HEADER PHOTORECEPTOR 28-JUL-98 3PYP TITLE PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYP; COMPND 5 OTHER_DETAILS: THIOESTER LINKAGE BETWEEN THE SULFUR OF CYS 69 AND COMPND 6 CARBOXY GROUP OF THE 4-HYDROXY CINNAMIC ACID CHROMOPHORE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 STRAIN: BN9626 KEYWDS PHOTORECEPTOR, LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS EXPDTA X-RAY DIFFRACTION AUTHOR U.K.GENICK,S.M.SOLTIS,P.KUHN,I.L.CANESTRELLI,E.D.GETZOFF REVDAT 4 09-AUG-23 3PYP 1 REMARK LINK REVDAT 3 29-NOV-17 3PYP 1 HELIX REVDAT 2 24-FEB-09 3PYP 1 VERSN REVDAT 1 01-JUN-99 3PYP 0 JRNL AUTH U.K.GENICK,S.M.SOLTIS,P.KUHN,I.L.CANESTRELLI,E.D.GETZOFF JRNL TITL STRUCTURE AT 0.85 A RESOLUTION OF AN EARLY PROTEIN JRNL TITL 2 PHOTOCYCLE INTERMEDIATE. JRNL REF NATURE V. 392 206 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9515969 JRNL DOI 10.1038/32462 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX-97 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : 5% RANDOMLY CHOSEN BY SHELX REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.133 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4249 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 80680 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.121 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3511 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 66807 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 : 137 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1133.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 943.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 18 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11379 REMARK 3 NUMBER OF RESTRAINTS : 15920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.038 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.098 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.112 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.064 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NUMBER OF PROTEIN AND SOLVENT ATOMS REMARK 3 CONTAINS DUAL CONFORMERS REMARK 4 REMARK 4 3PYP 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_1000179125. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 149 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84934 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : 0.52000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAME CRYSTAL LATTICE REMARK 200 MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2PHY REMARK 200 REMARK 200 REMARK: CRYSTALS IDENTICAL TO 2PHY REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 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 20.28050 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 20.28050 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 20.28050 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3002 LIES ON A SPECIAL POSITION. 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 H ASP A 19 HE22 GLN A 22 1.19 REMARK 500 HZ3 LYS A 78 O HOH A 3003 1.47 REMARK 500 OD1 ASP A 20 OE1 GLN A 41 2.02 REMARK 500 NZ LYS A 78 O HOH A 3003 2.09 REMARK 500 OD2 ASP A 20 O HOH A 3044 2.11 REMARK 500 O HOH A 1068 O HOH A 1069 2.14 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 ASP A 65 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 ASP A 65 CB - CG - OD1 ANGL. DEV. = -11.1 DEGREES REMARK 500 ASP A 65 CB - CG - OD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 CYS A 69 CA - CB - SG ANGL. DEV. = 12.8 DEGREES REMARK 500 TYR A 76 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 TYR A 76 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLU A 81 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 GLU A 81 CG - CD - OE1 ANGL. DEV. = 13.4 DEGREES REMARK 500 ASP A 97 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR A 98 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 TYR A 98 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET A 109 CG - SD - CE ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP A 116 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 124 NE - CZ - NH2 ANGL. DEV. = -4.7 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 HIS A 3 77.25 -101.78 REMARK 500 PHE A 75 -75.53 -131.44 REMARK 500 ASN A 89 97.87 -160.31 REMARK 500 ASP A 97 11.16 -140.97 REMARK 500 ASP A 97 24.03 -150.35 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 3PYP 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 34 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 FORMUL 3 HOH *137(H2 O) HELIX 1 1 ILE A 11 THR A 14 1 4 HELIX 2 2 ASP A 20 GLY A 25 1 6 HELIX 3 3 ALA A 44 THR A 50 1 7 HELIX 4 4 PRO A 54 VAL A 57 1 4 HELIX 5 5 PRO A 68 THR A 70 5 3 HELIX 6 6 TYR A 76 SER A 85 1 10 SHEET 1 A 5 ASN A 89 PHE A 96 0 SHEET 2 A 5 THR A 103 LYS A 111 -1 N MET A 109 O THR A 90 SHEET 3 A 5 TYR A 118 ARG A 124 -1 N LYS A 123 O LYS A 106 SHEET 4 A 5 GLY A 29 LEU A 33 -1 N LEU A 33 O TYR A 118 SHEET 5 A 5 ILE A 39 TYR A 42 -1 N GLN A 41 O GLN A 32 LINK SG ACYS A 69 C1 AHC4 A 126 1555 1555 1.84 LINK SG BCYS A 69 C1 BHC4 A 126 1555 1555 1.79 SITE 1 AC1 13 ILE A 31 TYR A 42 GLU A 46 THR A 50 SITE 2 AC1 13 ARG A 52 PHE A 62 VAL A 66 ALA A 67 SITE 3 AC1 13 PRO A 68 CYS A 69 THR A 70 PHE A 96 SITE 4 AC1 13 TYR A 98 CRYST1 66.224 66.224 40.561 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 0.015100 0.008718 0.000000 0.00000 SCALE2 0.000000 0.017436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024654 0.00000