HEADER TRANSFERASE 24-FEB-16 5IDM TITLE BIFUNCTIONAL HISTIDINE KINASE CCKA (DOMAIN, CA) IN COMPLEX WITH C-DI- TITLE 2 GMP AND AMPPNP/MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL CYCLE HISTIDINE KINASE CCKA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 378-547; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES; SOURCE 3 ORGANISM_TAXID: 155892; SOURCE 4 GENE: CCKA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS BIFUNCTIONAL, HISTIDINE KINASE, PHOSPHATASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.N.DUBEY,T.SCHIRMER REVDAT 3 21-SEP-22 5IDM 1 JRNL REMARK HETSYN LINK REVDAT 2 13-SEP-17 5IDM 1 REMARK REVDAT 1 05-OCT-16 5IDM 0 JRNL AUTH B.N.DUBEY,C.LORI,S.OZAKI,G.FUCILE,I.PLAZA-MENACHO,U.JENAL, JRNL AUTH 2 T.SCHIRMER JRNL TITL CYCLIC DI-GMP MEDIATES A HISTIDINE KINASE/PHOSPHATASE SWITCH JRNL TITL 2 BY NONCOVALENT DOMAIN CROSS-LINKING. JRNL REF SCI ADV V. 2 00823 2016 JRNL REFN ESSN 2375-2548 JRNL PMID 27652341 JRNL DOI 10.1126/SCIADV.1600823 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 27618 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1492 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1997 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2735 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 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) : 16.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.47000 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): 0.175 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.265 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2860 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2692 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3910 ; 1.628 ; 2.010 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6163 ; 1.276 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 347 ; 6.648 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;33.238 ;23.125 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 434 ;12.859 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;11.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3190 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 657 ; 0.005 ; 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): 1397 ; 0.948 ; 1.523 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1396 ; 0.948 ; 1.524 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1741 ; 1.659 ; 2.275 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 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 380 553 B 380 553 17980 0.140 0.050 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 : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 378 A 554 REMARK 3 RESIDUE RANGE : A 601 A 603 REMARK 3 RESIDUE RANGE : B 380 B 556 REMARK 3 RESIDUE RANGE : B 600 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8620 0.2060 -8.0340 REMARK 3 T TENSOR REMARK 3 T11: 0.0205 T22: 0.0180 REMARK 3 T33: 0.0088 T12: -0.0189 REMARK 3 T13: 0.0028 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.3250 L22: 1.1685 REMARK 3 L33: 0.2106 L12: -0.3611 REMARK 3 L13: 0.1812 L23: -0.0509 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: -0.0024 S13: -0.0154 REMARK 3 S21: -0.0139 S22: -0.0032 S23: -0.0195 REMARK 3 S31: -0.0235 S32: 0.0222 S33: -0.0014 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 : WITH TLS ADDED REMARK 4 REMARK 4 5IDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.9999 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM SULFATE, 28.4% REMARK 280 POLYETHYLENE GLYCOL 4000 AND 0.1 M MES PH 5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 28.14000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.14000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.05500 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 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 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 HIS A 555 REMARK 465 HIS A 556 REMARK 465 VAL B 378 REMARK 465 GLN B 379 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 PRO A 546 CG CD REMARK 470 PRO B 546 CG CD REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA B 442 REMARK 475 LYS B 443 REMARK 475 GLY B 444 REMARK 475 GLY B 445 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 ARG A 401 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 529 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 532 CG CD OE1 OE2 REMARK 480 ARG B 529 CG CD NE CZ NH1 NH2 REMARK 480 GLU B 532 CG CD OE1 OE2 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 OE2 GLU B 532 O HOH B 705 0.07 REMARK 500 OE2 GLU A 532 O HOH A 702 0.42 REMARK 500 OE1 GLU B 532 O HOH B 701 0.53 REMARK 500 NH2 ARG B 529 O HOH B 702 0.80 REMARK 500 NE ARG B 529 O HOH B 703 1.00 REMARK 500 CD ARG A 529 O HOH A 701 1.12 REMARK 500 NE ARG A 529 O HOH A 701 1.17 REMARK 500 CD GLU A 532 O HOH A 702 1.22 REMARK 500 CD ARG B 529 O HOH B 703 1.30 REMARK 500 CD GLU B 532 O HOH B 705 1.30 REMARK 500 CZ ARG B 529 O HOH B 702 1.39 REMARK 500 CZ ARG B 529 O HOH B 703 1.51 REMARK 500 NH1 ARG B 529 O HOH B 704 1.64 REMARK 500 O ALA B 441 N ALA B 442 1.69 REMARK 500 CG ARG A 529 O HOH A 701 1.76 REMARK 500 CD GLU B 532 O HOH B 701 1.79 REMARK 500 NH1 ARG B 529 O HOH B 702 1.86 REMARK 500 NH1 ARG B 529 O HOH B 703 1.98 REMARK 500 OE1 GLU A 532 O HOH A 702 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 NH2 ARG A 529 CG GLU B 402 2545 1.70 REMARK 500 NH2 ARG A 529 O ARG B 401 2545 1.75 REMARK 500 CZ ARG A 529 CG GLU B 402 2545 2.04 REMARK 500 NE ARG A 529 CD GLU B 402 2545 2.05 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 GLU A 532 CB GLU A 532 CG -0.355 REMARK 500 HIS A 553 C HIS A 553 O 0.140 REMARK 500 ALA B 441 C ALA B 442 N -0.466 REMARK 500 ARG B 529 CB ARG B 529 CG -0.626 REMARK 500 GLU B 532 CB GLU B 532 CG -0.204 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 GLU A 532 CA - CB - CG ANGL. DEV. = 21.8 DEGREES REMARK 500 ALA B 441 CA - C - N ANGL. DEV. = 16.1 DEGREES REMARK 500 ALA B 441 O - C - N ANGL. DEV. = -16.2 DEGREES REMARK 500 ARG B 529 CA - CB - CG ANGL. DEV. = 28.9 DEGREES REMARK 500 PRO B 546 N - CA - CB ANGL. DEV. = 7.3 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 ARG A 401 -137.43 63.29 REMARK 500 PHE A 496 -7.47 81.55 REMARK 500 ARG B 401 -149.81 64.96 REMARK 500 GLU B 402 23.97 -142.40 REMARK 500 LYS B 443 -60.75 -167.39 REMARK 500 PHE B 496 -9.16 82.08 REMARK 500 GLU B 532 -63.01 -120.09 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 HIS A 553 HIS A 554 133.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 553 -11.67 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 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 434 OD1 REMARK 620 2 ANP A 601 O1G 175.0 REMARK 620 3 ANP A 601 O1B 91.4 93.0 REMARK 620 4 ANP A 601 O2A 88.4 94.1 87.1 REMARK 620 5 HOH A 802 O 84.7 93.1 90.1 172.4 REMARK 620 6 HOH A 818 O 86.1 89.6 176.8 90.8 91.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 434 OD1 REMARK 620 2 ANP B 600 O2G 176.9 REMARK 620 3 ANP B 600 O2B 89.8 93.1 REMARK 620 4 ANP B 600 O2A 90.4 90.7 87.1 REMARK 620 5 HOH B 783 O 84.5 94.7 86.6 171.9 REMARK 620 6 HOH B 789 O 85.1 92.0 174.9 93.0 92.8 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 ANP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C2E A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP B 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 601 DBREF 5IDM A 378 547 UNP Q9X688 Q9X688_CAUVI 378 547 DBREF 5IDM B 378 547 UNP Q9X688 Q9X688_CAUVI 378 547 SEQADV 5IDM ALA A 548 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM LEU A 549 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM GLU A 550 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 551 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 552 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 553 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 554 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 555 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS A 556 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM ALA B 548 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM LEU B 549 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM GLU B 550 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 551 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 552 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 553 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 554 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 555 UNP Q9X688 EXPRESSION TAG SEQADV 5IDM HIS B 556 UNP Q9X688 EXPRESSION TAG SEQRES 1 A 179 VAL GLN ARG GLU VAL LEU ASP LEU GLY GLU LEU ILE SER SEQRES 2 A 179 GLU PHE GLU VAL LEU LEU ARG ARG LEU LEU ARG GLU ASP SEQRES 3 A 179 VAL LYS LEU ILE THR ASP TYR GLY ARG ASP LEU PRO GLN SEQRES 4 A 179 VAL ARG ALA ASP LYS SER GLN LEU GLU THR ALA VAL MET SEQRES 5 A 179 ASN LEU ALA VAL ASN ALA ARG ASP ALA VAL ARG ALA ALA SEQRES 6 A 179 LYS GLY GLY GLY VAL VAL ARG ILE ARG THR ALA ARG LEU SEQRES 7 A 179 THR ARG ASP GLU ALA ILE GLN LEU GLY PHE PRO ALA ALA SEQRES 8 A 179 ASP GLY ASP THR ALA PHE ILE GLU VAL SER ASP ASP GLY SEQRES 9 A 179 PRO GLY ILE PRO PRO ASP VAL MET GLY LYS ILE PHE ASP SEQRES 10 A 179 PRO PHE PHE THR THR LYS PRO VAL GLY GLU GLY THR GLY SEQRES 11 A 179 LEU GLY LEU ALA THR VAL TYR GLY ILE VAL LYS GLN SER SEQRES 12 A 179 ASP GLY TRP ILE HIS VAL HIS SER ARG PRO ASN GLU GLY SEQRES 13 A 179 ALA ALA PHE ARG ILE PHE LEU PRO VAL TYR GLU ALA PRO SEQRES 14 A 179 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 179 VAL GLN ARG GLU VAL LEU ASP LEU GLY GLU LEU ILE SER SEQRES 2 B 179 GLU PHE GLU VAL LEU LEU ARG ARG LEU LEU ARG GLU ASP SEQRES 3 B 179 VAL LYS LEU ILE THR ASP TYR GLY ARG ASP LEU PRO GLN SEQRES 4 B 179 VAL ARG ALA ASP LYS SER GLN LEU GLU THR ALA VAL MET SEQRES 5 B 179 ASN LEU ALA VAL ASN ALA ARG ASP ALA VAL ARG ALA ALA SEQRES 6 B 179 LYS GLY GLY GLY VAL VAL ARG ILE ARG THR ALA ARG LEU SEQRES 7 B 179 THR ARG ASP GLU ALA ILE GLN LEU GLY PHE PRO ALA ALA SEQRES 8 B 179 ASP GLY ASP THR ALA PHE ILE GLU VAL SER ASP ASP GLY SEQRES 9 B 179 PRO GLY ILE PRO PRO ASP VAL MET GLY LYS ILE PHE ASP SEQRES 10 B 179 PRO PHE PHE THR THR LYS PRO VAL GLY GLU GLY THR GLY SEQRES 11 B 179 LEU GLY LEU ALA THR VAL TYR GLY ILE VAL LYS GLN SER SEQRES 12 B 179 ASP GLY TRP ILE HIS VAL HIS SER ARG PRO ASN GLU GLY SEQRES 13 B 179 ALA ALA PHE ARG ILE PHE LEU PRO VAL TYR GLU ALA PRO SEQRES 14 B 179 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET ANP A 601 31 HET MG A 602 1 HET C2E A 603 46 HET ANP B 600 31 HET MG B 601 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM 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 ANP 2(C10 H17 N6 O12 P3) FORMUL 4 MG 2(MG 2+) FORMUL 5 C2E C20 H24 N10 O14 P2 FORMUL 8 HOH *406(H2 O) HELIX 1 AA1 LEU A 385 ARG A 401 1 17 HELIX 2 AA2 LYS A 421 ARG A 440 1 20 HELIX 3 AA3 ALA A 441 LYS A 443 5 3 HELIX 4 AA4 THR A 456 LEU A 463 1 8 HELIX 5 AA5 PRO A 485 GLY A 490 1 6 HELIX 6 AA6 LEU A 508 SER A 520 1 13 HELIX 7 AA7 LEU B 385 ARG B 401 1 17 HELIX 8 AA8 ASP B 420 ALA B 442 1 23 HELIX 9 AA9 THR B 456 LEU B 463 1 8 HELIX 10 AB1 PRO B 485 GLY B 490 1 6 HELIX 11 AB2 LEU B 508 SER B 520 1 13 SHEET 1 AA1 2 ARG A 380 ASP A 384 0 SHEET 2 AA1 2 GLN A 416 ASP A 420 -1 O VAL A 417 N LEU A 383 SHEET 1 AA2 5 LYS A 405 TYR A 410 0 SHEET 2 AA2 5 VAL A 447 LEU A 455 1 O VAL A 448 N ILE A 407 SHEET 3 AA2 5 THR A 472 ASP A 479 -1 O SER A 478 N ARG A 449 SHEET 4 AA2 5 ALA A 534 PRO A 541 -1 O ILE A 538 N ILE A 475 SHEET 5 AA2 5 TRP A 523 SER A 528 -1 N TRP A 523 O PHE A 539 SHEET 1 AA3 6 HIS A 551 HIS A 552 0 SHEET 2 AA3 6 VAL B 404 GLY B 411 -1 O TYR B 410 N HIS A 552 SHEET 3 AA3 6 GLY B 446 LEU B 455 1 O THR B 452 N GLY B 411 SHEET 4 AA3 6 THR B 472 ASP B 479 -1 O SER B 478 N ARG B 449 SHEET 5 AA3 6 GLY B 533 PRO B 541 -1 O ILE B 538 N ILE B 475 SHEET 6 AA3 6 TRP B 523 ARG B 529 -1 N TRP B 523 O PHE B 539 SHEET 1 AA4 2 GLU B 381 ASP B 384 0 SHEET 2 AA4 2 GLN B 416 ALA B 419 -1 O VAL B 417 N LEU B 383 LINK OD1 ASN A 434 MG MG A 602 1555 1555 2.09 LINK O1G ANP A 601 MG MG A 602 1555 1555 1.95 LINK O1B ANP A 601 MG MG A 602 1555 1555 2.07 LINK O2A ANP A 601 MG MG A 602 1555 1555 2.07 LINK MG MG A 602 O HOH A 802 1555 1555 2.12 LINK MG MG A 602 O HOH A 818 1555 1555 2.15 LINK OD1 ASN B 434 MG MG B 601 1555 1555 2.08 LINK O2G ANP B 600 MG MG B 601 1555 1555 1.99 LINK O2B ANP B 600 MG MG B 601 1555 1555 2.05 LINK O2A ANP B 600 MG MG B 601 1555 1555 2.05 LINK MG MG B 601 O HOH B 783 1555 1555 2.10 LINK MG MG B 601 O HOH B 789 1555 1555 2.23 SITE 1 AC1 27 ASN A 434 ALA A 438 ASP A 479 ILE A 484 SITE 2 AC1 27 PHE A 497 THR A 498 THR A 499 LYS A 500 SITE 3 AC1 27 GLY A 505 THR A 506 GLY A 507 LEU A 508 SITE 4 AC1 27 GLY A 509 LEU A 510 MG A 602 HOH A 727 SITE 5 AC1 27 HOH A 741 HOH A 761 HOH A 782 HOH A 793 SITE 6 AC1 27 HOH A 802 HOH A 812 HOH A 818 HOH A 821 SITE 7 AC1 27 HOH A 829 HOH A 840 HOH A 850 SITE 1 AC2 4 ASN A 434 ANP A 601 HOH A 802 HOH A 818 SITE 1 AC3 31 ALA A 442 LYS A 443 GLY A 445 TYR A 514 SITE 2 AC3 31 LYS A 518 TRP A 523 ILE A 524 HOH A 705 SITE 3 AC3 31 HOH A 710 HOH A 720 HOH A 736 HOH A 771 SITE 4 AC3 31 HOH A 780 HOH A 828 HOH A 836 HOH A 841 SITE 5 AC3 31 HOH A 844 HOH A 849 TYR B 514 TRP B 523 SITE 6 AC3 31 LEU B 549 GLU B 550 HIS B 551 HIS B 552 SITE 7 AC3 31 HIS B 553 HIS B 554 HIS B 555 HIS B 556 SITE 8 AC3 31 HOH B 730 HOH B 736 HOH B 770 SITE 1 AC4 25 ASN B 434 ALA B 438 ASP B 479 GLY B 483 SITE 2 AC4 25 ILE B 484 ILE B 492 PHE B 497 THR B 498 SITE 3 AC4 25 THR B 499 LYS B 500 THR B 506 GLY B 507 SITE 4 AC4 25 LEU B 508 GLY B 509 LEU B 510 PHE B 536 SITE 5 AC4 25 MG B 601 HOH B 723 HOH B 732 HOH B 753 SITE 6 AC4 25 HOH B 756 HOH B 761 HOH B 783 HOH B 789 SITE 7 AC4 25 HOH B 792 SITE 1 AC5 4 ASN B 434 ANP B 600 HOH B 783 HOH B 789 CRYST1 56.280 62.110 103.890 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 0.017768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009626 0.00000