PDB Short entry for 4HJ4 HEADER SIGNALING PROTEIN 12-OCT-12 4HJ4 TITLE CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES LOV PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOV PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES; SOURCE 3 ORGANISM_TAXID: 349102; SOURCE 4 STRAIN: ATCC 17025; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET28A KEYWDS LOV, PAS, HTH, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.R.CRANE,K.S.CONRAD,A.M.BILWES REVDAT 4 28-FEB-24 4HJ4 1 REMARK REVDAT 3 15-NOV-17 4HJ4 1 REMARK REVDAT 2 22-MAY-13 4HJ4 1 JRNL REVDAT 1 16-JAN-13 4HJ4 0 JRNL AUTH K.S.CONRAD,A.M.BILWES,B.R.CRANE JRNL TITL LIGHT-INDUCED SUBUNIT DISSOCIATION BY A LIGHT-OXYGEN-VOLTAGE JRNL TITL 2 DOMAIN PHOTORECEPTOR FROM RHODOBACTER SPHAEROIDES. JRNL REF BIOCHEMISTRY V. 52 378 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23252338 JRNL DOI 10.1021/BI3015373 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9886 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1025 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 29.8152 - 5.1630 1.00 1336 172 0.2300 0.2768 REMARK 3 2 5.1630 - 4.1015 1.00 1280 147 0.1931 0.2497 REMARK 3 3 4.1015 - 3.5840 1.00 1256 156 0.1642 0.2207 REMARK 3 4 3.5840 - 3.2567 1.00 1247 156 0.1697 0.2353 REMARK 3 5 3.2567 - 3.0236 1.00 1255 132 0.1816 0.2453 REMARK 3 6 3.0236 - 2.8454 1.00 1241 136 0.1896 0.2554 REMARK 3 7 2.8454 - 2.7030 0.99 1246 126 0.1892 0.2851 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.13 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 : 0.008 2841 REMARK 3 ANGLE : 1.234 3846 REMARK 3 CHIRALITY : 0.075 405 REMARK 3 PLANARITY : 0.006 516 REMARK 3 DIHEDRAL : 18.343 1060 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 4HJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9927 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG400, 0.15 M MGCL2, 0.1 M HEPES, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 32.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.25000 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 ALA B 1A REMARK 465 MET B 1 REMARK 465 ASP B 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 NH1 ARG A 10 O HOH A 302 1.93 REMARK 500 O THR B 148 O HOH B 307 2.12 REMARK 500 OD2 ASP B 70 O HOH B 302 2.15 REMARK 500 O LEU A 75 O HOH A 303 2.16 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 MET A 1 -143.51 -122.34 REMARK 500 PRO A 108 -52.02 -24.25 REMARK 500 SER A 127 72.43 -108.88 REMARK 500 ARG A 175 -70.99 -143.12 REMARK 500 CYS B 55 -7.48 -55.51 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HIA RELATED DB: PDB REMARK 900 RELATED ID: 4HJ3 RELATED DB: PDB REMARK 900 RELATED ID: 4HJ6 RELATED DB: PDB DBREF 4HJ4 A 1A 176 PDB 4HJ4 4HJ4 1 176 DBREF 4HJ4 B 1A 176 PDB 4HJ4 4HJ4 1 176 SEQRES 1 A 177 ALA MET ASP GLN LYS GLN PHE GLU LYS ILE ARG ALA VAL SEQRES 2 A 177 PHE ASP ARG SER GLY VAL ALA LEU THR LEU VAL ASP MET SEQRES 3 A 177 SER LEU PRO GLU GLN PRO LEU VAL LEU ALA ASN PRO PRO SEQRES 4 A 177 PHE LEU ARG MET THR GLY TYR THR GLU GLY GLN ILE LEU SEQRES 5 A 177 GLY PHE ASN CYS ARG PHE LEU GLN ARG GLY ASP GLU ASN SEQRES 6 A 177 ALA GLN ALA ARG ALA ASP ILE ARG ASP ALA LEU LYS LEU SEQRES 7 A 177 GLY ARG GLU LEU GLN VAL VAL LEU ARG ASN TYR ARG ALA SEQRES 8 A 177 ASN ASP GLU PRO PHE ASP ASN LEU LEU PHE LEU HIS PRO SEQRES 9 A 177 VAL GLY GLY ARG PRO ASP ALA PRO ASP TYR PHE LEU GLY SEQRES 10 A 177 SER GLN PHE GLU LEU GLY ARG SER GLY ASN SER GLU GLU SEQRES 11 A 177 ALA ALA ALA ALA GLY HIS ALA GLY ALA LEU THR GLY GLU SEQRES 12 A 177 LEU ALA ARG ILE GLY THR VAL ALA ALA ARG LEU GLU MET SEQRES 13 A 177 ASP SER ARG ARG HIS LEU ALA GLN ALA ALA ALA ALA LEU SEQRES 14 A 177 VAL ARG ALA TRP GLU ARG ARG GLY SEQRES 1 B 177 ALA MET ASP GLN LYS GLN PHE GLU LYS ILE ARG ALA VAL SEQRES 2 B 177 PHE ASP ARG SER GLY VAL ALA LEU THR LEU VAL ASP MET SEQRES 3 B 177 SER LEU PRO GLU GLN PRO LEU VAL LEU ALA ASN PRO PRO SEQRES 4 B 177 PHE LEU ARG MET THR GLY TYR THR GLU GLY GLN ILE LEU SEQRES 5 B 177 GLY PHE ASN CYS ARG PHE LEU GLN ARG GLY ASP GLU ASN SEQRES 6 B 177 ALA GLN ALA ARG ALA ASP ILE ARG ASP ALA LEU LYS LEU SEQRES 7 B 177 GLY ARG GLU LEU GLN VAL VAL LEU ARG ASN TYR ARG ALA SEQRES 8 B 177 ASN ASP GLU PRO PHE ASP ASN LEU LEU PHE LEU HIS PRO SEQRES 9 B 177 VAL GLY GLY ARG PRO ASP ALA PRO ASP TYR PHE LEU GLY SEQRES 10 B 177 SER GLN PHE GLU LEU GLY ARG SER GLY ASN SER GLU GLU SEQRES 11 B 177 ALA ALA ALA ALA GLY HIS ALA GLY ALA LEU THR GLY GLU SEQRES 12 B 177 LEU ALA ARG ILE GLY THR VAL ALA ALA ARG LEU GLU MET SEQRES 13 B 177 ASP SER ARG ARG HIS LEU ALA GLN ALA ALA ALA ALA LEU SEQRES 14 B 177 VAL ARG ALA TRP GLU ARG ARG GLY HET FMN A 201 31 HET FMN B 201 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *12(H2 O) HELIX 1 1 ASP A 2 ARG A 15 1 14 HELIX 2 2 ASN A 36 GLY A 44 1 9 HELIX 3 3 THR A 46 ILE A 50 5 5 HELIX 4 4 ASN A 54 GLN A 59 5 6 HELIX 5 5 ASN A 64 GLY A 78 1 15 HELIX 6 6 SER A 127 ILE A 146 1 20 HELIX 7 7 ALA A 150 ARG A 152 5 3 HELIX 8 8 LEU A 153 ARG A 174 1 22 HELIX 9 9 LYS B 4 ARG B 15 1 12 HELIX 10 10 ASN B 36 GLY B 44 1 9 HELIX 11 11 THR B 46 ILE B 50 5 5 HELIX 12 12 ASN B 54 GLN B 59 5 6 HELIX 13 13 ASN B 64 GLY B 78 1 15 HELIX 14 14 SER B 127 ARG B 145 1 19 HELIX 15 15 LEU B 153 ARG B 175 1 23 SHEET 1 A 5 LEU A 32 ALA A 35 0 SHEET 2 A 5 ALA A 19 ASP A 24 -1 N LEU A 22 O VAL A 33 SHEET 3 A 5 TYR A 113 LEU A 121 -1 O PHE A 114 N VAL A 23 SHEET 4 A 5 PRO A 94 VAL A 104 -1 N HIS A 102 O LEU A 115 SHEET 5 A 5 LEU A 81 TYR A 88 -1 N VAL A 83 O LEU A 99 SHEET 1 B 5 LEU B 32 ALA B 35 0 SHEET 2 B 5 THR B 21 ASP B 24 -1 N LEU B 22 O VAL B 33 SHEET 3 B 5 TYR B 113 LEU B 121 -1 O GLY B 116 N THR B 21 SHEET 4 B 5 PRO B 94 VAL B 104 -1 N VAL B 104 O TYR B 113 SHEET 5 B 5 LEU B 81 TYR B 88 -1 N LEU B 85 O ASN B 97 SITE 1 AC1 19 THR A 21 VAL A 23 ASN A 54 CYS A 55 SITE 2 AC1 19 ARG A 56 LEU A 58 GLN A 59 ARG A 68 SITE 3 AC1 19 ILE A 71 ARG A 72 LEU A 85 ASN A 87 SITE 4 AC1 19 ASN A 97 LEU A 99 LEU A 101 PHE A 114 SITE 5 AC1 19 LEU A 115 GLY A 116 GLN A 118 SITE 1 AC2 18 ARG A 79 ASN B 54 CYS B 55 ARG B 56 SITE 2 AC2 18 LEU B 58 GLN B 59 ARG B 68 ILE B 71 SITE 3 AC2 18 ARG B 72 LEU B 85 ASN B 87 ASN B 97 SITE 4 AC2 18 LEU B 99 LEU B 101 PHE B 114 LEU B 115 SITE 5 AC2 18 GLY B 116 GLN B 118 CRYST1 65.800 70.500 74.400 90.00 90.00 90.00 P 21 21 21 8 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 0.015198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013441 0.00000