HEADER SIGNALING PROTEIN 13-APR-18 6GB3 TITLE A FAST RECOVERING FULL-LENGTH LOV PROTEIN (DSLOV) FROM THE MARINE TITLE 2 PHOTOTROPHIC BACTERIUM DINOROSEOBACTER SHIBAE (DARK STATE) - M49S TITLE 3 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE BLUE-LIGHT PHOTORECEPTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: C-TERMINAL HEXA-HISTIDINE-TAGGED FUSION PROTEINS (TAG COMPND 7 SEQUENCE: LEHHHHHH) IN E. COLI BL21(DE3) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DINOROSEOBACTER SHIBAE (STRAIN DSM 16493 / SOURCE 3 NCIMB 14021 / DFL 12); SOURCE 4 ORGANISM_TAXID: 398580; SOURCE 5 STRAIN: DSM 16493 / NCIMB 14021 / DFL 12; SOURCE 6 GENE: DSHI_2006; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS LIGHT-OXYGEN-VOLTAGE, LOV, PAS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.GRANZIN,R.BATRA-SAFFERLING,K.ROELLEN REVDAT 3 17-JAN-24 6GB3 1 REMARK REVDAT 2 22-AUG-18 6GB3 1 JRNL REVDAT 1 18-JUL-18 6GB3 0 JRNL AUTH T.FETTWEISS,K.ROLLEN,J.GRANZIN,O.REINERS,S.ENDRES,T.DREPPER, JRNL AUTH 2 D.WILLBOLD,K.E.JAEGER,R.BATRA-SAFFERLING,U.KRAUSS JRNL TITL MECHANISTIC BASIS OF THE FAST DARK RECOVERY OF THE SHORT LOV JRNL TITL 2 PROTEIN DSLOV FROM DINOROSEOBACTER SHIBAE. JRNL REF BIOCHEMISTRY V. 57 4833 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29989797 JRNL DOI 10.1021/ACS.BIOCHEM.8B00645 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 12222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 632 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 45.5944 - 2.9950 0.99 2494 147 0.1485 0.1910 REMARK 3 2 2.9950 - 2.3773 0.96 2329 134 0.1618 0.2178 REMARK 3 3 2.3773 - 2.0768 0.93 2258 115 0.1487 0.2212 REMARK 3 4 2.0768 - 1.8869 0.91 2217 134 0.1465 0.2410 REMARK 3 5 1.8869 - 1.7516 0.95 2292 102 0.1663 0.2463 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.03 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 : 0.005 1003 REMARK 3 ANGLE : 0.774 1377 REMARK 3 CHIRALITY : 0.051 154 REMARK 3 PLANARITY : 0.005 180 REMARK 3 DIHEDRAL : 15.631 605 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 6GB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 45.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4KUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 1 M AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.93950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.48900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.93950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.48900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 19.25269 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -45.57749 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 A 601 LIES ON A SPECIAL POSITION. 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 ARG A 2 REMARK 465 ARG A 3 REMARK 465 HIS A 4 REMARK 465 TYR A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 LEU A 8 REMARK 465 ILE A 9 REMARK 465 ARG A 10 REMARK 465 ASN A 11 REMARK 465 THR A 12 REMARK 465 PRO A 13 REMARK 465 MET A 14 REMARK 465 PRO A 15 REMARK 465 ASP A 16 REMARK 465 THR A 17 REMARK 465 PRO A 18 REMARK 465 GLN A 19 REMARK 465 GLU A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS A 146 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 ASP A 31 CG OD1 OD2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 GLU A 65 CD OE1 OE2 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 CYS A 72 1.44 -68.86 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 FMN A 500 DBREF 6GB3 A 1 138 UNP A8LP63 A8LP63_DINSH 2 139 SEQADV 6GB3 SER A 49 UNP A8LP63 MET 50 ENGINEERED MUTATION SEQADV 6GB3 LEU A 139 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 GLU A 140 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 141 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 142 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 143 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 144 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 145 UNP A8LP63 EXPRESSION TAG SEQADV 6GB3 HIS A 146 UNP A8LP63 EXPRESSION TAG SEQRES 1 A 146 MET ARG ARG HIS TYR ARG ASP LEU ILE ARG ASN THR PRO SEQRES 2 A 146 MET PRO ASP THR PRO GLN ASP ILE ALA ASP LEU ARG ALA SEQRES 3 A 146 LEU LEU ASP GLU ASP GLU ALA GLU MET SER VAL VAL PHE SEQRES 4 A 146 SER ASP PRO SER GLN PRO ASP ASN PRO SER ILE TYR VAL SEQRES 5 A 146 SER ASP ALA PHE LEU VAL GLN THR GLY TYR THR LEU GLU SEQRES 6 A 146 GLU VAL LEU GLY ARG ASN CYS ARG PHE LEU GLN GLY PRO SEQRES 7 A 146 ASP THR ASN PRO HIS ALA VAL GLU ALA ILE ARG GLN GLY SEQRES 8 A 146 LEU LYS ALA GLU THR ARG PHE THR ILE ASP ILE LEU ASN SEQRES 9 A 146 TYR ARG LYS ASP GLY SER ALA PHE VAL ASN ARG LEU ARG SEQRES 10 A 146 ILE ARG PRO ILE TYR ASP PRO GLU GLY ASN LEU MET PHE SEQRES 11 A 146 PHE ALA GLY ALA GLN ASN PRO VAL LEU GLU HIS HIS HIS SEQRES 12 A 146 HIS HIS HIS HET FMN A 500 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *67(H2 O) HELIX 1 AA1 ASP A 23 LEU A 28 5 6 HELIX 2 AA2 ASP A 29 ALA A 33 5 5 HELIX 3 AA3 SER A 53 GLY A 61 1 9 HELIX 4 AA4 THR A 63 LEU A 68 1 6 HELIX 5 AA5 ASN A 71 GLN A 76 5 6 HELIX 6 AA6 ASN A 81 GLU A 95 1 15 SHEET 1 AA1 5 SER A 49 VAL A 52 0 SHEET 2 AA1 5 SER A 36 SER A 40 -1 N PHE A 39 O ILE A 50 SHEET 3 AA1 5 LEU A 128 PRO A 137 -1 O GLY A 133 N VAL A 38 SHEET 4 AA1 5 ALA A 111 TYR A 122 -1 N ARG A 115 O ASN A 136 SHEET 5 AA1 5 PHE A 98 TYR A 105 -1 N ILE A 102 O ASN A 114 SITE 1 AC1 20 SER A 40 ASN A 47 ASN A 71 CYS A 72 SITE 2 AC1 20 ARG A 73 LEU A 75 GLN A 76 VAL A 85 SITE 3 AC1 20 ILE A 88 ARG A 89 LEU A 92 ASN A 104 SITE 4 AC1 20 ASN A 114 LEU A 116 GLY A 133 GLN A 135 SITE 5 AC1 20 HOH A 625 HOH A 630 HOH A 649 HOH A 652 CRYST1 89.879 30.978 49.477 90.00 112.90 90.00 C 1 2 1 4 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 0.011126 0.000000 0.004699 0.00000 SCALE2 0.000000 0.032281 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021940 0.00000