HEADER SIGNALING PROTEIN 16-SEP-16 5GX9 TITLE PYP MUTANT - E46Q 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS PAS, LOV, PHOTORECEPTOR, LIGHT SENSOR, LBHB, SHB, CHROMOPHORE, KEYWDS 2 PHOTORECEPTOR PROTEIN, RECEPTOR, SENSORY TRANSDUCTION, SIGNALING KEYWDS 3 PROTEIN EXPDTA NEUTRON DIFFRACTION AUTHOR K.YONEZAWA REVDAT 4 08-NOV-23 5GX9 1 REMARK REVDAT 3 28-NOV-18 5GX9 1 REMARK REVDAT 2 13-SEP-17 5GX9 1 JRNL REVDAT 1 30-AUG-17 5GX9 0 JRNL AUTH K.YONEZAWA,N.SHIMIZU,K.KURIHARA,Y.YAMAZAKI,H.KAMIKUBO, JRNL AUTH 2 M.KATAOKA JRNL TITL NEUTRON CRYSTALLOGRAPHY OF PHOTOACTIVE YELLOW PROTEIN JRNL TITL 2 REVEALS UNUSUAL PROTONATION STATE OF ARG52 IN THE CRYSTAL JRNL REF SCI REP V. 7 9361 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28839266 JRNL DOI 10.1038/S41598-017-09718-9 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12RC1_2815) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 15983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1610 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 33.4533 - 3.3194 0.97 1399 164 0.1234 0.1444 REMARK 3 2 3.3194 - 2.6351 0.97 1369 154 0.1393 0.1701 REMARK 3 3 2.6351 - 2.3021 0.98 1373 149 0.1265 0.1802 REMARK 3 4 2.3021 - 2.0916 0.96 1354 155 0.1297 0.1839 REMARK 3 5 2.0916 - 1.9417 0.96 1318 144 0.1391 0.1824 REMARK 3 6 1.9417 - 1.8273 0.95 1333 147 0.1557 0.1999 REMARK 3 7 1.8273 - 1.7358 0.94 1317 143 0.1794 0.2490 REMARK 3 8 1.7358 - 1.6602 0.91 1273 145 0.1981 0.2340 REMARK 3 9 1.6602 - 1.5963 0.89 1214 134 0.2307 0.2715 REMARK 3 10 1.5963 - 1.5412 0.89 1239 140 0.2314 0.2612 REMARK 3 11 1.5412 - 1.4930 0.86 1184 135 0.2633 0.3283 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2326 REMARK 3 ANGLE : 1.233 4018 REMARK 3 CHIRALITY : 0.086 155 REMARK 3 PLANARITY : 0.010 419 REMARK 3 DIHEDRAL : 19.218 609 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 5GX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001631. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 10-JAN-09 REMARK 230 TEMPERATURE (KELVIN) : 295.0 REMARK 230 PH : 9.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-B REMARK 230 WAVELENGTH OR RANGE (A) : 2.6 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MACSCIENCE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 230 DATA SCALING SOFTWARE : NULL REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 15995 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.493 REMARK 230 RESOLUTION RANGE LOW (A) : 100.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 230 DATA REDUNDANCY : 2.200 REMARK 230 R MERGE (I) : 0.09500 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 7.7800 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 230 COMPLETENESS FOR SHELL (%) : 85.7 REMARK 230 DATA REDUNDANCY IN SHELL : 1.60 REMARK 230 R MERGE FOR SHELL (I) : 0.31800 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 2.400 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: 1OTA REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, SODIUM CHLORIDE, REMARK 280 SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, PH REMARK 280 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE REMARK 280 295K 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 20.49100 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 20.49100 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 20.49100 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 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 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 DH TYR A 42 O4' HC4 A 201 1.56 REMARK 500 OE1 GLN A 99 D2 DOD A 306 1.58 REMARK 500 OE1 GLN A 99 O DOD A 301 1.88 REMARK 500 O SER A 114 O DOD A 302 2.17 REMARK 500 OD1 ASP A 48 O DOD A 303 2.17 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 PHE A 75 -74.42 -129.96 REMARK 500 ASP A 97 16.03 -141.82 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 201 DBREF 5GX9 A 1 125 UNP P16113 PYP_HALHA 1 125 SEQADV 5GX9 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 201 17 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 FORMUL 3 DOD *80(D2 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 ASP A 34 -1 N GLN A 32 O LEU A 40 SHEET 3 AA1 5 SER A 117 ARG A 124 -1 O TYR A 118 N LEU A 33 SHEET 4 AA1 5 THR A 103 LYS A 111 -1 N LYS A 110 O TRP A 119 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 HC4 A 201 1555 1555 1.78 SITE 1 AC1 9 TYR A 42 GLN A 46 THR A 50 ARG A 52 SITE 2 AC1 9 ALA A 67 PRO A 68 CYS A 69 PHE A 96 SITE 3 AC1 9 TYR A 98 CRYST1 66.823 66.823 40.982 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 0.014965 0.008640 0.000000 0.00000 SCALE2 0.000000 0.017280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024401 0.00000