HEADER HYDROLASE, SIGNALING PROTEIN 27-FEB-09 3GFX TITLE KLEBSIELLA PNEUMONIAE BLRP1 PH 4.5 CALCIUM/CY-DIGMP COMPLEX 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 PLASMID KEYWDS TIM-BARREL, BLUF-DOMAIN, EAL-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 3GFX 1 REMARK SEQADV HETSYN LINK REVDAT 4 01-NOV-17 3GFX 1 REMARK REVDAT 3 19-JUN-13 3GFX 1 JRNL VERSN REVDAT 2 06-OCT-09 3GFX 1 HETATM REVDAT 1 23-JUN-09 3GFX 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32027 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1696 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1985 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6163 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 156 REMARK 3 SOLVENT ATOMS : 406 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.46000 REMARK 3 B22 (A**2) : -2.07000 REMARK 3 B33 (A**2) : 2.53000 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): 0.642 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.310 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.973 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6469 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8810 ; 1.323 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 780 ; 5.464 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;34.203 ;22.989 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1063 ;14.981 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;10.467 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 976 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4850 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2980 ; 0.155 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4442 ; 0.301 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 600 ; 0.143 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.142 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 55 ; 0.182 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.134 ; 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): 4032 ; 0.169 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6294 ; 0.297 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2870 ; 0.294 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2514 ; 0.533 ; 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 3GFX 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_1000051809. 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) : NULL 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) : 0.998 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 : 32027 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 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 34.50000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.50000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.45000 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: 8800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 ARG A 400 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 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: 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 GLU A 101 -165.49 -76.25 REMARK 500 PRO A 154 -115.65 -77.04 REMARK 500 LEU A 231 -64.70 59.75 REMARK 500 TYR A 246 77.92 -106.07 REMARK 500 HIS A 247 -54.09 -150.29 REMARK 500 CYS A 281 52.93 -151.47 REMARK 500 ASP B 19 98.31 -65.29 REMARK 500 LEU B 45 -26.83 -140.99 REMARK 500 THR B 90 31.80 -78.79 REMARK 500 THR B 102 -77.23 48.32 REMARK 500 ASP B 103 27.21 -143.86 REMARK 500 ASP B 135 63.33 -159.13 REMARK 500 PRO B 230 42.41 -49.82 REMARK 500 LEU B 231 -78.84 9.82 REMARK 500 HIS B 247 56.08 -113.77 REMARK 500 HIS B 248 136.65 -171.68 REMARK 500 CYS B 281 68.28 -151.37 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 GLN A 228 LEU A 229 140.46 REMARK 500 PRO B 230 LEU B 231 137.83 REMARK 500 LEU B 231 GLY B 232 -120.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 188 OE2 REMARK 620 2 ASN A 239 OD1 83.3 REMARK 620 3 GLU A 272 OE2 81.9 83.5 REMARK 620 4 ASP A 302 OD2 162.1 111.7 90.1 REMARK 620 5 HOH A 423 O 72.7 155.6 88.6 91.2 REMARK 620 6 C2E A 501 O2P 82.7 99.7 163.9 103.2 82.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 188 OE2 REMARK 620 2 ASN B 239 OD1 82.5 REMARK 620 3 GLU B 272 OE2 87.0 81.1 REMARK 620 4 ASP B 302 OD1 168.4 101.1 82.7 REMARK 620 5 HOH B 445 O 78.1 158.4 88.4 96.2 REMARK 620 6 C2E B 501 O2P 88.5 100.2 175.1 101.6 88.8 REMARK 620 N 1 2 3 4 5 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 1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GFY RELATED DB: PDB REMARK 900 KLEBSIELLA PNEUMONIAE BLRP1 WITH FMN AND CYCLIC DIGMP, NO METAL IONS 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 3GFX A 1 405 UNP A6T8V8 A6T8V8_KLEP7 1 405 DBREF 3GFX B 1 405 UNP A6T8V8 A6T8V8_KLEP7 1 405 SEQADV 3GFX ILE A -7 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER A -6 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX GLU A -5 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX PHE A -4 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX GLY A -3 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER A -2 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER A -1 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX ARG A 0 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX ILE B -7 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER B -6 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX GLU B -5 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX PHE B -4 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX GLY B -3 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER B -2 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX SER B -1 UNP A6T8V8 EXPRESSION TAG SEQADV 3GFX 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 FMN A1137 31 HET C2E A 501 46 HET CA A 503 1 HET FMN B1137 31 HET C2E B 501 46 HET CA B 503 1 HETNAM FMN FLAVIN MONONUCLEOTIDE 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 CA CALCIUM ION HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 C2E 2(C20 H24 N10 O14 P2) FORMUL 5 CA 2(CA 2+) FORMUL 9 HOH *406(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 TYR A 139 5 3 HELIX 8 8 PRO A 142 TRP A 150 5 9 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 LEU A 229 1 12 HELIX 13 13 LEU A 241 LEU A 245 5 5 HELIX 14 14 ASP A 250 ALA A 261 1 12 HELIX 15 15 ARG A 265 ASP A 267 5 3 HELIX 16 16 GLU A 275 THR A 280 1 6 HELIX 17 17 CYS A 281 GLY A 296 1 16 HELIX 18 18 SER A 309 PHE A 317 1 9 HELIX 19 19 ASP A 325 ARG A 330 1 6 HELIX 20 20 SER A 335 GLY A 353 1 19 HELIX 21 21 THR A 363 VAL A 373 1 11 HELIX 22 22 ASP B 19 LEU B 32 1 14 HELIX 23 23 GLU B 55 SER B 67 1 13 HELIX 24 24 ARG B 98 PHE B 100 5 3 HELIX 25 25 ASP B 103 SER B 113 1 11 HELIX 26 26 GLU B 119 ASN B 122 5 4 HELIX 27 27 ASP B 123 GLY B 136 1 14 HELIX 28 28 GLY B 137 TYR B 139 5 3 HELIX 29 29 PRO B 142 SER B 148 5 7 HELIX 30 30 SER B 198 ILE B 206 1 9 HELIX 31 31 ALA B 207 GLU B 209 5 3 HELIX 32 32 ASP B 210 SER B 218 1 9 HELIX 33 33 SER B 218 GLN B 228 1 11 HELIX 34 34 LEU B 241 HIS B 247 1 7 HELIX 35 35 ASP B 250 ALA B 262 1 13 HELIX 36 36 ARG B 265 ASP B 267 5 3 HELIX 37 37 GLU B 275 ILE B 279 1 5 HELIX 38 38 CYS B 281 GLY B 296 1 16 HELIX 39 39 GLY B 310 ARG B 316 5 7 HELIX 40 40 ASP B 325 ARG B 330 1 6 HELIX 41 41 SER B 335 GLY B 353 1 19 HELIX 42 42 THR B 363 VAL B 373 1 11 SHEET 1 A 5 HIS A 71 TYR A 81 0 SHEET 2 A 5 LEU A 2 VAL A 11 -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 LEU A 40 SHEET 1 B 2 MET A 151 MET A 152 0 SHEET 2 B 2 PRO A 397 VAL A 398 -1 O VAL A 398 N MET A 151 SHEET 1 C10 CYS A 387 LEU A 388 0 SHEET 2 C10 GLN A 170 GLU A 178 -1 N LEU A 173 O CYS A 387 SHEET 3 C10 LEU A 377 PHE A 378 -1 O PHE A 378 N VAL A 177 SHEET 4 C10 THR A 355 ALA A 358 1 N ALA A 358 O LEU A 377 SHEET 5 C10 LYS A 321 VAL A 324 1 N ILE A 322 O THR A 355 SHEET 6 C10 LYS A 298 PHE A 304 1 N ILE A 301 O LYS A 323 SHEET 7 C10 VAL A 269 THR A 274 1 N ILE A 271 O ALA A 300 SHEET 8 C10 GLN A 235 ASN A 239 1 N ILE A 238 O GLU A 272 SHEET 9 C10 ARG A 183 ARG A 192 1 N ALA A 189 O ALA A 237 SHEET 10 C10 GLN A 170 GLU A 178 -1 N ALA A 172 O LEU A 190 SHEET 1 D 5 HIS B 71 TYR B 81 0 SHEET 2 D 5 LEU B 2 VAL B 11 -1 N ARG B 8 O VAL B 75 SHEET 3 D 5 GLN B 46 THR B 54 -1 O LEU B 51 N LEU B 5 SHEET 4 D 5 THR B 37 PHE B 42 -1 N LEU B 41 O PHE B 48 SHEET 5 D 5 ARG B 93 ASP B 96 1 O LEU B 95 N LEU B 40 SHEET 1 E 2 TRP B 150 MET B 152 0 SHEET 2 E 2 PRO B 397 ALA B 399 -1 O VAL B 398 N MET B 151 SHEET 1 F10 CYS B 387 LEU B 388 0 SHEET 2 F10 GLN B 170 GLU B 178 -1 N LEU B 173 O CYS B 387 SHEET 3 F10 LEU B 377 PHE B 378 -1 O PHE B 378 N VAL B 177 SHEET 4 F10 THR B 355 ALA B 358 1 N ALA B 358 O LEU B 377 SHEET 5 F10 LYS B 321 VAL B 324 1 N ILE B 322 O THR B 355 SHEET 6 F10 LYS B 298 PHE B 304 1 N PHE B 304 O LYS B 323 SHEET 7 F10 VAL B 269 THR B 274 1 N VAL B 273 O ASP B 302 SHEET 8 F10 GLN B 235 ASN B 239 1 N ILE B 238 O GLU B 272 SHEET 9 F10 ARG B 183 ARG B 192 1 N PHE B 187 O ALA B 237 SHEET 10 F10 GLN B 170 GLU B 178 -1 N ILE B 176 O SER B 186 LINK OE2 GLU A 188 CA CA A 503 1555 1555 2.41 LINK OD1 ASN A 239 CA CA A 503 1555 1555 2.45 LINK OE2 GLU A 272 CA CA A 503 1555 1555 2.36 LINK OD2 ASP A 302 CA CA A 503 1555 1555 2.34 LINK O HOH A 423 CA CA A 503 1555 1555 2.64 LINK O2P C2E A 501 CA CA A 503 1555 1555 2.16 LINK OE2 GLU B 188 CA CA B 503 1555 1555 2.32 LINK OD1 ASN B 239 CA CA B 503 1555 1555 2.46 LINK OE2 GLU B 272 CA CA B 503 1555 1555 2.24 LINK OD1 ASP B 302 CA CA B 503 1555 1555 2.29 LINK O HOH B 445 CA CA B 503 1555 1555 2.43 LINK O2P C2E B 501 CA CA B 503 1555 1555 2.26 SITE 1 AC1 17 TYR A 7 ARG A 26 ALA A 27 LYS A 30 SITE 2 AC1 17 ASN A 31 GLN A 49 LEU A 61 GLU A 64 SITE 3 AC1 17 ILE A 65 ASP A 68 ARG A 70 HIS A 71 SITE 4 AC1 17 MET A 92 HOH A 524 HOH A 535 HOH A 546 SITE 5 AC1 17 HOH A 547 SITE 1 AC2 26 GLN A 174 GLU A 188 LEU A 190 ILE A 191 SITE 2 AC2 26 ARG A 192 PRO A 199 ASP A 215 LYS A 219 SITE 3 AC2 26 ASN A 239 ASP A 302 ASP A 303 GLY A 360 SITE 4 AC2 26 GLU A 362 GLY A 380 PHE A 381 PRO A 386 SITE 5 AC2 26 HOH A 406 HOH A 424 HOH A 437 HOH A 442 SITE 6 AC2 26 HOH A 462 CA A 503 GLN B 162 HIS B 163 SITE 7 AC2 26 PRO B 165 HOH B 446 SITE 1 AC3 6 GLU A 188 ASN A 239 GLU A 272 ASP A 302 SITE 2 AC3 6 HOH A 423 C2E A 501 SITE 1 AC4 15 TYR B 7 LEU B 23 ARG B 26 ALA B 27 SITE 2 AC4 15 LYS B 30 ASN B 31 PHE B 47 GLN B 49 SITE 3 AC4 15 LEU B 61 GLU B 64 ILE B 65 ASP B 68 SITE 4 AC4 15 ARG B 70 HIS B 71 MET B 92 SITE 1 AC5 21 GLN B 174 GLU B 188 LEU B 190 ILE B 191 SITE 2 AC5 21 ARG B 192 PRO B 199 ASP B 215 LYS B 219 SITE 3 AC5 21 ASN B 239 ASP B 302 ASP B 303 GLY B 360 SITE 4 AC5 21 VAL B 361 GLU B 362 GLY B 380 PHE B 381 SITE 5 AC5 21 PRO B 386 HOH B 414 HOH B 465 CA B 503 SITE 6 AC5 21 HOH B 582 SITE 1 AC6 6 GLU B 188 ASN B 239 GLU B 272 ASP B 302 SITE 2 AC6 6 HOH B 445 C2E B 501 CRYST1 69.000 96.900 128.500 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 0.014493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007782 0.00000