HEADER HYDROLASE, SIGNALING PROTEIN 27-FEB-09 3GFY TITLE KLEBSIELLA PNEUMONIAE BLRP1 WITH FMN AND CYCLIC DIGMP, NO METAL IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: KLEBSIELLA PNEUMONIAE BLRP1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH SOURCE 3 78578; SOURCE 4 ORGANISM_TAXID: 272620; SOURCE 5 GENE: BLRP1, KPN78578_15680, KPN_01598; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE-3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28-DERIVED KEYWDS TIM-BARREL, EAL DOMAIN, BLUF DOMAIN, HYDROLASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.BARENDS,E.HARTMANN,J.GRIESE,T.BEITLICH,N.KIRIENKO,D.RYJENKOV, AUTHOR 2 J.REINSTEIN,R.SHOEMAN,M.GOMELSKY,I.SCHLICHTING REVDAT 5 21-FEB-24 3GFY 1 REMARK SEQADV HETSYN REVDAT 4 01-NOV-17 3GFY 1 REMARK REVDAT 3 19-JUN-13 3GFY 1 JRNL VERSN REVDAT 2 06-OCT-09 3GFY 1 HETATM REVDAT 1 23-JUN-09 3GFY 0 JRNL AUTH T.R.BARENDS,E.HARTMANN,J.J.GRIESE,T.BEITLICH,N.V.KIRIENKO, JRNL AUTH 2 D.A.RYJENKOV,J.REINSTEIN,R.L.SHOEMAN,M.GOMELSKY, JRNL AUTH 3 I.SCHLICHTING JRNL TITL STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULATED JRNL TITL 2 CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. JRNL REF NATURE V. 459 1015 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19536266 JRNL DOI 10.1038/NATURE07966 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25028 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) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1800 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5874 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 154 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -1.73000 REMARK 3 B33 (A**2) : 1.06000 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): 1.979 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.373 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.281 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.779 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.872 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.846 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6170 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8396 ; 1.368 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 737 ; 5.691 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 270 ;32.988 ;22.815 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1021 ;14.245 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;12.604 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 925 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4618 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2685 ; 0.157 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4214 ; 0.302 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 340 ; 0.160 ; 0.500 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): 69 ; 0.134 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.198 ; 0.500 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): 3838 ; 0.318 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5972 ; 0.554 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2760 ; 0.521 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2422 ; 0.913 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3GFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98407 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25028 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 46.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2.0005 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN IN 5 MM CY-DIGMP, 5 MM CACL2, REMARK 280 25 MM TRIS-HCL PH 8.0, 40 MM NACL, 5 MM MGCL2, 2 MM EDTA, 2 MM REMARK 280 DTE, 5% GLYCEROL, RESERVOIR 0.1 M NA-AC BUFFER PH 4.5, 0.2 M CA- REMARK 280 ACETATE, 17-20%PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 34.21500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.53500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.53500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.21500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.26500 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: 6330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL 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 ILE A -7 REMARK 465 SER A -6 REMARK 465 GLU A -5 REMARK 465 PHE A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 ARG A 0 REMARK 465 PHE A 115 REMARK 465 GLY A 116 REMARK 465 VAL A 117 REMARK 465 THR A 118 REMARK 465 GLU A 119 REMARK 465 SER A 156 REMARK 465 GLY A 157 REMARK 465 VAL A 273 REMARK 465 THR A 274 REMARK 465 GLU A 275 REMARK 465 THR A 276 REMARK 465 GLU A 277 REMARK 465 VAL A 278 REMARK 465 ILE A 279 REMARK 465 THR A 280 REMARK 465 CYS A 281 REMARK 465 PHE A 282 REMARK 465 ASP A 303 REMARK 465 PHE A 304 REMARK 465 GLY A 305 REMARK 465 ALA A 306 REMARK 465 GLY A 307 REMARK 465 TYR A 308 REMARK 465 SER A 309 REMARK 465 GLY A 310 REMARK 465 LEU A 311 REMARK 465 SER A 312 REMARK 465 LEU A 313 REMARK 465 GLN A 401 REMARK 465 ALA A 402 REMARK 465 MET A 403 REMARK 465 ASP A 404 REMARK 465 LEU A 405 REMARK 465 ILE B -7 REMARK 465 SER B -6 REMARK 465 GLU B -5 REMARK 465 PHE B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 SER B -1 REMARK 465 ARG B 0 REMARK 465 PRO B 154 REMARK 465 ALA B 155 REMARK 465 SER B 156 REMARK 465 GLY B 157 REMARK 465 THR B 158 REMARK 465 ALA B 159 REMARK 465 THR B 274 REMARK 465 GLU B 275 REMARK 465 THR B 276 REMARK 465 GLU B 277 REMARK 465 VAL B 278 REMARK 465 ILE B 279 REMARK 465 THR B 280 REMARK 465 ILE B 301 REMARK 465 ASP B 302 REMARK 465 ASP B 303 REMARK 465 PHE B 304 REMARK 465 GLY B 305 REMARK 465 ALA B 306 REMARK 465 GLY B 307 REMARK 465 TYR B 308 REMARK 465 SER B 309 REMARK 465 GLY B 310 REMARK 465 LEU B 311 REMARK 465 SER B 312 REMARK 465 LEU B 313 REMARK 465 GLN B 401 REMARK 465 ALA B 402 REMARK 465 MET B 403 REMARK 465 ASP B 404 REMARK 465 LEU B 405 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ILE A 238 N - CA - C ANGL. DEV. = 20.6 DEGREES 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 PHE A 87 53.08 -114.54 REMARK 500 ASP A 103 -24.35 76.14 REMARK 500 ASP A 135 68.05 -153.47 REMARK 500 ILE A 238 126.23 -5.50 REMARK 500 GLN A 284 -43.25 70.94 REMARK 500 ARG A 316 55.25 -149.97 REMARK 500 THR B 90 91.31 171.98 REMARK 500 THR B 102 -85.19 61.33 REMARK 500 ASP B 135 64.83 -150.34 REMARK 500 PRO B 230 80.54 -66.23 REMARK 500 ASP B 250 81.18 -153.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 237 ILE A 238 57.67 REMARK 500 ARG A 316 PHE A 317 46.82 REMARK 500 THR B 90 GLY B 91 135.77 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 C2E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GFX RELATED DB: PDB REMARK 900 KLEBSIELLA PNEUMONIAE BLRP1 PH 4.5 CALCIUM/CY-DIGMP COMPLEX REMARK 900 RELATED ID: 3GFZ RELATED DB: PDB REMARK 900 KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX REMARK 900 RELATED ID: 3GG0 RELATED DB: PDB REMARK 900 KLEBSIELLA PNEUMONIAE BLRP1 PH 9.0 MANGANESE/CY-DIGMP COMPLEX REMARK 900 RELATED ID: 3GG1 RELATED DB: PDB REMARK 900 KLEBSIELLA PNEUMONIAE BLRP1 PH 8.0 CALCIUM/CY-DIGMP COMPLEX DBREF 3GFY A 1 405 UNP A6T8V8 A6T8V8_KLEP7 1 405 DBREF 3GFY B 1 405 UNP A6T8V8 A6T8V8_KLEP7 1 405 SEQADV 3GFY ILE A -7 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER A -6 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY GLU A -5 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY PHE A -4 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY GLY A -3 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER A -2 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER A -1 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY ARG A 0 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY ILE B -7 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER B -6 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY GLU B -5 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY PHE B -4 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY GLY B -3 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER B -2 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY SER B -1 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFY ARG B 0 UNP A6T8V8 EXPRESSION TAG SEQRES 1 A 413 ILE SER GLU PHE GLY SER SER ARG MET LEU THR THR LEU SEQRES 2 A 413 ILE TYR ARG SER GLN VAL HIS PRO ASP ARG PRO PRO VAL SEQRES 3 A 413 ASP LEU ASP ALA LEU VAL HIS ARG ALA SER SER LYS ASN SEQRES 4 A 413 LEU PRO LEU GLY ILE THR GLY ILE LEU LEU PHE ASN GLY SEQRES 5 A 413 LEU GLN PHE PHE GLN VAL LEU GLU GLY THR GLU GLU ALA SEQRES 6 A 413 LEU GLU SER LEU PHE SER GLU ILE GLN SER ASP PRO ARG SEQRES 7 A 413 HIS ARG ASP VAL VAL GLU LEU MET ARG ASP TYR SER ALA SEQRES 8 A 413 TYR ARG ARG PHE HIS GLY THR GLY MET ARG ILE LEU ASP SEQRES 9 A 413 LEU ARG LEU PHE GLU THR ASP GLY ALA LEU GLU GLU ILE SEQRES 10 A 413 LEU ARG PHE SER THR PHE GLY VAL THR GLU PRO VAL ASN SEQRES 11 A 413 ASP ARG MET PHE ARG LEU LEU SER ALA PHE ILE ALA ASP SEQRES 12 A 413 GLY GLY ARG TYR CYS LEU PRO GLU PRO LEU GLN PRO SER SEQRES 13 A 413 ARG TRP MET MET MET PRO ALA SER GLY THR ALA ALA PRO SEQRES 14 A 413 GLN HIS LEU PRO GLY GLN PRO CYS GLN PHE ALA LEU GLN SEQRES 15 A 413 ALA ILE VAL GLU PRO ALA LYS LYS ARG VAL SER SER PHE SEQRES 16 A 413 GLU ALA LEU ILE ARG SER PRO THR GLY GLY SER PRO VAL SEQRES 17 A 413 GLU MET PHE ALA ALA ILE ALA ALA GLU ASP ARG TYR ARG SEQRES 18 A 413 PHE ASP LEU GLU SER LYS ALA TYR ALA PHE ALA LEU ALA SEQRES 19 A 413 GLY GLN LEU PRO LEU GLY LYS HIS GLN LEU ALA ILE ASN SEQRES 20 A 413 LEU LEU PRO GLY SER LEU TYR HIS HIS PRO ASP ALA VAL SEQRES 21 A 413 GLY TRP LEU MET ASP SER LEU LEU ALA ALA GLY LEU ARG SEQRES 22 A 413 PRO ASP GLN VAL LEU ILE GLU VAL THR GLU THR GLU VAL SEQRES 23 A 413 ILE THR CYS PHE ASP GLN PHE ARG LYS VAL LEU LYS ALA SEQRES 24 A 413 LEU ARG VAL ALA GLY MET LYS LEU ALA ILE ASP ASP PHE SEQRES 25 A 413 GLY ALA GLY TYR SER GLY LEU SER LEU LEU THR ARG PHE SEQRES 26 A 413 GLN PRO ASP LYS ILE LYS VAL ASP ALA GLU LEU VAL ARG SEQRES 27 A 413 ASP ILE HIS ILE SER GLY THR LYS GLN ALA ILE VAL ALA SEQRES 28 A 413 SER VAL VAL ARG CYS CYS GLU ASP LEU GLY ILE THR VAL SEQRES 29 A 413 VAL ALA GLU GLY VAL GLU THR LEU GLU GLU TRP CYS TRP SEQRES 30 A 413 LEU GLN SER VAL GLY ILE ARG LEU PHE GLN GLY PHE LEU SEQRES 31 A 413 PHE SER ARG PRO CYS LEU ASN GLY ILE GLY GLU ILE CYS SEQRES 32 A 413 TRP PRO VAL ALA ARG GLN ALA MET ASP LEU SEQRES 1 B 413 ILE SER GLU PHE GLY SER SER ARG MET LEU THR THR LEU SEQRES 2 B 413 ILE TYR ARG SER GLN VAL HIS PRO ASP ARG PRO PRO VAL SEQRES 3 B 413 ASP LEU ASP ALA LEU VAL HIS ARG ALA SER SER LYS ASN SEQRES 4 B 413 LEU PRO LEU GLY ILE THR GLY ILE LEU LEU PHE ASN GLY SEQRES 5 B 413 LEU GLN PHE PHE GLN VAL LEU GLU GLY THR GLU GLU ALA SEQRES 6 B 413 LEU GLU SER LEU PHE SER GLU ILE GLN SER ASP PRO ARG SEQRES 7 B 413 HIS ARG ASP VAL VAL GLU LEU MET ARG ASP TYR SER ALA SEQRES 8 B 413 TYR ARG ARG PHE HIS GLY THR GLY MET ARG ILE LEU ASP SEQRES 9 B 413 LEU ARG LEU PHE GLU THR ASP GLY ALA LEU GLU GLU ILE SEQRES 10 B 413 LEU ARG PHE SER THR PHE GLY VAL THR GLU PRO VAL ASN SEQRES 11 B 413 ASP ARG MET PHE ARG LEU LEU SER ALA PHE ILE ALA ASP SEQRES 12 B 413 GLY GLY ARG TYR CYS LEU PRO GLU PRO LEU GLN PRO SER SEQRES 13 B 413 ARG TRP MET MET MET PRO ALA SER GLY THR ALA ALA PRO SEQRES 14 B 413 GLN HIS LEU PRO GLY GLN PRO CYS GLN PHE ALA LEU GLN SEQRES 15 B 413 ALA ILE VAL GLU PRO ALA LYS LYS ARG VAL SER SER PHE SEQRES 16 B 413 GLU ALA LEU ILE ARG SER PRO THR GLY GLY SER PRO VAL SEQRES 17 B 413 GLU MET PHE ALA ALA ILE ALA ALA GLU ASP ARG TYR ARG SEQRES 18 B 413 PHE ASP LEU GLU SER LYS ALA TYR ALA PHE ALA LEU ALA SEQRES 19 B 413 GLY GLN LEU PRO LEU GLY LYS HIS GLN LEU ALA ILE ASN SEQRES 20 B 413 LEU LEU PRO GLY SER LEU TYR HIS HIS PRO ASP ALA VAL SEQRES 21 B 413 GLY TRP LEU MET ASP SER LEU LEU ALA ALA GLY LEU ARG SEQRES 22 B 413 PRO ASP GLN VAL LEU ILE GLU VAL THR GLU THR GLU VAL SEQRES 23 B 413 ILE THR CYS PHE ASP GLN PHE ARG LYS VAL LEU LYS ALA SEQRES 24 B 413 LEU ARG VAL ALA GLY MET LYS LEU ALA ILE ASP ASP PHE SEQRES 25 B 413 GLY ALA GLY TYR SER GLY LEU SER LEU LEU THR ARG PHE SEQRES 26 B 413 GLN PRO ASP LYS ILE LYS VAL ASP ALA GLU LEU VAL ARG SEQRES 27 B 413 ASP ILE HIS ILE SER GLY THR LYS GLN ALA ILE VAL ALA SEQRES 28 B 413 SER VAL VAL ARG CYS CYS GLU ASP LEU GLY ILE THR VAL SEQRES 29 B 413 VAL ALA GLU GLY VAL GLU THR LEU GLU GLU TRP CYS TRP SEQRES 30 B 413 LEU GLN SER VAL GLY ILE ARG LEU PHE GLN GLY PHE LEU SEQRES 31 B 413 PHE SER ARG PRO CYS LEU ASN GLY ILE GLY GLU ILE CYS SEQRES 32 B 413 TRP PRO VAL ALA ARG GLN ALA MET ASP LEU HET C2E A 501 46 HET FMN A 504 31 HET C2E B 501 46 HET FMN B 504 31 HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 C2E 2(C20 H24 N10 O14 P2) FORMUL 4 FMN 2(C17 H21 N4 O9 P) FORMUL 7 HOH *50(H2 O) HELIX 1 1 ASP A 19 LEU A 32 1 14 HELIX 2 2 PRO A 33 GLY A 35 5 3 HELIX 3 3 GLU A 55 SER A 67 1 13 HELIX 4 4 ARG A 98 PHE A 100 5 3 HELIX 5 5 ASP A 103 SER A 113 1 11 HELIX 6 6 ASP A 123 GLY A 136 1 14 HELIX 7 7 GLY A 137 CYS A 140 5 4 HELIX 8 8 PRO A 142 SER A 148 5 7 HELIX 9 9 SER A 198 ILE A 206 1 9 HELIX 10 10 ALA A 207 GLU A 209 5 3 HELIX 11 11 ASP A 210 SER A 218 1 9 HELIX 12 12 SER A 218 GLN A 228 1 11 HELIX 13 13 LEU A 241 HIS A 247 1 7 HELIX 14 14 ASP A 250 ALA A 261 1 12 HELIX 15 15 ARG A 265 GLN A 268 5 4 HELIX 16 16 GLN A 284 GLY A 296 1 13 HELIX 17 17 ASP A 325 ARG A 330 1 6 HELIX 18 18 SER A 335 GLY A 353 1 19 HELIX 19 19 THR A 363 VAL A 373 1 11 HELIX 20 20 ASP B 19 LEU B 32 1 14 HELIX 21 21 GLU B 55 SER B 67 1 13 HELIX 22 22 ARG B 98 PHE B 100 5 3 HELIX 23 23 ASP B 103 SER B 113 1 11 HELIX 24 24 GLU B 119 ASN B 122 5 4 HELIX 25 25 ASP B 123 GLY B 136 1 14 HELIX 26 26 GLY B 137 TYR B 139 5 3 HELIX 27 27 PRO B 142 SER B 148 5 7 HELIX 28 28 PRO B 179 LYS B 182 5 4 HELIX 29 29 SER B 198 ALA B 205 1 8 HELIX 30 30 ALA B 207 GLU B 209 5 3 HELIX 31 31 ASP B 210 LEU B 229 1 20 HELIX 32 32 LEU B 241 HIS B 247 1 7 HELIX 33 33 ASP B 250 ALA B 262 1 13 HELIX 34 34 ARG B 265 ASP B 267 5 3 HELIX 35 35 CYS B 281 GLY B 296 1 16 HELIX 36 36 ASP B 325 ARG B 330 1 6 HELIX 37 37 SER B 335 GLY B 353 1 19 HELIX 38 38 THR B 363 VAL B 373 1 11 SHEET 1 A 5 ARG A 72 TYR A 81 0 SHEET 2 A 5 LEU A 2 GLN A 10 -1 N ARG A 8 O VAL A 75 SHEET 3 A 5 GLN A 46 THR A 54 -1 O LEU A 51 N LEU A 5 SHEET 4 A 5 THR A 37 PHE A 42 -1 N LEU A 41 O PHE A 48 SHEET 5 A 5 ILE A 94 ASP A 96 1 O LEU A 95 N PHE A 42 SHEET 1 B 2 TRP A 150 PRO A 154 0 SHEET 2 B 2 CYS A 395 ALA A 399 -1 O VAL A 398 N MET A 151 SHEET 1 C 4 GLN A 235 ALA A 237 0 SHEET 2 C 4 ARG A 183 ARG A 192 1 N ALA A 189 O ALA A 237 SHEET 3 C 4 GLN A 170 GLU A 178 -1 N GLU A 178 O ARG A 183 SHEET 4 C 4 CYS A 387 LEU A 388 -1 O CYS A 387 N LEU A 173 SHEET 1 D 5 LEU A 270 ILE A 271 0 SHEET 2 D 5 LYS A 298 ILE A 301 1 O ALA A 300 N ILE A 271 SHEET 3 D 5 LYS A 321 VAL A 324 1 O LYS A 323 N ILE A 301 SHEET 4 D 5 THR A 355 ALA A 358 1 O VAL A 357 N VAL A 324 SHEET 5 D 5 LEU A 377 PHE A 378 1 O LEU A 377 N ALA A 358 SHEET 1 E 5 HIS B 71 TYR B 81 0 SHEET 2 E 5 LEU B 2 VAL B 11 -1 N ARG B 8 O VAL B 75 SHEET 3 E 5 GLN B 46 THR B 54 -1 O GLY B 53 N THR B 3 SHEET 4 E 5 THR B 37 PHE B 42 -1 N THR B 37 O GLU B 52 SHEET 5 E 5 ARG B 93 ASP B 96 1 O LEU B 95 N LEU B 40 SHEET 1 F 2 TRP B 150 MET B 152 0 SHEET 2 F 2 PRO B 397 ALA B 399 -1 O VAL B 398 N MET B 151 SHEET 1 G 6 LYS B 298 ALA B 300 0 SHEET 2 G 6 VAL B 269 GLU B 272 1 N ILE B 271 O LYS B 298 SHEET 3 G 6 GLN B 235 ASN B 239 1 N ILE B 238 O GLU B 272 SHEET 4 G 6 ARG B 183 ARG B 192 1 N PHE B 187 O ALA B 237 SHEET 5 G 6 GLN B 170 GLU B 178 -1 N ILE B 176 O SER B 185 SHEET 6 G 6 CYS B 387 LEU B 388 -1 O CYS B 387 N LEU B 173 SHEET 1 H 3 LYS B 321 VAL B 324 0 SHEET 2 H 3 THR B 355 GLU B 359 1 O THR B 355 N ILE B 322 SHEET 3 H 3 PHE B 378 GLN B 379 1 O GLN B 379 N ALA B 358 CISPEP 1 LEU A 229 PRO A 230 0 -10.18 SITE 1 AC1 23 GLN A 174 GLU A 188 LEU A 190 ILE A 191 SITE 2 AC1 23 ARG A 192 PRO A 199 ASP A 215 LYS A 219 SITE 3 AC1 23 ASN A 239 LEU A 241 ASP A 302 GLU A 359 SITE 4 AC1 23 GLY A 360 VAL A 361 GLU A 362 GLY A 380 SITE 5 AC1 23 PHE A 381 PRO A 386 HOH A 408 GLN B 162 SITE 6 AC1 23 HIS B 163 PRO B 165 HOH B 415 SITE 1 AC2 13 TYR A 7 ARG A 26 ALA A 27 LYS A 30 SITE 2 AC2 13 ASN A 31 GLN A 49 LEU A 61 GLU A 64 SITE 3 AC2 13 ILE A 65 ASP A 68 ARG A 70 HIS A 71 SITE 4 AC2 13 MET A 92 SITE 1 AC3 19 GLN B 174 GLU B 188 LEU B 190 ILE B 191 SITE 2 AC3 19 ARG B 192 PRO B 199 ASP B 215 LYS B 219 SITE 3 AC3 19 ASN B 239 ASP B 283 GLU B 359 GLY B 360 SITE 4 AC3 19 VAL B 361 GLU B 362 GLY B 380 PHE B 381 SITE 5 AC3 19 PRO B 386 HOH B 411 HOH B 435 SITE 1 AC4 14 TYR B 7 LEU B 23 ARG B 26 ALA B 27 SITE 2 AC4 14 LYS B 30 ASN B 31 PHE B 47 GLN B 49 SITE 3 AC4 14 LEU B 61 GLU B 64 ILE B 65 ASP B 68 SITE 4 AC4 14 ARG B 70 HIS B 71 CRYST1 68.430 96.530 127.070 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 0.014613 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007870 0.00000