HEADER SIGNALING PROTEIN 30-JUN-06 2HJ9 TITLE CRYSTAL STRUCTURE OF THE AUTOINDUCER-2-BOUND FORM OF VIBRIO HARVEYI TITLE 2 LUXP COMPLEXED WITH THE PERIPLASMIC DOMAIN OF LUXQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOINDUCER 2-BINDING PERIPLASMIC PROTEIN LUXP; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AUTOINDUCER 2 SENSOR KINASE/PHOSPHATASE LUXQ; COMPND 7 CHAIN: C, D; COMPND 8 FRAGMENT: PERIPLASMIC DOMAIN (RESIDUES 53-271); COMPND 9 EC: 3.1.3.-; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 3 ORGANISM_TAXID: 669; SOURCE 4 GENE: LUXP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 12 ORGANISM_TAXID: 669; SOURCE 13 GENE: LUXQ; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS PERIPLASMIC BINDING PROTEIN, PER/ARNT/SIMPLE-MINDED (PAS) FOLD, KEYWDS 2 AUTOINDUCER-2 (AI-2), QUORUM SENSING, HISTIDINE SENSOR KINASE, KEYWDS 3 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.B.NEIDITCH,F.M.HUGHSON REVDAT 3 14-FEB-24 2HJ9 1 REMARK REVDAT 2 24-FEB-09 2HJ9 1 VERSN REVDAT 1 26-SEP-06 2HJ9 0 JRNL AUTH M.B.NEIDITCH,M.J.FEDERLE,A.J.POMPEANI,R.C.KELLY,D.L.SWEM, JRNL AUTH 2 P.D.JEFFREY,B.L.BASSLER,F.M.HUGHSON JRNL TITL LIGAND-INDUCED ASYMMETRY IN HISTIDINE SENSOR KINASE COMPLEX JRNL TITL 2 REGULATES QUORUM SENSING. JRNL REF CELL(CAMBRIDGE,MASS.) V. 126 1095 2006 JRNL REFN ISSN 0092-8674 JRNL PMID 16990134 JRNL DOI 10.1016/J.CELL.2006.07.032 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 52723 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2827 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3720 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 192 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8672 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 394 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : -1.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.369 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.266 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8900 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12106 ; 1.458 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1074 ; 6.238 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 451 ;39.190 ;24.501 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1463 ;17.414 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 49 ;17.858 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1350 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6837 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4218 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 6094 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 559 ; 0.170 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 43 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.143 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 5514 ; 0.726 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8747 ; 1.302 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3817 ; 1.764 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3359 ; 2.775 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2HJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55573 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 MIXTURE OF PROTEIN (20 MG/ML IN 20 REMARK 280 MM TRIS-HCL (PH 7.5), 150 MM NACL) AND WELL SOLUTION (27.5% (W/V) REMARK 280 PEG 400, 100 MM POTASSIUM NITRATE, 100 MM 2- REMARK 280 MORPHOLINOETHANESULFONIC ACID MONOHYDRATE (PH 6.0), 100 M 4,5- REMARK 280 DIHYDROXY-2,3-PENTANE DIONE, AND 1 MM BORIC ACID), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 182.66400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.95800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.95800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 273.99600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.95800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.95800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 91.33200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.95800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.95800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 273.99600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.95800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.95800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.33200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 182.66400 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 PRO B 109 REMARK 465 ASN B 110 REMARK 465 ALA B 111 REMARK 465 ASP B 112 REMARK 465 ILE B 113 REMARK 465 LYS B 114 REMARK 465 GLN B 115 REMARK 465 GLN B 116 REMARK 465 SER B 117 REMARK 465 LEU B 118 REMARK 465 GLY C 51 REMARK 465 LYS C 239 REMARK 465 SER C 240 REMARK 465 SER C 241 REMARK 465 ASP C 242 REMARK 465 LYS C 243 REMARK 465 ARG C 244 REMARK 465 LEU C 245 REMARK 465 ASP C 246 REMARK 465 LYS C 247 REMARK 465 ASP C 271 REMARK 465 GLY D 51 REMARK 465 SER D 52 REMARK 465 LYS D 53 REMARK 465 GLN D 54 REMARK 465 GLN D 55 REMARK 465 THR D 56 REMARK 465 SER D 57 REMARK 465 ARG D 238 REMARK 465 LYS D 239 REMARK 465 SER D 240 REMARK 465 SER D 241 REMARK 465 ASP D 242 REMARK 465 LYS D 243 REMARK 465 ARG D 244 REMARK 465 LEU D 245 REMARK 465 ASP D 246 REMARK 465 LYS D 247 REMARK 465 ASP D 271 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 LEU D 202 OG SER D 206 2.02 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 PRO A 62 152.41 -49.30 REMARK 500 ASN A 110 19.71 59.34 REMARK 500 PHE A 133 -154.94 -139.14 REMARK 500 LYS A 169 -6.40 77.35 REMARK 500 ASP A 257 51.28 -97.01 REMARK 500 ARG A 281 26.79 -141.40 REMARK 500 GLU A 282 8.61 -69.48 REMARK 500 GLN B 76 31.35 71.71 REMARK 500 SER B 126 3.62 -64.97 REMARK 500 LYS B 127 62.76 38.65 REMARK 500 ASP B 136 -41.74 -134.30 REMARK 500 PRO B 172 153.80 -44.86 REMARK 500 PHE B 206 -161.43 -72.00 REMARK 500 ASP B 257 73.14 -100.19 REMARK 500 ARG B 281 51.37 -118.85 REMARK 500 MET B 311 66.94 -67.17 REMARK 500 ARG C 91 29.51 49.72 REMARK 500 ASP C 119 -149.52 -106.05 REMARK 500 ASN C 216 -88.02 50.31 REMARK 500 SER C 217 43.20 -157.71 REMARK 500 ASP D 107 55.57 -158.53 REMARK 500 HIS D 110 60.96 -118.42 REMARK 500 TRP D 125 138.77 -177.79 REMARK 500 PRO D 177 2.16 -68.30 REMARK 500 PRO D 229 27.69 -67.95 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 AI2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AI2 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZHH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO FORM OF VIBRIO HARVEYI LUXP COMPLEXED REMARK 900 WITH THE PERIPLASMIC DOMAIN OF LUXQ REMARK 900 RELATED ID: 1JX6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LUXP FROM VIBRIO HARVEYI COMPLEXED WITH REMARK 900 AUTOINDUCER-2 REMARK 900 RELATED ID: 2HJE RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE TWO HETEROLOGOUS LUXQ N-TERMINAL RESIDUES (GLY-SER) REMARK 999 ARE DERIVED FROM THE THROMBIN CLEAVAGE SIGNAL. REMARK 999 LUXP RESIDUES 22-26 ARE DELETED. DBREF 2HJ9 A 27 365 UNP P54300 LUXP_VIBHA 27 365 DBREF 2HJ9 B 27 365 UNP P54300 LUXP_VIBHA 27 365 DBREF 2HJ9 C 53 271 UNP P54302 LUXQ_VIBHA 53 271 DBREF 2HJ9 D 53 271 UNP P54302 LUXQ_VIBHA 53 271 SEQADV 2HJ9 GLY C 51 UNP P54302 SEE REMARK 999 SEQADV 2HJ9 SER C 52 UNP P54302 SEE REMARK 999 SEQADV 2HJ9 GLY D 51 UNP P54302 SEE REMARK 999 SEQADV 2HJ9 SER D 52 UNP P54302 SEE REMARK 999 SEQRES 1 A 339 GLY TYR TRP GLY TYR GLN GLU PHE LEU ASP GLU PHE PRO SEQRES 2 A 339 GLU GLN ARG ASN LEU THR ASN ALA LEU SER GLU ALA VAL SEQRES 3 A 339 ARG ALA GLN PRO VAL PRO LEU SER LYS PRO THR GLN ARG SEQRES 4 A 339 PRO ILE LYS ILE SER VAL VAL TYR PRO GLY GLN GLN VAL SEQRES 5 A 339 SER ASP TYR TRP VAL ARG ASN ILE ALA SER PHE GLU LYS SEQRES 6 A 339 ARG LEU TYR LYS LEU ASN ILE ASN TYR GLN LEU ASN GLN SEQRES 7 A 339 VAL PHE THR ARG PRO ASN ALA ASP ILE LYS GLN GLN SER SEQRES 8 A 339 LEU SER LEU MET GLU ALA LEU LYS SER LYS SER ASP TYR SEQRES 9 A 339 LEU ILE PHE THR LEU ASP THR THR ARG HIS ARG LYS PHE SEQRES 10 A 339 VAL GLU HIS VAL LEU ASP SER THR ASN THR LYS LEU ILE SEQRES 11 A 339 LEU GLN ASN ILE THR THR PRO VAL ARG GLU TRP ASP LYS SEQRES 12 A 339 HIS GLN PRO PHE LEU TYR VAL GLY PHE ASP HIS ALA GLU SEQRES 13 A 339 GLY SER ARG GLU LEU ALA THR GLU PHE GLY LYS PHE PHE SEQRES 14 A 339 PRO LYS HIS THR TYR TYR SER VAL LEU TYR PHE SER GLU SEQRES 15 A 339 GLY TYR ILE SER ASP VAL ARG GLY ASP THR PHE ILE HIS SEQRES 16 A 339 GLN VAL ASN ARG ASP ASN ASN PHE GLU LEU GLN SER ALA SEQRES 17 A 339 TYR TYR THR LYS ALA THR LYS GLN SER GLY TYR ASP ALA SEQRES 18 A 339 ALA LYS ALA SER LEU ALA LYS HIS PRO ASP VAL ASP PHE SEQRES 19 A 339 ILE TYR ALA CYS SER THR ASP VAL ALA LEU GLY ALA VAL SEQRES 20 A 339 ASP ALA LEU ALA GLU LEU GLY ARG GLU ASP ILE MET ILE SEQRES 21 A 339 ASN GLY TRP GLY GLY GLY SER ALA GLU LEU ASP ALA ILE SEQRES 22 A 339 GLN LYS GLY ASP LEU ASP ILE THR VAL MET ARG MET ASN SEQRES 23 A 339 ASP ASP THR GLY ILE ALA MET ALA GLU ALA ILE LYS TRP SEQRES 24 A 339 ASP LEU GLU ASP LYS PRO VAL PRO THR VAL TYR SER GLY SEQRES 25 A 339 ASP PHE GLU ILE VAL THR LYS ALA ASP SER PRO GLU ARG SEQRES 26 A 339 ILE GLU ALA LEU LYS LYS ARG ALA PHE ARG TYR SER ASP SEQRES 27 A 339 ASN SEQRES 1 B 339 GLY TYR TRP GLY TYR GLN GLU PHE LEU ASP GLU PHE PRO SEQRES 2 B 339 GLU GLN ARG ASN LEU THR ASN ALA LEU SER GLU ALA VAL SEQRES 3 B 339 ARG ALA GLN PRO VAL PRO LEU SER LYS PRO THR GLN ARG SEQRES 4 B 339 PRO ILE LYS ILE SER VAL VAL TYR PRO GLY GLN GLN VAL SEQRES 5 B 339 SER ASP TYR TRP VAL ARG ASN ILE ALA SER PHE GLU LYS SEQRES 6 B 339 ARG LEU TYR LYS LEU ASN ILE ASN TYR GLN LEU ASN GLN SEQRES 7 B 339 VAL PHE THR ARG PRO ASN ALA ASP ILE LYS GLN GLN SER SEQRES 8 B 339 LEU SER LEU MET GLU ALA LEU LYS SER LYS SER ASP TYR SEQRES 9 B 339 LEU ILE PHE THR LEU ASP THR THR ARG HIS ARG LYS PHE SEQRES 10 B 339 VAL GLU HIS VAL LEU ASP SER THR ASN THR LYS LEU ILE SEQRES 11 B 339 LEU GLN ASN ILE THR THR PRO VAL ARG GLU TRP ASP LYS SEQRES 12 B 339 HIS GLN PRO PHE LEU TYR VAL GLY PHE ASP HIS ALA GLU SEQRES 13 B 339 GLY SER ARG GLU LEU ALA THR GLU PHE GLY LYS PHE PHE SEQRES 14 B 339 PRO LYS HIS THR TYR TYR SER VAL LEU TYR PHE SER GLU SEQRES 15 B 339 GLY TYR ILE SER ASP VAL ARG GLY ASP THR PHE ILE HIS SEQRES 16 B 339 GLN VAL ASN ARG ASP ASN ASN PHE GLU LEU GLN SER ALA SEQRES 17 B 339 TYR TYR THR LYS ALA THR LYS GLN SER GLY TYR ASP ALA SEQRES 18 B 339 ALA LYS ALA SER LEU ALA LYS HIS PRO ASP VAL ASP PHE SEQRES 19 B 339 ILE TYR ALA CYS SER THR ASP VAL ALA LEU GLY ALA VAL SEQRES 20 B 339 ASP ALA LEU ALA GLU LEU GLY ARG GLU ASP ILE MET ILE SEQRES 21 B 339 ASN GLY TRP GLY GLY GLY SER ALA GLU LEU ASP ALA ILE SEQRES 22 B 339 GLN LYS GLY ASP LEU ASP ILE THR VAL MET ARG MET ASN SEQRES 23 B 339 ASP ASP THR GLY ILE ALA MET ALA GLU ALA ILE LYS TRP SEQRES 24 B 339 ASP LEU GLU ASP LYS PRO VAL PRO THR VAL TYR SER GLY SEQRES 25 B 339 ASP PHE GLU ILE VAL THR LYS ALA ASP SER PRO GLU ARG SEQRES 26 B 339 ILE GLU ALA LEU LYS LYS ARG ALA PHE ARG TYR SER ASP SEQRES 27 B 339 ASN SEQRES 1 C 221 GLY SER LYS GLN GLN THR SER ALA LEU ILE HIS ASN ILE SEQRES 2 C 221 PHE ASP SER HIS PHE ALA ALA ILE GLN ILE HIS HIS ASP SEQRES 3 C 221 SER ASN SER LYS SER GLU VAL ILE ARG ASP PHE TYR THR SEQRES 4 C 221 ASP ARG ASP THR ASP VAL LEU ASN PHE PHE PHE LEU SER SEQRES 5 C 221 ILE ASP GLN SER ASP PRO SER HIS THR PRO GLU PHE ARG SEQRES 6 C 221 PHE LEU THR ASP HIS LYS GLY ILE ILE TRP ASP ASP GLY SEQRES 7 C 221 ASN ALA HIS PHE TYR GLY VAL ASN ASP LEU ILE LEU ASP SEQRES 8 C 221 SER LEU ALA ASN ARG VAL SER PHE SER ASN ASN TRP TYR SEQRES 9 C 221 TYR ILE ASN VAL MET THR SER ILE GLY SER ARG HIS MET SEQRES 10 C 221 LEU VAL ARG ARG VAL PRO ILE LEU ASP PRO SER THR GLY SEQRES 11 C 221 GLU VAL LEU GLY PHE SER PHE ASN ALA VAL VAL LEU ASP SEQRES 12 C 221 ASN ASN PHE ALA LEU MET GLU LYS LEU LYS SER GLU SER SEQRES 13 C 221 ASN VAL ASP ASN VAL VAL LEU VAL ALA ASN SER VAL PRO SEQRES 14 C 221 LEU ALA ASN SER LEU ILE GLY ASP GLU PRO TYR ASN VAL SEQRES 15 C 221 ALA ASP VAL LEU GLN ARG LYS SER SER ASP LYS ARG LEU SEQRES 16 C 221 ASP LYS LEU LEU VAL ILE GLU THR PRO ILE VAL VAL ASN SEQRES 17 C 221 ALA VAL THR THR GLU LEU CYS LEU LEU THR VAL GLN ASP SEQRES 1 D 221 GLY SER LYS GLN GLN THR SER ALA LEU ILE HIS ASN ILE SEQRES 2 D 221 PHE ASP SER HIS PHE ALA ALA ILE GLN ILE HIS HIS ASP SEQRES 3 D 221 SER ASN SER LYS SER GLU VAL ILE ARG ASP PHE TYR THR SEQRES 4 D 221 ASP ARG ASP THR ASP VAL LEU ASN PHE PHE PHE LEU SER SEQRES 5 D 221 ILE ASP GLN SER ASP PRO SER HIS THR PRO GLU PHE ARG SEQRES 6 D 221 PHE LEU THR ASP HIS LYS GLY ILE ILE TRP ASP ASP GLY SEQRES 7 D 221 ASN ALA HIS PHE TYR GLY VAL ASN ASP LEU ILE LEU ASP SEQRES 8 D 221 SER LEU ALA ASN ARG VAL SER PHE SER ASN ASN TRP TYR SEQRES 9 D 221 TYR ILE ASN VAL MET THR SER ILE GLY SER ARG HIS MET SEQRES 10 D 221 LEU VAL ARG ARG VAL PRO ILE LEU ASP PRO SER THR GLY SEQRES 11 D 221 GLU VAL LEU GLY PHE SER PHE ASN ALA VAL VAL LEU ASP SEQRES 12 D 221 ASN ASN PHE ALA LEU MET GLU LYS LEU LYS SER GLU SER SEQRES 13 D 221 ASN VAL ASP ASN VAL VAL LEU VAL ALA ASN SER VAL PRO SEQRES 14 D 221 LEU ALA ASN SER LEU ILE GLY ASP GLU PRO TYR ASN VAL SEQRES 15 D 221 ALA ASP VAL LEU GLN ARG LYS SER SER ASP LYS ARG LEU SEQRES 16 D 221 ASP LYS LEU LEU VAL ILE GLU THR PRO ILE VAL VAL ASN SEQRES 17 D 221 ALA VAL THR THR GLU LEU CYS LEU LEU THR VAL GLN ASP HET AI2 A 501 13 HET AI2 B 502 13 HETNAM AI2 3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2, HETNAM 2 AI2 2,6,6A-TETRAOL HETSYN AI2 (2S,3R,4S)-2-METHYL-3,4-DIHYDROXY-OXOLAN-2,3-DIOXY- HETSYN 2 AI2 BORATE FORMUL 5 AI2 2(C5 H10 B O7 1-) FORMUL 7 HOH *394(H2 O) HELIX 1 1 GLY A 30 PHE A 38 1 9 HELIX 2 2 PHE A 38 ALA A 54 1 17 HELIX 3 3 ASP A 80 LEU A 96 1 17 HELIX 4 4 ASP A 112 SER A 126 1 15 HELIX 5 5 THR A 137 LEU A 148 1 12 HELIX 6 6 VAL A 164 ASP A 168 5 5 HELIX 7 7 ASP A 179 PHE A 195 1 17 HELIX 8 8 GLY A 209 ASN A 228 1 20 HELIX 9 9 THR A 240 HIS A 255 1 16 HELIX 10 10 SER A 265 LEU A 279 1 15 HELIX 11 11 GLY A 292 LYS A 301 1 10 HELIX 12 12 ASP A 313 GLU A 328 1 16 HELIX 13 13 SER A 348 PHE A 360 1 13 HELIX 14 14 GLY B 30 PHE B 38 1 9 HELIX 15 15 PHE B 38 ALA B 54 1 17 HELIX 16 16 ASP B 80 LEU B 96 1 17 HELIX 17 17 LEU B 120 LYS B 125 1 6 HELIX 18 18 THR B 137 THR B 151 1 15 HELIX 19 19 VAL B 164 ASP B 168 5 5 HELIX 20 20 ASP B 179 PHE B 195 1 17 HELIX 21 21 GLY B 209 ASN B 228 1 20 HELIX 22 22 THR B 240 HIS B 255 1 16 HELIX 23 23 SER B 265 LEU B 279 1 15 HELIX 24 24 GLY B 292 LYS B 301 1 10 HELIX 25 25 ASP B 313 GLU B 328 1 16 HELIX 26 26 SER B 348 PHE B 360 1 13 HELIX 27 27 SER C 52 SER C 79 1 28 HELIX 28 28 SER C 81 ARG C 91 1 11 HELIX 29 29 ASP C 92 ASP C 107 1 16 HELIX 30 30 PRO C 108 THR C 111 5 4 HELIX 31 31 ASN C 129 GLY C 134 5 6 HELIX 32 32 ASN C 136 VAL C 147 1 12 HELIX 33 33 ASN C 195 ASN C 207 1 13 HELIX 34 34 ASN C 231 GLN C 237 1 7 HELIX 35 35 LEU D 59 SER D 79 1 21 HELIX 36 36 SER D 81 ARG D 91 1 11 HELIX 37 37 ASP D 92 ASP D 107 1 16 HELIX 38 38 ASN D 129 GLY D 134 5 6 HELIX 39 39 ASN D 136 VAL D 147 1 12 HELIX 40 40 ASN D 195 SER D 206 1 12 HELIX 41 41 ASN D 231 LEU D 236 1 6 SHEET 1 A 6 TYR A 100 PHE A 106 0 SHEET 2 A 6 ILE A 67 TYR A 73 1 N ILE A 69 O GLN A 101 SHEET 3 A 6 TYR A 130 THR A 134 1 O ILE A 132 N SER A 70 SHEET 4 A 6 LYS A 154 GLN A 158 1 O ILE A 156 N PHE A 133 SHEET 5 A 6 LEU A 174 GLY A 177 1 O LEU A 174 N LEU A 157 SHEET 6 A 6 VAL A 335 SER A 337 1 O TYR A 336 N TYR A 175 SHEET 1 B 7 MET A 285 ILE A 286 0 SHEET 2 B 7 PHE A 260 ALA A 263 1 N ILE A 261 O MET A 285 SHEET 3 B 7 TYR A 200 LEU A 204 1 N LEU A 204 O TYR A 262 SHEET 4 B 7 GLU A 230 TYR A 235 1 O GLN A 232 N TYR A 201 SHEET 5 B 7 GLU D 181 VAL D 191 -1 O VAL D 182 N ALA A 234 SHEET 6 B 7 PHE D 114 ASP D 119 -1 N PHE D 116 O PHE D 187 SHEET 7 B 7 GLY D 122 ASP D 126 -1 O TRP D 125 N LEU D 117 SHEET 1 C 7 MET A 285 ILE A 286 0 SHEET 2 C 7 PHE A 260 ALA A 263 1 N ILE A 261 O MET A 285 SHEET 3 C 7 TYR A 200 LEU A 204 1 N LEU A 204 O TYR A 262 SHEET 4 C 7 GLU A 230 TYR A 235 1 O GLN A 232 N TYR A 201 SHEET 5 C 7 GLU D 181 VAL D 191 -1 O VAL D 182 N ALA A 234 SHEET 6 C 7 GLY D 163 LEU D 175 -1 N ILE D 174 O LEU D 183 SHEET 7 C 7 TYR D 154 THR D 160 -1 N ILE D 156 O MET D 167 SHEET 1 D 2 ILE A 306 ARG A 310 0 SHEET 2 D 2 PHE A 340 THR A 344 -1 O GLU A 341 N MET A 309 SHEET 1 E 6 TYR B 100 PHE B 106 0 SHEET 2 E 6 ILE B 67 TYR B 73 1 N ILE B 67 O GLN B 101 SHEET 3 E 6 TYR B 130 THR B 134 1 O ILE B 132 N SER B 70 SHEET 4 E 6 LYS B 154 GLN B 158 1 O ILE B 156 N LEU B 131 SHEET 5 E 6 LEU B 174 PHE B 178 1 O LEU B 174 N LEU B 157 SHEET 6 E 6 VAL B 335 GLY B 338 1 O TYR B 336 N TYR B 175 SHEET 1 F 4 GLU B 230 TYR B 235 0 SHEET 2 F 4 TYR B 200 LEU B 204 1 N TYR B 201 O GLN B 232 SHEET 3 F 4 PHE B 260 ALA B 263 1 O TYR B 262 N LEU B 204 SHEET 4 F 4 MET B 285 ILE B 286 1 O MET B 285 N ILE B 261 SHEET 1 G 2 ILE B 306 ARG B 310 0 SHEET 2 G 2 PHE B 340 THR B 344 -1 O GLU B 341 N MET B 309 SHEET 1 H 5 ILE C 123 ASP C 126 0 SHEET 2 H 5 PHE C 114 THR C 118 -1 N LEU C 117 O TRP C 125 SHEET 3 H 5 VAL C 182 VAL C 191 -1 O PHE C 187 N PHE C 116 SHEET 4 H 5 GLY C 163 LEU C 175 -1 N ILE C 174 O GLY C 184 SHEET 5 H 5 TYR C 154 THR C 160 -1 N VAL C 158 O ARG C 165 SHEET 1 I 4 VAL C 218 ASN C 222 0 SHEET 2 I 4 ASN C 210 ALA C 215 -1 N LEU C 213 O LEU C 220 SHEET 3 I 4 VAL C 260 VAL C 269 -1 O LEU C 267 N VAL C 212 SHEET 4 I 4 VAL C 250 VAL C 257 -1 N THR C 253 O LEU C 266 SHEET 1 J 4 VAL D 218 ASN D 222 0 SHEET 2 J 4 ASN D 210 ALA D 215 -1 N ALA D 215 O VAL D 218 SHEET 3 J 4 VAL D 260 VAL D 269 -1 O LEU D 267 N VAL D 212 SHEET 4 J 4 VAL D 250 VAL D 257 -1 N VAL D 257 O VAL D 260 SITE 1 AC1 11 GLN A 77 SER A 79 TYR A 81 TRP A 82 SITE 2 AC1 11 ASN A 159 ARG A 215 SER A 265 THR A 266 SITE 3 AC1 11 TRP A 289 ARG A 310 HOH A 538 SITE 1 AC2 11 GLN B 77 SER B 79 TYR B 81 TRP B 82 SITE 2 AC2 11 ASN B 159 ARG B 215 SER B 265 THR B 266 SITE 3 AC2 11 TRP B 289 ARG B 310 HOH B 510 CRYST1 83.916 83.916 365.328 90.00 90.00 90.00 P 43 21 2 16 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 0.011917 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002737 0.00000