HEADER HYDROLASE 02-MAY-13 4KIE TITLE CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC TITLE 2 PHOSPHODIESTERASE YAHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC DI-GMP PHOSPHODIESTERASE YAHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EAL DOMAIN CONTAINING RESIDUES 96-372; COMPND 5 EC: 3.1.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YAHA, B0315, JW0307; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS PGPG, PHOSPHODIESTERASE, TIM-BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SUNDRIYAL,T.SCHIRMER REVDAT 4 20-SEP-23 4KIE 1 REMARK SEQADV REVDAT 3 14-MAY-14 4KIE 1 JRNL REVDAT 2 12-FEB-14 4KIE 1 JRNL REMARK REVDAT 1 29-JAN-14 4KIE 0 JRNL AUTH A.SUNDRIYAL,C.MASSA,D.SAMORAY,F.ZEHENDER,T.SHARPE,U.JENAL, JRNL AUTH 2 T.SCHIRMER JRNL TITL INHERENT REGULATION OF EAL DOMAIN-CATALYZED HYDROLYSIS OF JRNL TITL 2 SECOND MESSENGER CYCLIC DI-GMP. JRNL REF J.BIOL.CHEM. V. 289 6978 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24451384 JRNL DOI 10.1074/JBC.M113.516195 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1726 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2340 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.57000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.28000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.381 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2214 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2124 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3005 ; 1.445 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4910 ; 0.795 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.825 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;36.243 ;25.051 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 354 ;13.677 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;25.512 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 332 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2480 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 492 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 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 98 A 358 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2854 -18.2126 -24.3855 REMARK 3 T TENSOR REMARK 3 T11: 0.0019 T22: 0.0075 REMARK 3 T33: 0.0543 T12: 0.0002 REMARK 3 T13: 0.0063 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.4432 L22: 0.4183 REMARK 3 L33: 0.2172 L12: -0.1825 REMARK 3 L13: 0.0540 L23: -0.0164 REMARK 3 S TENSOR REMARK 3 S11: -0.0193 S12: -0.0152 S13: -0.1081 REMARK 3 S21: 0.0105 S22: 0.0318 S23: 0.0058 REMARK 3 S31: 0.0116 S32: -0.0205 S33: -0.0125 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 4KIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA CCP4_3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34026 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.140 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7220 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.14 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: 2R6O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-ACETATE PH 4.6 AND 40% REMARK 280 PEG200, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.81300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.90900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.36150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.81300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.90900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.36150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.81300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.90900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.36150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.81300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.90900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.36150 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 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 516 LIES ON A SPECIAL POSITION. 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 MET A 95 REMARK 465 HIS A 96 REMARK 465 ARG A 97 REMARK 465 LYS A 359 REMARK 465 ALA A 360 REMARK 465 GLY A 361 REMARK 465 GLY A 362 REMARK 465 ALA A 363 REMARK 465 ALA A 364 REMARK 465 ALA A 365 REMARK 465 LEU A 366 REMARK 465 GLU A 367 REMARK 465 HIS A 368 REMARK 465 HIS A 369 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 150 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O1 PGE A 401 O HOH A 702 3554 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 310 CD ARG A 310 NE -0.136 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 310 CG - CD - NE ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 310 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 310 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 310 NE - CZ - NH2 ANGL. DEV. = -11.1 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 ALA A 132 -130.50 47.80 REMARK 500 PHE A 159 -19.86 -145.07 REMARK 500 SER A 344 136.28 -172.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 310 0.07 SIDE CHAIN 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 PGE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LJ3 RELATED DB: PDB REMARK 900 RELATED ID: 4LYK RELATED DB: PDB DBREF 4KIE A 96 362 UNP P21514 YAHA_ECOLI 96 362 SEQADV 4KIE MET A 95 UNP P21514 INITIATING METHIONINE SEQADV 4KIE ALA A 363 UNP P21514 EXPRESSION TAG SEQADV 4KIE ALA A 364 UNP P21514 EXPRESSION TAG SEQADV 4KIE ALA A 365 UNP P21514 EXPRESSION TAG SEQADV 4KIE LEU A 366 UNP P21514 EXPRESSION TAG SEQADV 4KIE GLU A 367 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 368 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 369 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 370 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 371 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 372 UNP P21514 EXPRESSION TAG SEQADV 4KIE HIS A 373 UNP P21514 EXPRESSION TAG SEQRES 1 A 279 MET HIS ARG TYR ILE ASN ASP ASN HIS TYR HIS HIS ILE SEQRES 2 A 279 VAL THR PRO GLU ALA ILE SER LEU ALA LEU GLU ASN HIS SEQRES 3 A 279 GLU PHE LYS PRO TRP ILE GLN PRO VAL PHE CYS ALA GLN SEQRES 4 A 279 THR GLY VAL LEU THR GLY CYS GLU VAL LEU VAL ARG TRP SEQRES 5 A 279 GLU HIS PRO GLN THR GLY ILE ILE PRO PRO ASP GLN PHE SEQRES 6 A 279 ILE PRO LEU ALA GLU SER SER GLY LEU ILE VAL ILE MET SEQRES 7 A 279 THR ARG GLN LEU MET LYS GLN THR ALA ASP ILE LEU MET SEQRES 8 A 279 PRO VAL LYS HIS LEU LEU PRO ASP ASN PHE HIS ILE GLY SEQRES 9 A 279 ILE ASN VAL SER ALA GLY CYS PHE LEU ALA ALA GLY PHE SEQRES 10 A 279 GLU LYS GLU CYS LEU ASN LEU VAL ASN LYS LEU GLY ASN SEQRES 11 A 279 ASP LYS ILE LYS LEU VAL LEU GLU LEU THR GLU ARG ASN SEQRES 12 A 279 PRO ILE PRO VAL THR PRO GLU ALA ARG ALA ILE PHE ASP SEQRES 13 A 279 SER LEU HIS GLN HIS ASN ILE THR PHE ALA LEU ASP ASP SEQRES 14 A 279 PHE GLY THR GLY TYR ALA THR TYR ARG TYR LEU GLN ALA SEQRES 15 A 279 PHE PRO VAL ASP PHE ILE LYS ILE ASP LYS SER PHE VAL SEQRES 16 A 279 GLN MET ALA SER VAL ASP GLU ILE SER GLY HIS ILE VAL SEQRES 17 A 279 ASP ASN ILE VAL GLU LEU ALA ARG LYS PRO GLY LEU SER SEQRES 18 A 279 ILE VAL ALA GLU GLY VAL GLU THR GLN GLU GLN ALA ASP SEQRES 19 A 279 LEU MET ILE GLY LYS GLY VAL HIS PHE LEU GLN GLY TYR SEQRES 20 A 279 LEU TYR SER PRO PRO VAL PRO GLY ASN LYS PHE ILE SER SEQRES 21 A 279 GLU TRP VAL MET LYS ALA GLY GLY ALA ALA ALA LEU GLU SEQRES 22 A 279 HIS HIS HIS HIS HIS HIS HET PGE A 401 10 HET PGE A 402 10 HET PGE A 403 10 HET PGE A 404 10 HET PGE A 405 10 HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 PGE 5(C6 H14 O4) FORMUL 7 HOH *213(H2 O) HELIX 1 1 THR A 109 ASN A 119 1 11 HELIX 2 2 PRO A 155 GLN A 158 5 4 HELIX 3 3 PHE A 159 GLY A 167 1 9 HELIX 4 4 LEU A 168 MET A 185 1 18 HELIX 5 5 PRO A 186 LEU A 191 5 6 HELIX 6 6 SER A 202 ALA A 208 1 7 HELIX 7 7 GLY A 210 GLY A 223 1 14 HELIX 8 8 THR A 242 HIS A 255 1 14 HELIX 9 9 GLY A 267 PHE A 277 1 11 HELIX 10 10 ASP A 285 SER A 293 1 9 HELIX 11 11 ASP A 295 ALA A 309 1 15 HELIX 12 12 THR A 323 LYS A 333 1 11 HELIX 13 13 GLY A 349 VAL A 357 1 9 SHEET 1 A 4 GLY A 152 ILE A 154 0 SHEET 2 A 4 LEU A 137 HIS A 148 -1 N TRP A 146 O ILE A 154 SHEET 3 A 4 PHE A 122 CYS A 131 -1 N TRP A 125 O LEU A 143 SHEET 4 A 4 VAL A 347 PRO A 348 -1 O VAL A 347 N ILE A 126 SHEET 1 B10 GLY A 152 ILE A 154 0 SHEET 2 B10 LEU A 137 HIS A 148 -1 N TRP A 146 O ILE A 154 SHEET 3 B10 PHE A 195 ASN A 200 1 O GLY A 198 N VAL A 142 SHEET 4 B10 ILE A 227 THR A 234 1 O GLU A 232 N ILE A 199 SHEET 5 B10 THR A 258 ASP A 263 1 O ALA A 260 N LEU A 233 SHEET 6 B10 PHE A 281 ILE A 284 1 O LYS A 283 N LEU A 261 SHEET 7 B10 SER A 315 ALA A 318 1 O VAL A 317 N ILE A 284 SHEET 8 B10 PHE A 337 LEU A 338 1 O PHE A 337 N ALA A 318 SHEET 9 B10 PHE A 122 CYS A 131 -1 N PHE A 130 O LEU A 338 SHEET 10 B10 VAL A 347 PRO A 348 -1 O VAL A 347 N ILE A 126 SSBOND 1 CYS A 131 CYS A 131 1555 2555 2.31 CISPEP 1 PRO A 149 GLN A 150 0 -16.53 SITE 1 AC1 8 PRO A 278 VAL A 279 LEU A 308 LYS A 311 SITE 2 AC1 8 HOH A 525 HOH A 556 HOH A 697 HOH A 702 SITE 1 AC2 10 VAL A 129 THR A 138 GLY A 139 GLU A 141 SITE 2 AC2 10 HIS A 196 GLU A 232 LYS A 283 PHE A 337 SITE 3 AC2 10 GLN A 339 HOH A 501 SITE 1 AC3 8 VAL A 142 ILE A 160 THR A 173 LEU A 176 SITE 2 AC3 8 ILE A 199 ASN A 200 HOH A 511 HOH A 625 SITE 1 AC4 4 GLU A 147 ARG A 246 HOH A 668 HOH A 710 SITE 1 AC5 6 HIS A 106 VAL A 108 TRP A 146 HIS A 148 SITE 2 AC5 6 HOH A 534 HOH A 667 CRYST1 73.626 87.818 94.723 90.00 90.00 90.00 I 2 2 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 0.013582 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010557 0.00000