HEADER HYDROLASE 17-NOV-16 5MF5 TITLE PA3825-EAL MG-CDG STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIGUANYLATE PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: AO964_02925; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: LEMO21 KEYWDS EAL, PHOSPHODIESTERASE, BIOFILM FORMATION, P AERUGINOSA, PA3825, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.HORRELL,D.BELLINI,R.STRANGE,A.WAGNER,M.WALSH REVDAT 4 17-JAN-24 5MF5 1 REMARK HETSYN REVDAT 3 03-JUL-19 5MF5 1 SOURCE REMARK REVDAT 2 01-MAR-17 5MF5 1 JRNL REVDAT 1 21-DEC-16 5MF5 0 SPRSDE 21-DEC-16 5MF5 4Y9Q JRNL AUTH D.BELLINI,S.HORRELL,A.HUTCHIN,C.W.PHIPPEN,R.W.STRANGE,Y.CAI, JRNL AUTH 2 A.WAGNER,J.S.WEBB,I.TEWS,M.A.WALSH JRNL TITL DIMERISATION INDUCED FORMATION OF THE ACTIVE SITE AND THE JRNL TITL 2 IDENTIFICATION OF THREE METAL SITES IN JRNL TITL 3 EAL-PHOSPHODIESTERASES. JRNL REF SCI REP V. 7 42166 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28186120 JRNL DOI 10.1038/SREP42166 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27262 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1427 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1940 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 1.08000 REMARK 3 B33 (A**2) : -2.16000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.020 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2182 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2069 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2964 ; 1.637 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4753 ; 1.001 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 270 ; 5.822 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;35.718 ;22.959 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;12.807 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.659 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 330 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2452 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 495 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1062 ; 2.372 ; 3.093 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1061 ; 2.372 ; 3.090 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1338 ; 3.511 ; 4.614 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5MF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.6 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 29.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 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: MOLREP REMARK 200 STARTING MODEL: 4Y9O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SODIUM PHOSPHATE MONOBASIC, 1.2 REMARK 280 M POTASSIUM PHOSPHATE DIBASIC AND 0.1 M SODIUM ACETATE PH 4.5, REMARK 280 0.2 M MAGNESIUM CHLORIDE, PH 7.1, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 67.86500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.29500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 101.79750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.29500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.93250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.29500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.79750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.29500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.29500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.93250 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 67.86500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 451 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 259 CB CG CD OE1 NE2 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 HOH A 441 O HOH A 510 1.80 REMARK 500 O HOH A 441 O HOH A 519 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 243 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = -3.6 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 57 -20.90 -140.07 REMARK 500 CYS A 104 32.33 -94.69 REMARK 500 ILE A 192 -46.45 -141.44 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 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 39 OE2 REMARK 620 2 ASN A 98 OD1 87.9 REMARK 620 3 GLU A 130 OE1 84.7 94.4 REMARK 620 4 ASP A 160 OD2 167.6 85.8 85.1 REMARK 620 5 C2E A 301 O21 98.6 88.3 175.9 91.9 REMARK 620 6 HOH A 459 O 84.6 169.3 92.5 103.0 85.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 40 O REMARK 620 2 C2E A 301 O6 133.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD1 REMARK 620 2 ASP A 183 OD1 90.0 REMARK 620 3 C2E A 301 O11 85.8 175.7 REMARK 620 4 HOH A 401 O 67.6 116.0 61.7 REMARK 620 5 HOH A 468 O 157.9 80.8 102.9 98.4 REMARK 620 N 1 2 3 4 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y9O RELATED DB: PDB REMARK 900 RELATED ID: 4Y9M RELATED DB: PDB REMARK 900 RELATED ID: 4Y9N RELATED DB: PDB REMARK 900 RELATED ID: 4Y9P RELATED DB: PDB REMARK 900 RELATED ID: 4Y8E RELATED DB: PDB DBREF1 5MF5 A 5 261 UNP A0A140SMD7_PSEAI DBREF2 5MF5 A A0A140SMD7 259 514 SEQADV 5MF5 GLN A 259 UNP A0A140SMD GLY 513 CONFLICT SEQRES 1 A 256 ALA SER PRO SER SER GLU LEU ARG ARG ALA LEU GLU ALA SEQRES 2 A 256 ASN GLU PHE ILE PRO TYR TYR GLN PRO LEU SER PRO GLY SEQRES 3 A 256 GLN GLY GLY ARG TRP ILE GLY VAL GLU VAL LEU MET ARG SEQRES 4 A 256 TRP ARG HIS PRO ARG GLU GLY LEU ILE ARG PRO ASP LEU SEQRES 5 A 256 PHE ILE PRO PHE ALA GLU ARG SER GLY LEU ILE VAL PRO SEQRES 6 A 256 MET THR ARG ALA LEU MET ARG GLN VAL ALA GLU ASP LEU SEQRES 7 A 256 GLY GLY HIS ALA GLY LYS LEU GLU PRO GLY PHE HIS ILE SEQRES 8 A 256 GLY PHE ASN ILE SER ALA THR HIS CYS HIS GLU LEU ALA SEQRES 9 A 256 LEU VAL ASP ASP CYS ARG GLU LEU LEU ALA ALA PHE PRO SEQRES 10 A 256 PRO GLY HIS ILE THR LEU VAL LEU GLU LEU THR GLU ARG SEQRES 11 A 256 GLU LEU ILE GLU SER SER GLU VAL THR ASP ARG LEU PHE SEQRES 12 A 256 ASP GLU LEU HIS ALA LEU GLY VAL LYS ILE ALA ILE ASP SEQRES 13 A 256 ASP PHE GLY THR GLY HIS SER SER LEU ALA TYR LEU ARG SEQRES 14 A 256 LYS PHE GLN VAL ASP CYS LEU LYS ILE ASP GLN SER PHE SEQRES 15 A 256 VAL ALA ARG ILE GLY ILE ASP THR LEU SER GLY HIS ILE SEQRES 16 A 256 LEU ASP SER ILE VAL GLU LEU SER ALA LYS LEU ASP LEU SEQRES 17 A 256 ASP ILE VAL ALA GLU GLY VAL GLU THR PRO GLU GLN ARG SEQRES 18 A 256 ASP TYR LEU ALA ALA ARG GLY VAL ASP TYR LEU GLN GLY SEQRES 19 A 256 TYR LEU ILE GLY ARG PRO MET PRO LEU GLU SER LEU LEU SEQRES 20 A 256 SER SER LEU THR VAL GLN GLU GLN GLN HET C2E A 301 46 HET MG A 302 1 HET MG A 303 1 HET MG A 304 1 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 MG MAGNESIUM ION HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 C2E C20 H24 N10 O14 P2 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *168(H2 O) HELIX 1 AA1 SER A 6 ALA A 17 1 12 HELIX 2 AA2 ARG A 53 LEU A 56 5 4 HELIX 3 AA3 PHE A 57 SER A 64 1 8 HELIX 4 AA4 LEU A 66 GLY A 83 1 18 HELIX 5 AA5 GLY A 84 LEU A 89 5 6 HELIX 6 AA6 SER A 100 GLU A 106 5 7 HELIX 7 AA7 LEU A 107 ALA A 119 1 13 HELIX 8 AA8 SER A 140 GLY A 154 1 15 HELIX 9 AA9 SER A 168 PHE A 175 1 8 HELIX 10 AB1 ASP A 183 ALA A 188 1 6 HELIX 11 AB2 ASP A 193 ASP A 211 1 19 HELIX 12 AB3 THR A 221 ARG A 231 1 11 HELIX 13 AB4 PRO A 246 GLN A 261 1 15 SHEET 1 AA110 GLY A 50 ILE A 52 0 SHEET 2 AA110 GLY A 37 HIS A 46 -1 N TRP A 44 O ILE A 52 SHEET 3 AA110 PHE A 93 ASN A 98 1 O GLY A 96 N VAL A 40 SHEET 4 AA110 ILE A 125 THR A 132 1 O GLU A 130 N PHE A 97 SHEET 5 AA110 LYS A 156 PHE A 162 1 O ALA A 158 N LEU A 129 SHEET 6 AA110 CYS A 179 ILE A 182 1 O LYS A 181 N ILE A 159 SHEET 7 AA110 ASP A 213 ALA A 216 1 O VAL A 215 N ILE A 182 SHEET 8 AA110 TYR A 235 LEU A 236 1 O TYR A 235 N ALA A 216 SHEET 9 AA110 PHE A 20 PRO A 29 -1 N SER A 28 O LEU A 236 SHEET 10 AA110 GLY A 37 HIS A 46 -1 O GLU A 39 N GLN A 25 LINK OE2 GLU A 39 MG MG A 303 1555 1555 2.21 LINK O VAL A 40 MG MG A 302 1555 1555 2.34 LINK OD1 ASN A 98 MG MG A 303 1555 1555 2.31 LINK OE1 GLU A 130 MG MG A 303 1555 1555 2.17 LINK OD2 ASP A 160 MG MG A 303 1555 1555 2.18 LINK OD1 ASP A 161 MG MG A 304 1555 1555 2.23 LINK OD1 ASP A 183 MG MG A 304 1555 1555 2.27 LINK O6 C2E A 301 MG MG A 302 1555 1555 2.38 LINK O21 C2E A 301 MG MG A 303 1555 1555 2.17 LINK O11 C2E A 301 MG MG A 304 1555 1555 2.31 LINK MG MG A 303 O HOH A 459 1555 1555 2.17 LINK MG MG A 304 O HOH A 401 1555 1555 2.16 LINK MG MG A 304 O HOH A 468 1555 1555 2.20 SITE 1 AC1 32 GLN A 25 GLU A 39 LEU A 41 MET A 42 SITE 2 AC1 32 ARG A 43 ARG A 53 PRO A 54 ASP A 55 SITE 3 AC1 32 LEU A 74 ASN A 98 ASP A 160 ASP A 161 SITE 4 AC1 32 GLN A 184 GLU A 217 GLY A 218 GLU A 220 SITE 5 AC1 32 GLY A 238 TYR A 239 PRO A 244 MG A 302 SITE 6 AC1 32 MG A 303 MG A 304 HOH A 401 HOH A 403 SITE 7 AC1 32 HOH A 412 HOH A 418 HOH A 459 HOH A 461 SITE 8 AC1 32 HOH A 501 HOH A 509 HOH A 511 HOH A 523 SITE 1 AC2 3 VAL A 40 ASN A 98 C2E A 301 SITE 1 AC3 6 GLU A 39 ASN A 98 GLU A 130 ASP A 160 SITE 2 AC3 6 C2E A 301 HOH A 459 SITE 1 AC4 6 ASP A 161 ASP A 183 GLU A 217 C2E A 301 SITE 2 AC4 6 HOH A 401 HOH A 468 CRYST1 64.590 64.590 135.730 90.00 90.00 90.00 P 43 21 2 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 0.015482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007368 0.00000