PDB Short entry for 1XFQ HEADER SIGNALING PROTEIN 15-SEP-04 1XFQ TITLE STRUCTURE OF THE BLUE SHIFTED INTERMEDIATE STATE OF THE PHOTOACTIVE TITLE 2 YELLOW PROTEIN LACKING THE N-TERMINAL PART COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 26-125; COMPND 5 SYNONYM: PYP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 ORGANISM_TAXID: 1053; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PAS DOMAIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.BERNARD,K.HOUBEN,N.M.DERIX,D.MARKS,M.A.VAN DER HORST, AUTHOR 2 K.J.HELLINGWERF,R.BOELENS,R.KAPTEIN,N.A.VAN NULAND REVDAT 3 02-MAR-22 1XFQ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1XFQ 1 VERSN REVDAT 1 16-AUG-05 1XFQ 0 JRNL AUTH C.BERNARD,K.HOUBEN,N.M.DERIX,D.MARKS,M.A.VAN DER HORST, JRNL AUTH 2 K.J.HELLINGWERF,R.BOELENS,R.KAPTEIN,N.A.VAN NULAND JRNL TITL THE SOLUTION STRUCTURE OF A TRANSIENT PHOTORECEPTOR JRNL TITL 2 INTERMEDIATE: DELTA25 PHOTOACTIVE YELLOW PROTEIN JRNL REF STRUCTURE V. 13 953 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16004868 JRNL DOI 10.1016/J.STR.2005.04.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, CNS 1.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XFQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030311. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50MM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DELTA25-PYP, 15N-13C, 50MM REMARK 210 PHOSPHATE BUFFER; 1MM DELTA25- REMARK 210 PYP 15N, 50MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA; CBCA(CO)NH; 3D 15N TOCSY REMARK 210 -HSQC; 3D_15N-SEPARATED_NOESY; REMARK 210 2D NOESY; 2D TOCSY; HNCO; HNCACB; REMARK 210 13C FILTERED 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0.4, CNS 1.2 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 GLU A 19 REMARK 465 SER A 20 REMARK 465 ASP A 21 REMARK 465 ASP A 22 REMARK 465 ASP A 23 REMARK 465 ASP A 24 REMARK 465 LYS A 25 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 ILE A 31 CA ILE A 31 CB -0.205 REMARK 500 1 ILE A 39 CA ILE A 39 CB -0.216 REMARK 500 1 ILE A 49 CA ILE A 49 CB -0.219 REMARK 500 1 THR A 50 CA THR A 50 CB -0.197 REMARK 500 1 VAL A 57 CA VAL A 57 CB -0.213 REMARK 500 1 ILE A 58 CA ILE A 58 CB -0.205 REMARK 500 1 VAL A 66 CA VAL A 66 CB -0.211 REMARK 500 1 THR A 70 CA THR A 70 CB -0.207 REMARK 500 1 VAL A 83 CA VAL A 83 CB -0.217 REMARK 500 1 THR A 90 CA THR A 90 CB -0.195 REMARK 500 1 THR A 95 CA THR A 95 CB -0.209 REMARK 500 1 THR A 101 CA THR A 101 CB -0.210 REMARK 500 1 THR A 103 CA THR A 103 CB -0.216 REMARK 500 1 VAL A 105 CA VAL A 105 CB -0.218 REMARK 500 1 VAL A 107 CA VAL A 107 CB -0.217 REMARK 500 1 VAL A 120 CA VAL A 120 CB -0.210 REMARK 500 1 VAL A 122 CA VAL A 122 CB -0.208 REMARK 500 1 VAL A 125 CA VAL A 125 CB -0.216 REMARK 500 2 ILE A 31 CA ILE A 31 CB -0.214 REMARK 500 2 ILE A 39 CA ILE A 39 CB -0.213 REMARK 500 2 ILE A 49 CA ILE A 49 CB -0.212 REMARK 500 2 THR A 50 CA THR A 50 CB -0.209 REMARK 500 2 VAL A 57 CA VAL A 57 CB -0.216 REMARK 500 2 ILE A 58 CA ILE A 58 CB -0.198 REMARK 500 2 VAL A 66 CA VAL A 66 CB -0.212 REMARK 500 2 THR A 70 CA THR A 70 CB -0.196 REMARK 500 2 VAL A 83 CA VAL A 83 CB -0.216 REMARK 500 2 THR A 90 CA THR A 90 CB -0.204 REMARK 500 2 THR A 95 CA THR A 95 CB -0.212 REMARK 500 2 THR A 101 CA THR A 101 CB -0.204 REMARK 500 2 THR A 103 CA THR A 103 CB -0.213 REMARK 500 2 VAL A 105 CA VAL A 105 CB -0.212 REMARK 500 2 VAL A 107 CA VAL A 107 CB -0.212 REMARK 500 2 VAL A 120 CA VAL A 120 CB -0.210 REMARK 500 2 VAL A 122 CA VAL A 122 CB -0.214 REMARK 500 2 VAL A 125 CA VAL A 125 CB -0.213 REMARK 500 3 ILE A 31 CA ILE A 31 CB -0.215 REMARK 500 3 ILE A 39 CA ILE A 39 CB -0.215 REMARK 500 3 ILE A 49 CA ILE A 49 CB -0.208 REMARK 500 3 THR A 50 CA THR A 50 CB -0.208 REMARK 500 3 VAL A 57 CA VAL A 57 CB -0.205 REMARK 500 3 ILE A 58 CA ILE A 58 CB -0.206 REMARK 500 3 VAL A 66 CA VAL A 66 CB -0.207 REMARK 500 3 THR A 70 CA THR A 70 CB -0.211 REMARK 500 3 VAL A 83 CA VAL A 83 CB -0.220 REMARK 500 3 THR A 90 CA THR A 90 CB -0.193 REMARK 500 3 THR A 95 CA THR A 95 CB -0.198 REMARK 500 3 THR A 101 CA THR A 101 CB -0.213 REMARK 500 3 THR A 103 CA THR A 103 CB -0.210 REMARK 500 3 VAL A 105 CA VAL A 105 CB -0.213 REMARK 500 REMARK 500 THIS ENTRY HAS 360 BOND DEVIATIONS. 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 ALA A 44 -32.53 176.18 REMARK 500 1 GLU A 46 40.46 -147.45 REMARK 500 1 LYS A 55 32.20 -99.05 REMARK 500 1 ILE A 58 166.66 50.73 REMARK 500 1 TYR A 76 -113.60 50.40 REMARK 500 1 ASN A 87 48.65 -157.18 REMARK 500 1 TYR A 98 -166.51 -100.31 REMARK 500 1 MET A 100 33.40 -95.74 REMARK 500 2 ALA A 44 13.04 -170.20 REMARK 500 2 PRO A 54 36.94 -83.40 REMARK 500 2 ILE A 58 73.53 37.85 REMARK 500 2 PHE A 62 79.09 34.82 REMARK 500 2 VAL A 66 78.72 54.79 REMARK 500 2 ALA A 67 105.95 -39.56 REMARK 500 2 GLU A 74 43.65 -80.10 REMARK 500 2 TYR A 76 -96.98 52.22 REMARK 500 2 ASN A 87 54.63 -164.00 REMARK 500 2 LEU A 88 96.11 -65.37 REMARK 500 2 ASP A 97 -168.14 63.94 REMARK 500 2 TYR A 98 2.84 -155.74 REMARK 500 2 LEU A 113 1.27 -67.07 REMARK 500 2 SER A 117 151.32 179.25 REMARK 500 3 GLU A 46 103.18 67.57 REMARK 500 3 ILE A 49 47.75 33.97 REMARK 500 3 GLN A 56 44.32 -107.16 REMARK 500 3 LYS A 60 90.45 -69.25 REMARK 500 3 ALA A 67 110.27 -38.22 REMARK 500 3 CYS A 69 179.43 61.94 REMARK 500 3 TYR A 76 -106.30 54.15 REMARK 500 3 ASN A 87 55.75 -162.85 REMARK 500 3 LEU A 88 83.61 -69.07 REMARK 500 3 ASP A 97 -123.18 -84.44 REMARK 500 3 MET A 100 21.72 48.25 REMARK 500 3 PRO A 102 -73.84 -80.07 REMARK 500 4 GLN A 56 -46.94 -161.81 REMARK 500 4 ASP A 65 120.21 -172.07 REMARK 500 4 VAL A 66 37.33 -150.35 REMARK 500 4 ALA A 67 106.45 61.86 REMARK 500 4 SER A 72 79.29 57.02 REMARK 500 4 GLU A 74 -49.92 -167.63 REMARK 500 4 ASN A 87 50.19 -158.89 REMARK 500 4 TYR A 98 -149.37 177.50 REMARK 500 4 PRO A 102 86.82 -56.41 REMARK 500 5 ALA A 27 145.39 69.35 REMARK 500 5 GLU A 46 -178.82 68.14 REMARK 500 5 THR A 50 49.22 -95.00 REMARK 500 5 ILE A 58 73.44 38.70 REMARK 500 5 LYS A 64 141.64 -170.15 REMARK 500 5 ASN A 87 62.61 -169.96 REMARK 500 5 LEU A 88 102.35 -38.45 REMARK 500 REMARK 500 THIS ENTRY HAS 221 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 HC4 A 169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XFN RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE GROUND STATE DBREF 1XFQ A 26 125 UNP P16113 PYP_ECTHA 26 125 SEQADV 1XFQ HIS A 13 UNP P16113 EXPRESSION TAG SEQADV 1XFQ HIS A 14 UNP P16113 EXPRESSION TAG SEQADV 1XFQ HIS A 15 UNP P16113 EXPRESSION TAG SEQADV 1XFQ HIS A 16 UNP P16113 EXPRESSION TAG SEQADV 1XFQ HIS A 17 UNP P16113 EXPRESSION TAG SEQADV 1XFQ HIS A 18 UNP P16113 EXPRESSION TAG SEQADV 1XFQ GLU A 19 UNP P16113 EXPRESSION TAG SEQADV 1XFQ SER A 20 UNP P16113 EXPRESSION TAG SEQADV 1XFQ ASP A 21 UNP P16113 EXPRESSION TAG SEQADV 1XFQ ASP A 22 UNP P16113 EXPRESSION TAG SEQADV 1XFQ ASP A 23 UNP P16113 EXPRESSION TAG SEQADV 1XFQ ASP A 24 UNP P16113 EXPRESSION TAG SEQADV 1XFQ LYS A 25 UNP P16113 EXPRESSION TAG SEQRES 1 A 113 HIS HIS HIS HIS HIS HIS GLU SER ASP ASP ASP ASP LYS SEQRES 2 A 113 LEU ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN SEQRES 3 A 113 ILE LEU GLN TYR ASN ALA ALA GLU GLY ASP ILE THR GLY SEQRES 4 A 113 ARG ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS SEQRES 5 A 113 ASP VAL ALA PRO CYS THR ASP SER PRO GLU PHE TYR GLY SEQRES 6 A 113 LYS PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR SEQRES 7 A 113 MET PHE GLU TYR THR PHE ASP TYR GLN MET THR PRO THR SEQRES 8 A 113 LYS VAL LYS VAL HIS MET LYS LYS ALA LEU SER GLY ASP SEQRES 9 A 113 SER TYR TRP VAL PHE VAL LYS ARG VAL HET HC4 A 169 18 HETNAM HC4 4'-HYDROXYCINNAMIC ACID HETSYN HC4 PARA-COUMARIC ACID FORMUL 2 HC4 C9 H8 O3 HELIX 1 1 LYS A 78 GLY A 86 1 9 SHEET 1 A 5 ILE A 39 ASN A 43 0 SHEET 2 A 5 ALA A 30 ASP A 34 -1 N ALA A 30 O ASN A 43 SHEET 3 A 5 SER A 117 ARG A 124 -1 O VAL A 120 N ILE A 31 SHEET 4 A 5 VAL A 105 LYS A 111 -1 N LYS A 110 O TRP A 119 SHEET 5 A 5 THR A 90 TYR A 94 -1 N PHE A 92 O VAL A 107 LINK SG CYS A 69 C1 HC4 A 169 1555 1555 1.82 SITE 1 AC1 1 CYS A 69 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