 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 1T18 1 REMARK REVDAT 3 09-SEP-15 1T18 1 VERSN REVDAT 2 24-FEB-09 1T18 1 VERSN REVDAT 1 18-JAN-05 1T18 0 JRNL AUTH S.RAJAGOPAL,S.ANDERSON,V.SRAJER,M.SCHMIDT,R.PAHL,K.MOFFAT JRNL TITL A STRUCTURAL PATHWAY FOR SIGNALING IN THE E46Q MUTANT OF JRNL TITL 2 PHOTOACTIVE YELLOW PROTEIN JRNL REF STRUCTURE V. 13 55 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15642261 JRNL DOI 10.1016/J.STR.2004.10.016 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.229 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.240 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 13.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1682 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13889 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.229 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.240 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 13.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1671 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 12533 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 : 0 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 987.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 125 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3953 REMARK 3 NUMBER OF RESTRAINTS : 11012 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.062 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.077 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.027 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.060 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T18 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : LAUEVIEW REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 20.50100 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 20.50100 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 20.50100 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 VAL A 125 C VAL A 125 OXT 0.329 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 2 ASP A 65 CB - CG - OD1 ANGL. DEV. = -7.0 DEGREES REMARK 500 2 ASP A 65 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 TYR A 76 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 TYR A 94 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 TYR A 94 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 MET A 109 CG - SD - CE ANGL. DEV. = -10.3 DEGREES REMARK 500 2 GLY A 115 N - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 2 ARG A 124 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 ARG A 124 NE - CZ - NH2 ANGL. DEV. = -8.1 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 1 PHE A 75 -74.18 -123.79 REMARK 500 1 ASP A 97 20.41 -140.69 REMARK 500 1 ASP A 116 55.19 -98.59 REMARK 500 2 PHE A 75 -76.15 -130.94 REMARK 500 2 ASN A 89 97.44 -160.49 REMARK 500 2 ASP A 97 17.21 -143.89 REMARK 500 2 ASP A 116 58.77 -119.63 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: 1T19 RELATED DB: PDB REMARK 900 RELATED ID: 1T1A RELATED DB: PDB REMARK 900 RELATED ID: 1T1B RELATED DB: PDB REMARK 900 RELATED ID: 1T1C RELATED DB: PDB DBREF 1T18 A 1 125 UNP P16113 PYP_ECTHA 1 125 SEQADV 1T18 GLN A 46 UNP P16113 GLU 46 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 GLN 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 HELIX 1 1 ASP A 10 LEU A 15 1 6 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 ALA A 67 ASP A 71 5 5 HELIX 6 6 PHE A 75 GLY A 86 1 12 SHEET 1 A 5 ILE A 39 TYR A 42 0 SHEET 2 A 5 GLY A 29 ASP A 34 -1 N GLN A 32 O LEU A 40 SHEET 3 A 5 SER A 117 ARG A 124 -1 O TYR A 118 N LEU A 33 SHEET 4 A 5 THR A 103 LYS A 111 -1 N HIS A 108 O PHE A 121 SHEET 5 A 5 ASN A 89 PHE A 96 -1 N PHE A 92 O VAL A 107 LINK SG CYS A 69 C1 HC4 A 169 1555 1555 1.79 SITE 1 AC1 9 TYR A 42 THR A 50 ARG A 52 VAL A 66 SITE 2 AC1 9 ALA A 67 CYS A 69 THR A 70 PHE A 96 SITE 3 AC1 9 TYR A 98 CRYST1 66.917 66.917 41.002 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 0.014944 0.008628 0.000000 0.00000 SCALE2 0.000000 0.017256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024389 0.00000 MODEL 1