HEADER SIGNALING PROTEIN 10-OCT-19 6UMZ TITLE CRYSTAL STRUCTURE OF PHOTOACTIVE YELLOW PROTEIN (PYP); 3-BR-P-COUMARIC TITLE 2 ACID CHROMOPHORE 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_TAXID: 1053; SOURCE 4 GENE: PYP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PHOTOACTIVE YELLOW PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.-Y.LIN,M.G.ROMEI,S.G.BOXER REVDAT 4 11-OCT-23 6UMZ 1 JRNL REVDAT 3 04-NOV-20 6UMZ 1 JRNL REVDAT 2 19-AUG-20 6UMZ 1 JRNL REVDAT 1 15-JUL-20 6UMZ 0 JRNL AUTH M.G.ROMEI,C.Y.LIN,S.G.BOXER JRNL TITL STRUCTURAL AND SPECTROSCOPIC CHARACTERIZATION OF PHOTOACTIVE JRNL TITL 2 YELLOW PROTEIN AND PHOTOSWITCHABLE FLUORESCENT PROTEIN JRNL TITL 3 CONSTRUCTS CONTAINING HEAVY ATOMS. JRNL REF J PHOTOCHEM PHOTOBIOL A CHEM V. 401 12738 2020 JRNL REFN ISSN 1010-6030 JRNL PMID 32753830 JRNL DOI 10.1016/J.JPHOTOCHEM.2020.112738 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13RC2_2986 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 69337 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.0480 - 2.1689 1.00 5258 155 0.1461 0.1460 REMARK 3 2 2.1689 - 1.7216 0.99 5137 151 0.1278 0.1423 REMARK 3 3 1.7216 - 1.5040 0.99 5089 152 0.1182 0.1291 REMARK 3 4 1.5040 - 1.3664 0.98 5061 152 0.1098 0.1292 REMARK 3 5 1.3664 - 1.2685 0.98 5011 148 0.1040 0.1389 REMARK 3 6 1.2685 - 1.1937 0.97 4973 151 0.1006 0.1018 REMARK 3 7 1.1937 - 1.1339 0.97 4951 146 0.0948 0.1001 REMARK 3 8 1.1339 - 1.0846 0.96 4933 144 0.0991 0.1178 REMARK 3 9 1.0846 - 1.0428 0.96 4874 144 0.1052 0.1101 REMARK 3 10 1.0428 - 1.0068 0.95 4835 146 0.1136 0.1177 REMARK 3 11 1.0068 - 0.9753 0.90 4631 137 0.1327 0.1545 REMARK 3 12 0.9753 - 0.9475 0.86 4411 128 0.1627 0.2095 REMARK 3 13 0.9475 - 0.9225 0.83 4206 125 0.1786 0.1886 REMARK 3 14 0.9225 - 0.9000 0.78 3970 118 0.2183 0.2460 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.02 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6UMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000244868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.885570 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69351 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 33.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 60.10 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.5 REMARK 200 DATA REDUNDANCY IN SHELL : 24.20 REMARK 200 R MERGE FOR SHELL (I) : 2.01100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1NWZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE, PH 6.0, 1 M REMARK 280 NACL, 1.9 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 20.28850 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 20.28850 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 20.28850 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A -2 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 O HOH A 386 O HOH A 414 2.13 REMARK 500 OD2 ASP A 20 O HOH A 301 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 336 O HOH A 420 6664 2.18 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 MET A 109 CG - SD - CE ANGL. DEV. = -21.7 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 ASP A 65 -67.47 -109.13 REMARK 500 PHE A 75 -75.62 -128.17 REMARK 500 ASN A 87 29.00 -140.27 REMARK 500 ASN A 87 28.66 -140.09 REMARK 500 ASN A 89 88.39 -166.71 REMARK 500 ASP A 97 12.74 -142.05 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 QBV A 201 DBREF 6UMZ A 1 125 UNP P16113 PYP_HALHA 1 125 SEQADV 6UMZ GLY A -2 UNP P16113 EXPRESSION TAG SEQADV 6UMZ SER A -1 UNP P16113 EXPRESSION TAG SEQADV 6UMZ HIS A 0 UNP P16113 EXPRESSION TAG SEQRES 1 A 128 GLY SER HIS MET GLU HIS VAL ALA PHE GLY SER GLU ASP SEQRES 2 A 128 ILE GLU ASN THR LEU ALA LYS MET ASP ASP GLY GLN LEU SEQRES 3 A 128 ASP GLY LEU ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP SEQRES 4 A 128 GLY ASN ILE LEU GLN TYR ASN ALA ALA GLU GLY ASP ILE SEQRES 5 A 128 THR GLY ARG ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE SEQRES 6 A 128 PHE LYS ASP VAL ALA PRO CYS THR ASP SER PRO GLU PHE SEQRES 7 A 128 TYR GLY LYS PHE LYS GLU GLY VAL ALA SER GLY ASN LEU SEQRES 8 A 128 ASN THR MET PHE GLU TYR THR PHE ASP TYR GLN MET THR SEQRES 9 A 128 PRO THR LYS VAL LYS VAL HIS MET LYS LYS ALA LEU SER SEQRES 10 A 128 GLY ASP SER TYR TRP VAL PHE VAL LYS ARG VAL HET QBV A 201 17 HETNAM QBV (2E)-3-(3-BROMO-4-HYDROXYPHENYL)PROP-2-ENOIC ACID FORMUL 2 QBV C9 H7 BR O3 FORMUL 3 HOH *150(H2 O) HELIX 1 AA1 ASP A 10 ALA A 16 1 7 HELIX 2 AA2 ASP A 19 ASP A 24 1 6 HELIX 3 AA3 ASN A 43 GLY A 51 1 9 HELIX 4 AA4 ASP A 53 ILE A 58 1 6 HELIX 5 AA5 ALA A 67 ASP A 71 5 5 HELIX 6 AA6 PHE A 75 GLY A 86 1 12 SHEET 1 AA1 5 ILE A 39 TYR A 42 0 SHEET 2 AA1 5 GLY A 29 LEU A 33 -1 N GLN A 32 O LEU A 40 SHEET 3 AA1 5 TYR A 118 ARG A 124 -1 O TYR A 118 N LEU A 33 SHEET 4 AA1 5 THR A 103 LYS A 111 -1 N HIS A 108 O PHE A 121 SHEET 5 AA1 5 ASN A 89 PHE A 96 -1 N PHE A 92 O VAL A 107 LINK SG CYS A 69 C1 QBV A 201 1555 1555 1.77 SITE 1 AC1 11 TYR A 42 GLU A 46 THR A 50 ARG A 52 SITE 2 AC1 11 PHE A 62 VAL A 66 ALA A 67 PRO A 68 SITE 3 AC1 11 CYS A 69 PHE A 96 TYR A 98 CRYST1 65.767 65.767 40.577 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 0.015205 0.008779 0.000000 0.00000 SCALE2 0.000000 0.017557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024645 0.00000