HEADER TRANSFERASE 22-SEP-09 2KOI TITLE REFINED SOLUTION STRUCTURE OF A CYANOBACTERIAL PHYTOCHROME GAF DOMAIN TITLE 2 IN THE RED LIGHT-ABSORBING GROUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GAF DOMAIN (UNP RESIDUES 31-200); COMPND 5 SYNONYM: SYB-CPH1(GAF); COMPND 6 EC: 2.7.13.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 321332; SOURCE 4 STRAIN: JA-2-3B'A(2-13); SOURCE 5 GENE: CYB_2465; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-4T KEYWDS PHYTOCHROME, GAF DOMAIN, PHYCOCYANOBILIN, PCB, BACTERIOPHYTOCHROME, KEYWDS 2 CYANOBACTERIAL PHYTOCHROME, KINASE, PHOSPHOPROTEIN, TRANSFERASE, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, PSI-2, CENTER FOR EUKARYOTIC KEYWDS 4 STRUCTURAL GENOMICS, CESG, STRUCTURAL GENOMICS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.C.CORNILESCU,G.CORNILESCU,A.T.ULIJASZ,R.D.VIERSTRA,J.L.MARKLEY, AUTHOR 2 CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 5 13-JUL-11 2KOI 1 VERSN REVDAT 4 26-JAN-10 2KOI 1 JRNL REVDAT 3 19-JAN-10 2KOI 1 JRNL REVDAT 2 29-DEC-09 2KOI 1 JRNL REVDAT 1 03-NOV-09 2KOI 0 JRNL AUTH A.T.ULIJASZ,G.CORNILESCU,C.C.CORNILESCU,J.ZHANG,M.RIVERA, JRNL AUTH 2 J.L.MARKLEY,R.D.VIERSTRA JRNL TITL STRUCTURAL BASIS FOR THE PHOTOCONVERSION OF A PHYTOCHROME TO JRNL TITL 2 THE ACTIVATED PFR FORM JRNL REF NATURE V. 463 250 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20075921 JRNL DOI 10.1038/NATURE08671 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.CORNILESCU,A.T.ULIJASZ,C.C.CORNILESCU,J.L.MARKLEY, REMARK 1 AUTH 2 R.D.VIERSTRA REMARK 1 TITL SOLUTION STRUCTURE OF A CYANOBACTERIAL PHYTOCHROME GAF REMARK 1 TITL 2 DOMAIN IN THE RED-LIGHT-ABSORBING GROUND STATE REMARK 1 REF J.MOL.BIOL. V. 383 403 2008 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 18762196 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KOI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-09. REMARK 100 THE RCSB ID CODE IS RCSB101375. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 306 REMARK 210 PH : 8.5; 8.5 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.7 MM [U-13C; U-15N] SYB- REMARK 210 CPH1(GAF), 1.7 MM REMARK 210 PHYCOCYANOBILIN, 10 MM [U-2H] REMARK 210 TRIS-DCL, 0.03 % SODIUM AZIDE, REMARK 210 93% H2O/7% D2O; 2 MM SYB- REMARK 210 CPH1(GAF), 2 MM [U-15N] REMARK 210 PHYCOCYANOBILIN, 10 MM [U-2H] REMARK 210 TRIS-DCL, 0.03 % SODIUM AZIDE, REMARK 210 93% H2O/7% D2O; 1 MM SYB- REMARK 210 CPH1(GAF), 1 MM [U-13C] REMARK 210 PHYCOCYANOBILIN, 10 MM [U-2H] REMARK 210 TRIS-DCL, 0.03 % SODIUM AZIDE, REMARK 210 100% D2O; 1 MM [U-13C; U-15N] SYB REMARK 210 -CPH1(GAF), 1 MM PHYCOCYANOBILIN, REMARK 210 10 MM [U-2H] TRIS-DCL, 0.03 % REMARK 210 SODIUM AZIDE-16, 93% H2O/7% D2O; REMARK 210 0.5 MM SYB-CPH1(GAF), 0.5 MM [U- REMARK 210 13C] PHYCOCYANOBILIN, 10 MM [U- REMARK 210 2H] TRIS-DCL, 0.03 % SODIUM REMARK 210 AZIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HNCO ANTIPHASE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRDRAW, PIPP, X-PLOR_ REMARK 210 NIH, VNMRJ, MOLMOL, PROCHECKNMR REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR REMARK 210 DYNAMICS, INTERNAL VARIABLE REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 HG SER A 168 HE2 HIS A 170 1.39 REMARK 500 HZ3 LYS A 52 HBB2 CYC A 203 1.45 REMARK 500 HE2 HIS A 139 HMA3 CYC A 203 1.45 REMARK 500 O ALA A 188 H SER A 192 1.48 REMARK 500 O HIS A 141 H SER A 145 1.54 REMARK 500 HB2 PRO A 88 H GLU A 89 1.56 REMARK 500 H PHE A 56 O TRP A 163 1.57 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 1 GLU A 72 17.91 53.60 REMARK 500 1 PRO A 88 -115.84 -45.63 REMARK 500 1 GLU A 89 -51.68 -157.00 REMARK 500 1 PRO A 116 -25.71 -36.79 REMARK 500 1 ARG A 124 -14.39 -45.92 REMARK 500 1 LEU A 127 -110.88 39.27 REMARK 500 1 PRO A 130 168.42 -41.65 REMARK 500 1 LEU A 131 11.06 -63.07 REMARK 500 1 ASP A 136 160.86 -41.68 REMARK 500 1 HIS A 159 -122.47 58.34 REMARK 500 1 ARG A 174 80.98 -164.40 REMARK 500 2 GLU A 72 6.04 -59.94 REMARK 500 2 PRO A 88 -97.75 -39.60 REMARK 500 2 GLU A 89 -39.86 -165.71 REMARK 500 2 VAL A 100 107.38 -168.80 REMARK 500 2 GLU A 117 102.87 56.88 REMARK 500 2 TRP A 119 -19.60 -152.83 REMARK 500 2 LEU A 121 3.18 56.90 REMARK 500 2 ARG A 124 -3.62 -49.33 REMARK 500 2 LEU A 127 -117.88 50.11 REMARK 500 2 PRO A 130 173.35 -42.97 REMARK 500 2 LEU A 131 14.46 -64.17 REMARK 500 2 PRO A 137 -20.71 -37.80 REMARK 500 2 HIS A 159 -122.04 60.17 REMARK 500 2 ARG A 174 81.62 -172.91 REMARK 500 3 GLU A 72 0.67 57.41 REMARK 500 3 PRO A 88 -95.43 -39.18 REMARK 500 3 GLU A 89 -46.90 -162.91 REMARK 500 3 VAL A 106 -19.74 -49.66 REMARK 500 3 GLU A 117 84.55 59.61 REMARK 500 3 LEU A 121 35.52 -71.66 REMARK 500 3 ARG A 124 -14.21 -45.79 REMARK 500 3 LEU A 127 -80.93 59.22 REMARK 500 3 PRO A 130 167.76 -40.97 REMARK 500 3 LEU A 131 9.96 -57.84 REMARK 500 3 PRO A 137 -17.56 -37.91 REMARK 500 3 HIS A 159 -123.56 61.79 REMARK 500 4 GLU A 72 44.10 26.34 REMARK 500 4 PRO A 88 -92.65 -75.70 REMARK 500 4 GLU A 89 -37.70 -167.58 REMARK 500 4 PRO A 116 87.62 -37.74 REMARK 500 4 GLU A 117 94.92 44.57 REMARK 500 4 SER A 118 0.36 -157.31 REMARK 500 4 LEU A 127 -107.43 44.68 REMARK 500 4 LEU A 131 -12.73 -47.69 REMARK 500 4 PRO A 137 -35.79 -39.08 REMARK 500 4 HIS A 159 -125.44 58.38 REMARK 500 5 GLU A 72 11.26 -61.67 REMARK 500 5 PRO A 88 -84.80 -40.38 REMARK 500 5 GLU A 89 -30.89 -172.41 REMARK 500 REMARK 500 THIS ENTRY HAS 216 RAMACHANDRAN OUTLIERS. 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 CYC A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.102706 RELATED DB: TARGETDB DBREF 2KOI A 31 200 UNP Q2JIZ5 Q2JIZ5_SYNJB 31 200 SEQADV 2KOI SER A 201 UNP Q2JIZ5 EXPRESSION TAG SEQADV 2KOI LEU A 202 UNP Q2JIZ5 EXPRESSION TAG SEQRES 1 A 172 LEU ASP GLN ILE LEU ARG ALA THR VAL GLU GLU VAL ARG SEQRES 2 A 172 ALA PHE LEU GLY THR ASP ARG VAL LYS VAL TYR ARG PHE SEQRES 3 A 172 ASP PRO GLU GLY HIS GLY THR VAL VAL ALA GLU ALA ARG SEQRES 4 A 172 GLY GLY GLU ARG LEU PRO SER LEU LEU GLY LEU THR PHE SEQRES 5 A 172 PRO ALA GLY ASP ILE PRO GLU GLU ALA ARG ARG LEU PHE SEQRES 6 A 172 ARG LEU ALA GLN VAL ARG VAL ILE VAL ASP VAL GLU ALA SEQRES 7 A 172 GLN SER ARG SER ILE SER GLN PRO GLU SER TRP GLY LEU SEQRES 8 A 172 SER ALA ARG VAL PRO LEU GLY GLU PRO LEU GLN ARG PRO SEQRES 9 A 172 VAL ASP PRO CYS HIS VAL HIS TYR LEU LYS SER MET GLY SEQRES 10 A 172 VAL ALA SER SER LEU VAL VAL PRO LEU MET HIS HIS GLN SEQRES 11 A 172 GLU LEU TRP GLY LEU LEU VAL SER HIS HIS ALA GLU PRO SEQRES 12 A 172 ARG PRO TYR SER GLN GLU GLU LEU GLN VAL VAL GLN LEU SEQRES 13 A 172 LEU ALA ASP GLN VAL SER ILE ALA ILE ALA GLN ALA GLU SEQRES 14 A 172 LEU SER LEU HET CYC A 203 81 HETNAM CYC PHYCOCYANOBILIN FORMUL 2 CYC C33 H40 N4 O6 HELIX 1 1 LEU A 31 GLY A 47 1 17 HELIX 2 2 PRO A 83 ILE A 87 5 5 HELIX 3 3 GLU A 89 ALA A 98 1 10 HELIX 4 4 GLY A 120 VAL A 125 5 6 HELIX 5 5 ASP A 136 SER A 145 1 10 HELIX 6 6 SER A 177 LEU A 202 1 26 SHEET 1 A 6 THR A 81 PHE A 82 0 SHEET 2 A 6 GLY A 62 ARG A 69 -1 N GLY A 62 O PHE A 82 SHEET 3 A 6 ARG A 50 PHE A 56 -1 N VAL A 53 O ALA A 66 SHEET 4 A 6 GLU A 161 HIS A 170 -1 O TRP A 163 N PHE A 56 SHEET 5 A 6 SER A 150 HIS A 158 -1 N VAL A 154 O LEU A 166 SHEET 6 A 6 ARG A 101 VAL A 102 -1 N ARG A 101 O VAL A 153 LINK SG CYS A 138 CAC CYC A 203 1555 1555 1.84 SITE 1 AC1 14 LYS A 52 TYR A 54 PHE A 82 ILE A 87 SITE 2 AC1 14 PRO A 88 ALA A 91 PHE A 95 ARG A 101 SITE 3 AC1 14 PRO A 134 VAL A 135 ASP A 136 CYS A 138 SITE 4 AC1 14 HIS A 139 LEU A 165 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1