HEADER SIGNALING PROTEIN 17-FEB-15 4Y9P TITLE PA3825-EAL CA-CDG STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PA3825-EAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 255-517; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: PA3825; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EAL, CYCLIC DI-GMP, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.BELLINI,S.HORRELL,A.WAGNER,R.STRANGE,M.A.WALSH REVDAT 4 10-JAN-24 4Y9P 1 HETSYN LINK REVDAT 3 30-AUG-17 4Y9P 1 REMARK LINK SITE ATOM REVDAT 2 23-NOV-16 4Y9P 1 JRNL REVDAT 1 09-MAR-16 4Y9P 0 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 MUCR AND PA3825 EAL-PHOSPHODIESTERASE DOMAINS FROM JRNL TITL 2 PSEUDOMONAS AERUGINOSA SUGGEST ROLES FOR THREE METALS IN THE JRNL TITL 3 ACTIVE SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 19345 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1060 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) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1421 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : 0.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.559 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.284 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.243 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.255 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4142 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3950 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5640 ; 1.999 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9088 ; 1.509 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 7.869 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;39.225 ;23.209 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 687 ;17.627 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;20.168 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 633 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4609 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 929 ; 0.006 ; 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): 2023 ; 5.773 ; 4.372 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2022 ; 5.754 ; 4.371 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2527 ; 7.819 ; 6.536 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2528 ; 7.820 ; 6.540 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2119 ; 7.136 ; 4.981 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2118 ; 7.125 ; 4.982 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3114 ;10.152 ; 7.240 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4723 ;13.209 ;36.417 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4724 ;13.208 ;36.420 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 6 262 B 6 262 28262 0.13 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0420 -0.9450 -21.3870 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.0829 REMARK 3 T33: 0.1937 T12: -0.0184 REMARK 3 T13: 0.0390 T23: 0.0768 REMARK 3 L TENSOR REMARK 3 L11: 3.6479 L22: 3.0628 REMARK 3 L33: 2.0896 L12: -0.3626 REMARK 3 L13: -0.0287 L23: 1.0264 REMARK 3 S TENSOR REMARK 3 S11: -0.0410 S12: -0.1016 S13: -0.2977 REMARK 3 S21: -0.1183 S22: 0.0100 S23: -0.4529 REMARK 3 S31: 0.2349 S32: 0.2329 S33: 0.0310 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): -35.0110 -0.7030 -19.5730 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.0761 REMARK 3 T33: 0.0704 T12: -0.0694 REMARK 3 T13: 0.0505 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 3.3119 L22: 2.6506 REMARK 3 L33: 3.4189 L12: 0.0376 REMARK 3 L13: 0.3182 L23: -0.8504 REMARK 3 S TENSOR REMARK 3 S11: -0.0690 S12: -0.2492 S13: -0.2260 REMARK 3 S21: 0.0755 S22: 0.0311 S23: 0.3425 REMARK 3 S31: 0.5691 S32: -0.4411 S33: 0.0379 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4Y9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19345 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 84.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.94500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 4Y8E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-11% ISO-PROPANOL, 0.1 M MES PH 6.5, REMARK 280 0.1 M SODIUM ACETATE PH 4.5 AND 0.2 M CALCIUM ACETATE., PH 5.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.11500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.11500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.70000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 165 REMARK 465 HIS A 166 REMARK 465 SER A 167 REMARK 465 SER A 168 REMARK 465 LEU A 169 REMARK 465 ALA A 170 REMARK 465 TYR A 171 REMARK 465 LEU A 172 REMARK 465 ALA A 262 REMARK 465 SER A 263 REMARK 465 SER B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 VAL B 4 REMARK 465 GLY B 165 REMARK 465 HIS B 166 REMARK 465 SER B 167 REMARK 465 SER B 168 REMARK 465 LEU B 169 REMARK 465 ALA B 262 REMARK 465 SER B 263 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 HIS A 46 O GLU A 49 2.15 REMARK 500 O HOH A 406 O HOH A 427 2.19 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 76 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 104 CA - CB - SG ANGL. DEV. = -12.6 DEGREES REMARK 500 LEU B 51 CB - CG - CD2 ANGL. DEV. = 10.2 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 ASN A 18 68.34 18.33 REMARK 500 GLU A 90 130.61 -37.06 REMARK 500 GLU A 106 157.71 58.36 REMARK 500 ILE A 137 157.40 -45.85 REMARK 500 GLU A 138 -46.99 83.72 REMARK 500 GLU A 141 -85.05 64.00 REMARK 500 THR A 143 30.90 -67.21 REMARK 500 ASP A 144 75.70 -116.24 REMARK 500 LYS A 174 -107.90 82.24 REMARK 500 PHE A 175 175.88 18.59 REMARK 500 ASN B 18 69.60 17.56 REMARK 500 GLU B 106 121.20 -178.09 REMARK 500 LEU B 109 -37.76 -37.09 REMARK 500 GLU B 138 49.90 -84.51 REMARK 500 TYR B 171 -28.16 -9.12 REMARK 500 GLN B 176 83.63 34.71 REMARK 500 ASP B 193 98.50 -169.89 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 GLU A 106 LEU A 107 -147.05 REMARK 500 GLU A 141 VAL A 142 -147.10 REMARK 500 ALA B 5 SER B 6 -146.41 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 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 39 OE2 REMARK 620 2 ASN A 98 OD1 82.9 REMARK 620 3 GLU A 130 OE1 80.3 84.3 REMARK 620 4 ASP A 160 OD1 150.0 124.4 89.5 REMARK 620 5 ASP A 160 OD2 157.7 80.0 84.0 44.4 REMARK 620 6 C2E A 304 O2P 89.0 89.1 168.0 102.5 104.8 REMARK 620 7 HOH A 414 O 82.5 164.6 88.5 68.9 112.8 95.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 135 OE1 REMARK 620 2 HOH A 422 O 81.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 161 OD1 REMARK 620 2 ASP A 183 OD1 66.7 REMARK 620 3 GLU A 217 OE1 101.7 138.2 REMARK 620 4 C2E A 304 O1P 60.5 119.3 81.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 39 OE2 REMARK 620 2 ASN B 98 OD1 83.3 REMARK 620 3 GLU B 130 OE1 80.6 89.6 REMARK 620 4 ASP B 160 OD1 147.6 128.4 91.9 REMARK 620 5 ASP B 160 OD2 163.0 83.2 89.0 45.3 REMARK 620 6 C2E B 304 O21 86.8 90.0 167.4 98.2 103.5 REMARK 620 7 HOH B 401 O 77.3 159.5 93.6 71.8 117.0 82.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE B 99 O REMARK 620 2 GLU B 135 OE1 69.3 REMARK 620 3 GLU B 135 OE2 75.1 44.0 REMARK 620 4 HOH B 421 O 95.0 97.9 141.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 160 OD1 REMARK 620 2 ASP B 161 OD1 92.2 REMARK 620 3 GLU B 217 OE1 122.6 98.3 REMARK 620 4 GLU B 217 OE2 79.0 138.2 56.4 REMARK 620 5 C2E B 304 O11 99.9 75.5 137.4 146.1 REMARK 620 6 HOH B 401 O 78.2 162.7 99.0 54.6 91.8 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y9M RELATED DB: PDB REMARK 900 4Y9M IS THE SAME PROTEIN WITH NO LIGAND OR METALS BOUND. REMARK 900 RELATED ID: 4Y9N RELATED DB: PDB REMARK 900 4Y9N IS THE SAME PROTEIN CO-CRYSTALLISED WITH MAGNESIUM CHLORIDE REMARK 900 BUT WITH NO LIGAND OR METALS BOUND. REMARK 900 RELATED ID: 4Y8E RELATED DB: PDB REMARK 900 4Y8E IS THE SAME PROTEIN CO-CRYSTALLISED WITH CALCIUM CHLORIDE REMARK 900 WITHOUT A LIGAND. REMARK 900 RELATED ID: 4Y9O RELATED DB: PDB REMARK 900 4Y9O IS THE SAME PROTEIN CO-CRYSTALLISED WITH MANGANESE CHLORIDE REMARK 900 BUT WITH NO LIGAND OR METALS BOUND. DBREF 4Y9P A 1 263 UNP Q9HXH7 Q9HXH7_PSEAE 255 517 DBREF 4Y9P B 1 263 UNP Q9HXH7 Q9HXH7_PSEAE 255 517 SEQRES 1 A 263 SER ARG ARG VAL ALA SER PRO SER SER GLU LEU ARG ARG SEQRES 2 A 263 ALA LEU GLU ALA ASN GLU PHE ILE PRO TYR TYR GLN PRO SEQRES 3 A 263 LEU SER PRO GLY GLN GLY GLY ARG TRP ILE GLY VAL GLU SEQRES 4 A 263 VAL LEU MET ARG TRP ARG HIS PRO ARG GLU GLY LEU ILE SEQRES 5 A 263 ARG PRO ASP LEU PHE ILE PRO PHE ALA GLU ARG SER GLY SEQRES 6 A 263 LEU ILE VAL PRO MET THR ARG ALA LEU MET ARG GLN VAL SEQRES 7 A 263 ALA GLU ASP LEU GLY GLY HIS ALA GLY LYS LEU GLU PRO SEQRES 8 A 263 GLY PHE HIS ILE GLY PHE ASN ILE SER ALA THR HIS CYS SEQRES 9 A 263 HIS GLU LEU ALA LEU VAL ASP ASP CYS ARG GLU LEU LEU SEQRES 10 A 263 ALA ALA PHE PRO PRO GLY HIS ILE THR LEU VAL LEU GLU SEQRES 11 A 263 LEU THR GLU ARG GLU LEU ILE GLU SER SER GLU VAL THR SEQRES 12 A 263 ASP ARG LEU PHE ASP GLU LEU HIS ALA LEU GLY VAL LYS SEQRES 13 A 263 ILE ALA ILE ASP ASP PHE GLY THR GLY HIS SER SER LEU SEQRES 14 A 263 ALA TYR LEU ARG LYS PHE GLN VAL ASP CYS LEU LYS ILE SEQRES 15 A 263 ASP GLN SER PHE VAL ALA ARG ILE GLY ILE ASP THR LEU SEQRES 16 A 263 SER GLY HIS ILE LEU ASP SER ILE VAL GLU LEU SER ALA SEQRES 17 A 263 LYS LEU ASP LEU ASP ILE VAL ALA GLU GLY VAL GLU THR SEQRES 18 A 263 PRO GLU GLN ARG ASP TYR LEU ALA ALA ARG GLY VAL ASP SEQRES 19 A 263 TYR LEU GLN GLY TYR LEU ILE GLY ARG PRO MET PRO LEU SEQRES 20 A 263 GLU SER LEU LEU SER SER LEU THR VAL GLN GLU GLY GLN SEQRES 21 A 263 GLY ALA SER SEQRES 1 B 263 SER ARG ARG VAL ALA SER PRO SER SER GLU LEU ARG ARG SEQRES 2 B 263 ALA LEU GLU ALA ASN GLU PHE ILE PRO TYR TYR GLN PRO SEQRES 3 B 263 LEU SER PRO GLY GLN GLY GLY ARG TRP ILE GLY VAL GLU SEQRES 4 B 263 VAL LEU MET ARG TRP ARG HIS PRO ARG GLU GLY LEU ILE SEQRES 5 B 263 ARG PRO ASP LEU PHE ILE PRO PHE ALA GLU ARG SER GLY SEQRES 6 B 263 LEU ILE VAL PRO MET THR ARG ALA LEU MET ARG GLN VAL SEQRES 7 B 263 ALA GLU ASP LEU GLY GLY HIS ALA GLY LYS LEU GLU PRO SEQRES 8 B 263 GLY PHE HIS ILE GLY PHE ASN ILE SER ALA THR HIS CYS SEQRES 9 B 263 HIS GLU LEU ALA LEU VAL ASP ASP CYS ARG GLU LEU LEU SEQRES 10 B 263 ALA ALA PHE PRO PRO GLY HIS ILE THR LEU VAL LEU GLU SEQRES 11 B 263 LEU THR GLU ARG GLU LEU ILE GLU SER SER GLU VAL THR SEQRES 12 B 263 ASP ARG LEU PHE ASP GLU LEU HIS ALA LEU GLY VAL LYS SEQRES 13 B 263 ILE ALA ILE ASP ASP PHE GLY THR GLY HIS SER SER LEU SEQRES 14 B 263 ALA TYR LEU ARG LYS PHE GLN VAL ASP CYS LEU LYS ILE SEQRES 15 B 263 ASP GLN SER PHE VAL ALA ARG ILE GLY ILE ASP THR LEU SEQRES 16 B 263 SER GLY HIS ILE LEU ASP SER ILE VAL GLU LEU SER ALA SEQRES 17 B 263 LYS LEU ASP LEU ASP ILE VAL ALA GLU GLY VAL GLU THR SEQRES 18 B 263 PRO GLU GLN ARG ASP TYR LEU ALA ALA ARG GLY VAL ASP SEQRES 19 B 263 TYR LEU GLN GLY TYR LEU ILE GLY ARG PRO MET PRO LEU SEQRES 20 B 263 GLU SER LEU LEU SER SER LEU THR VAL GLN GLU GLY GLN SEQRES 21 B 263 GLY ALA SER HET CA A 301 1 HET CA A 302 1 HET CA A 303 1 HET C2E A 304 46 HET CA B 301 1 HET CA B 302 1 HET CA B 303 1 HET C2E B 304 46 HETNAM CA CALCIUM ION 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) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 3 CA 6(CA 2+) FORMUL 6 C2E 2(C20 H24 N10 O14 P2) FORMUL 11 HOH *56(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 GLY A 65 1 9 HELIX 4 AA4 LEU A 66 GLY A 83 1 18 HELIX 5 AA5 HIS A 85 LEU A 89 5 5 HELIX 6 AA6 ALA A 101 HIS A 105 5 5 HELIX 7 AA7 GLU A 106 LEU A 107 5 2 HELIX 8 AA8 ALA A 108 ALA A 119 1 12 HELIX 9 AA9 GLU A 133 ILE A 137 1 5 HELIX 10 AB1 ASP A 144 LEU A 153 1 10 HELIX 11 AB2 ASP A 183 ARG A 189 1 7 HELIX 12 AB3 ASP A 193 ASP A 211 1 19 HELIX 13 AB4 THR A 221 ARG A 231 1 11 HELIX 14 AB5 PRO A 246 GLY A 259 1 14 HELIX 15 AB6 SER B 6 ALA B 17 1 12 HELIX 16 AB7 ARG B 53 LEU B 56 5 4 HELIX 17 AB8 PHE B 57 GLY B 65 1 9 HELIX 18 AB9 LEU B 66 GLY B 83 1 18 HELIX 19 AC1 HIS B 85 LEU B 89 5 5 HELIX 20 AC2 ALA B 101 HIS B 105 5 5 HELIX 21 AC3 LEU B 107 ALA B 118 1 12 HELIX 22 AC4 GLU B 133 GLU B 138 1 6 HELIX 23 AC5 SER B 140 ALA B 152 1 13 HELIX 24 AC6 ASP B 183 ARG B 189 1 7 HELIX 25 AC7 ASP B 193 ASP B 211 1 19 HELIX 26 AC8 THR B 221 ARG B 231 1 11 HELIX 27 AC9 PRO B 246 GLY B 259 1 14 SHEET 1 AA110 LEU A 51 ILE A 52 0 SHEET 2 AA110 GLY A 37 ARG A 45 -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 THR A 126 N ILE A 95 SHEET 5 AA110 LYS A 156 PHE A 162 1 O ASP A 160 N LEU A 131 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 ARG A 45 -1 O LEU A 41 N TYR A 23 SHEET 1 AA210 GLY B 50 ILE B 52 0 SHEET 2 AA210 GLY B 37 HIS B 46 -1 N TRP B 44 O ILE B 52 SHEET 3 AA210 PHE B 93 ASN B 98 1 O GLY B 96 N VAL B 40 SHEET 4 AA210 ILE B 125 THR B 132 1 O THR B 126 N ILE B 95 SHEET 5 AA210 LYS B 156 PHE B 162 1 O ASP B 160 N LEU B 131 SHEET 6 AA210 CYS B 179 ILE B 182 1 O LYS B 181 N ILE B 159 SHEET 7 AA210 ASP B 213 ALA B 216 1 O VAL B 215 N ILE B 182 SHEET 8 AA210 TYR B 235 LEU B 236 1 O TYR B 235 N ALA B 216 SHEET 9 AA210 PHE B 20 PRO B 29 -1 N SER B 28 O LEU B 236 SHEET 10 AA210 GLY B 37 HIS B 46 -1 O ARG B 43 N ILE B 21 LINK OE2 GLU A 39 CA CA A 303 1555 1555 2.19 LINK OD1 ASN A 98 CA CA A 303 1555 1555 2.36 LINK OE1 GLU A 130 CA CA A 303 1555 1555 2.31 LINK OE1 GLU A 135 CA CA A 301 1555 1555 3.16 LINK OD1 ASP A 160 CA CA A 303 1555 1555 3.10 LINK OD2 ASP A 160 CA CA A 303 1555 1555 2.18 LINK OD1 ASP A 161 CA CA A 302 1555 1555 2.18 LINK OD1 ASP A 183 CA CA A 302 1555 1555 3.07 LINK OE1 GLU A 217 CA CA A 302 1555 1555 2.37 LINK CA CA A 301 O HOH A 422 1555 1555 2.53 LINK CA CA A 302 O1P C2E A 304 1555 1555 2.97 LINK CA CA A 303 O2P C2E A 304 1555 1555 2.17 LINK CA CA A 303 O HOH A 414 1555 1555 2.31 LINK OE2 GLU B 39 CA CA B 302 1555 1555 2.27 LINK OD1 ASN B 98 CA CA B 302 1555 1555 2.32 LINK O ILE B 99 CA CA B 301 1555 1555 2.99 LINK OE1 GLU B 130 CA CA B 302 1555 1555 2.17 LINK OE1 GLU B 135 CA CA B 301 1555 1555 2.76 LINK OE2 GLU B 135 CA CA B 301 1555 1555 3.03 LINK OD1 ASP B 160 CA CA B 302 1555 1555 3.14 LINK OD2 ASP B 160 CA CA B 302 1555 1555 2.13 LINK OD1 ASP B 160 CA CA B 303 1555 1555 2.31 LINK OD1 ASP B 161 CA CA B 303 1555 1555 2.30 LINK OE1 GLU B 217 CA CA B 303 1555 1555 2.07 LINK OE2 GLU B 217 CA CA B 303 1555 1555 2.58 LINK CA CA B 301 O HOH B 421 1555 1555 2.52 LINK CA CA B 302 O21 C2E B 304 1555 1555 2.09 LINK CA CA B 302 O HOH B 401 1555 1555 2.32 LINK CA CA B 303 O11 C2E B 304 1555 1555 2.40 LINK CA CA B 303 O HOH B 401 1555 1555 2.83 SITE 1 AC1 3 ILE A 99 GLU A 135 HOH A 422 SITE 1 AC2 5 ASP A 161 ASP A 183 GLN A 184 GLU A 217 SITE 2 AC2 5 C2E A 304 SITE 1 AC3 6 GLU A 39 ASN A 98 GLU A 130 ASP A 160 SITE 2 AC3 6 C2E A 304 HOH A 414 SITE 1 AC4 22 GLN A 25 GLU A 39 LEU A 41 MET A 42 SITE 2 AC4 22 ARG A 43 ARG A 53 PRO A 54 ASP A 55 SITE 3 AC4 22 GLU A 62 ASN A 98 ASP A 160 ASP A 161 SITE 4 AC4 22 GLN A 184 GLU A 217 GLY A 218 GLU A 220 SITE 5 AC4 22 GLY A 238 TYR A 239 PRO A 244 CA A 302 SITE 6 AC4 22 CA A 303 ARG B 243 SITE 1 AC5 3 ILE B 99 GLU B 135 HOH B 421 SITE 1 AC6 6 GLU B 39 ASN B 98 GLU B 130 ASP B 160 SITE 2 AC6 6 C2E B 304 HOH B 401 SITE 1 AC7 5 ASP B 160 ASP B 161 GLU B 217 C2E B 304 SITE 2 AC7 5 HOH B 401 SITE 1 AC8 22 ARG A 243 GLN B 25 GLU B 39 LEU B 41 SITE 2 AC8 22 MET B 42 ARG B 43 PRO B 54 ASP B 55 SITE 3 AC8 22 LEU B 74 ASN B 98 SER B 100 ASP B 160 SITE 4 AC8 22 ASP B 161 GLN B 184 GLY B 218 GLU B 220 SITE 5 AC8 22 GLY B 238 TYR B 239 PRO B 244 CA B 302 SITE 6 AC8 22 CA B 303 HOH B 401 CRYST1 112.230 59.400 92.780 90.00 115.03 90.00 C 1 2 1 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 0.008910 0.000000 0.004161 0.00000 SCALE2 0.000000 0.016835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011895 0.00000