HEADER SIGNALING PROTEIN 22-MAY-13 4KUK TITLE A SUPERFAST RECOVERING FULL-LENGTH LOV PROTEIN FROM THE MARINE TITLE 2 PHOTOTROPHIC BACTERIUM DINOROSEOBACTER SHIBAE (DARK STATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BLUE-LIGHT PHOTORECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LIGHT-OXYGEN-VOLTAGE (LOV) PHOTORECEPTOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DINOROSEOBACTER SHIBAE; SOURCE 3 ORGANISM_TAXID: 398580; SOURCE 4 STRAIN: DFL 12; SOURCE 5 GENE: DSHI_2006; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT-DSLOV KEYWDS PAS DOMAIN, LIGHT-OXYGEN-VOLTAGE, LOV, FMN BINDING, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.CIRCOLONE,J.GRANZIN,A.STADLER,U.KRAUSS,T.DREPPER,S.ENDRES,E.KNIEPS- AUTHOR 2 GRUENHAGEN,A.WIRTZ,D.WILLBOLD,R.BATRA-SAFFERLING,K.-E.JAEGER REVDAT 5 20-SEP-23 4KUK 1 REMARK SEQADV LINK REVDAT 4 29-APR-15 4KUK 1 JRNL REVDAT 3 01-APR-15 4KUK 1 JRNL REVDAT 2 04-MAR-15 4KUK 1 JRNL REVDAT 1 26-NOV-14 4KUK 0 JRNL AUTH S.ENDRES,J.GRANZIN,F.CIRCOLONE,A.STADLER,U.KRAUSS,T.DREPPER, JRNL AUTH 2 V.SVENSSON,E.KNIEPS-GRUNHAGEN,A.WIRTZ,A.COUSIN,P.TIELEN, JRNL AUTH 3 D.WILLBOLD,K.E.JAEGER,R.BATRA-SAFFERLING JRNL TITL STRUCTURE AND FUNCTION OF A SHORT LOV PROTEIN FROM THE JRNL TITL 2 MARINE PHOTOTROPHIC BACTERIUM DINOROSEOBACTER SHIBAE. JRNL REF BMC MICROBIOL V. 15 30 2015 JRNL REFN ESSN 1471-2180 JRNL PMID 25887755 JRNL DOI 10.1186/S12866-015-0365-0 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 19910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1016 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 45.4197 - 2.8693 0.99 2781 172 0.1451 0.1730 REMARK 3 2 2.8693 - 2.2775 1.00 2748 137 0.1399 0.2025 REMARK 3 3 2.2775 - 1.9896 1.00 2722 143 0.1166 0.1770 REMARK 3 4 1.9896 - 1.8077 1.00 2696 150 0.1087 0.1485 REMARK 3 5 1.8077 - 1.6781 1.00 2715 137 0.1132 0.1814 REMARK 3 6 1.6781 - 1.5792 1.00 2688 144 0.1112 0.1852 REMARK 3 7 1.5792 - 1.5000 0.94 2544 133 0.1095 0.2075 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.08 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 : 0.012 1040 REMARK 3 ANGLE : 1.330 1426 REMARK 3 CHIRALITY : 0.088 157 REMARK 3 PLANARITY : 0.008 190 REMARK 3 DIHEDRAL : 15.387 393 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 4KUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : DIAMOND(001) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19912 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2V0U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M MAGNESIUM CHLORIDE, 8% PGA-LM, REMARK 280 0.1 M SODIUM ACETATE, PH 5.0, 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 44.98900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.29750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.98900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.29750 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: 3430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 19.29932 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -45.40025 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 396 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 397 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 402 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 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 350 O HOH A 372 2.16 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 RBF A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KUO RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CONFORMATION A OF RESIDUE A ARG 97 IS METHYLATED (NMM) AND REMARK 999 CONFORMATION B IS NOT. DBREF 4KUK A 1 138 UNP A8LP63 A8LP63_DINSH 2 139 SEQADV 4KUK LEU A 139 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK GLU A 140 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK HIS A 141 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK HIS A 142 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK HIS A 143 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK HIS A 144 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK HIS A 145 UNP A8LP63 EXPRESSION TAG SEQADV 4KUK 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 MET 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 NMM 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 MODRES 4KUK NMM A 97 ARG HET NMM A 97 12 HET RBF A 201 27 HET ACY A 202 4 HETNAM NMM (2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC HETNAM 2 NMM ACID HETNAM RBF RIBOFLAVIN HETNAM ACY ACETIC ACID HETSYN NMM L-NMMA HETSYN RBF RIBOFLAVINE; VITAMIN B2 FORMUL 1 NMM C7 H16 N4 O2 FORMUL 2 RBF C17 H20 N4 O6 FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *112(H2 O) HELIX 1 1 ASP A 23 LEU A 28 5 6 HELIX 2 2 SER A 53 GLY A 61 1 9 HELIX 3 3 THR A 63 LEU A 68 1 6 HELIX 4 4 ASN A 71 GLN A 76 5 6 HELIX 5 5 ASN A 81 GLU A 95 1 15 SHEET 1 A 5 MET A 49 VAL A 52 0 SHEET 2 A 5 SER A 36 SER A 40 -1 N PHE A 39 O ILE A 50 SHEET 3 A 5 LEU A 128 PRO A 137 -1 O GLY A 133 N VAL A 38 SHEET 4 A 5 ALA A 111 TYR A 122 -1 N ILE A 121 O MET A 129 SHEET 5 A 5 PHE A 98 TYR A 105 -1 N PHE A 98 O ILE A 118 LINK C THR A 96 N ANMM A 97 1555 1555 1.33 LINK C ANMM A 97 N PHE A 98 1555 1555 1.33 SITE 1 AC1 21 VAL A 38 SER A 40 ASN A 47 ASN A 71 SITE 2 AC1 21 CYS A 72 ARG A 73 LEU A 75 GLN A 76 SITE 3 AC1 21 VAL A 85 ILE A 88 LEU A 92 ASN A 104 SITE 4 AC1 21 ASN A 114 LEU A 116 PHE A 131 GLY A 133 SITE 5 AC1 21 GLN A 135 ACY A 202 HOH A 313 HOH A 345 SITE 6 AC1 21 HOH A 353 SITE 1 AC2 6 ASN A 47 ASN A 71 ARG A 73 LEU A 92 SITE 2 AC2 6 RBF A 201 HOH A 366 CRYST1 89.978 30.595 49.332 90.00 113.03 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 0.011114 0.000000 0.004724 0.00000 SCALE2 0.000000 0.032685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022026 0.00000