HEADER BIOSYNTHETIC PROTEIN 09-NOV-17 5YRP TITLE CRYSTAL STRUCTURE OF THE EAL DOMAIN OF MYCOBACTERIUM SMEGMATIS DCPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSORY BOX/RESPONSE REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EAL DOMAIN; COMPND 5 SYNONYM: C-DI-GMP HYDROLYSIS PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS C-DI-GMP, DIGUANYLATE CYCLASE, PHOSPHODIESTERASE, GAF, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHEN,N.LI,Y.LUO,Y.L.JIANG,C.Z.ZHOU,Y.CHEN,Q.LI REVDAT 3 06-NOV-24 5YRP 1 REMARK REVDAT 2 22-NOV-23 5YRP 1 LINK REVDAT 1 09-MAY-18 5YRP 0 JRNL AUTH H.J.CHEN,N.LI,Y.LUO,Y.L.JIANG,C.Z.ZHOU,Y.CHEN,Q.LI JRNL TITL THE GDP-SWITCHED GAF DOMAIN OF DCPA MODULATES THE CONCERTED JRNL TITL 2 SYNTHESIS/HYDROLYSIS OF C-DI-GMP INMYCOBACTERIUM SMEGMATIS. JRNL REF BIOCHEM. J. V. 475 1295 2018 JRNL REFN ESSN 1470-8728 JRNL PMID 29555845 JRNL DOI 10.1042/BCJ20180079 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 101.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13688 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) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 733 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) : 2.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 934 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3370 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.70000 REMARK 3 B22 (A**2) : 3.70000 REMARK 3 B33 (A**2) : -7.41000 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.471 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.445 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.648 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.843 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3418 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3438 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4641 ; 0.959 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7857 ; 0.679 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 4.767 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;34.153 ;22.955 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 561 ;11.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;13.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 568 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3830 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.001 ; 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): 1784 ; 1.734 ; 6.860 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1783 ; 1.735 ; 6.859 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2223 ; 3.003 ;10.288 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2224 ; 3.002 ;10.288 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1634 ; 1.668 ; 7.072 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1635 ; 1.667 ; 7.072 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2419 ; 2.808 ;10.534 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3849 ; 5.702 ;55.069 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3846 ; 5.684 ;55.066 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 : 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 REMARK 4 REMARK 4 5YRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14428 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 101.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4RNH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% POLYETHYLENE GLYCOL 6000, 0.1M REMARK 280 MGCL2, 0.1M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 64.52650 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 82.76750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 64.52650 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 82.76750 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 64.52650 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 82.76750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 64.52650 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 82.76750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 64.52650 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 82.76750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 64.52650 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 82.76750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 64.52650 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 82.76750 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 64.52650 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 64.52650 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.76750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ILE A 360 REMARK 465 GLU A 361 REMARK 465 GLY A 362 REMARK 465 GLY A 363 REMARK 465 GLU A 390 REMARK 465 HIS A 391 REMARK 465 PRO A 392 REMARK 465 THR A 393 REMARK 465 ARG A 394 REMARK 465 GLY A 395 REMARK 465 LEU A 396 REMARK 465 LEU A 397 REMARK 465 SER A 398 REMARK 465 PRO A 399 REMARK 465 ASP A 400 REMARK 465 SER A 401 REMARK 465 PHE A 402 REMARK 465 ILE A 403 REMARK 465 GLY A 404 REMARK 465 VAL A 405 REMARK 465 ALA A 406 REMARK 465 GLU A 407 REMARK 465 SER A 408 REMARK 465 ARG B 388 REMARK 465 TRP B 389 REMARK 465 GLU B 390 REMARK 465 HIS B 391 REMARK 465 PRO B 392 REMARK 465 THR B 393 REMARK 465 ARG B 394 REMARK 465 GLY B 395 REMARK 465 LEU B 396 REMARK 465 LEU B 397 REMARK 465 SER B 398 REMARK 465 PRO B 399 REMARK 465 ASP B 400 REMARK 465 SER B 401 REMARK 465 PHE B 402 REMARK 465 ILE B 403 REMARK 465 GLY B 404 REMARK 465 VAL B 405 REMARK 465 ALA B 406 REMARK 465 GLU B 407 REMARK 465 SER B 408 REMARK 465 ILE B 409 REMARK 465 ASN B 410 REMARK 465 LEU B 411 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 SER A 480 43.38 -74.15 REMARK 500 GLU B 414 79.85 -104.13 REMARK 500 VAL B 451 28.41 49.06 REMARK 500 GLN B 484 -178.22 -67.48 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 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 384 OE2 REMARK 620 2 ASN A 444 OD1 76.4 REMARK 620 3 GLU A 476 OE2 79.0 69.3 REMARK 620 4 ASP A 506 OD1 145.0 71.0 77.9 REMARK 620 5 ASP A 506 OD2 142.4 116.6 74.2 51.5 REMARK 620 6 HOH A 804 O 76.6 134.0 138.7 136.6 107.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 384 OE1 REMARK 620 2 GLU B 384 OE2 51.2 REMARK 620 3 GLU B 476 OE2 78.4 70.3 REMARK 620 4 ASP B 506 OD1 137.0 148.6 81.6 REMARK 620 5 ASP B 506 OD2 140.3 104.6 62.8 48.0 REMARK 620 6 HOH B 809 O 124.2 131.1 154.8 73.9 95.5 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 MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 701 DBREF 5YRP A 360 606 UNP A0QUG3 A0QUG3_MYCS2 360 606 DBREF 5YRP B 360 606 UNP A0QUG3 A0QUG3_MYCS2 360 606 SEQRES 1 A 247 ILE GLU GLY GLY ALA LEU VAL LEU HIS TYR LEU PRO GLU SEQRES 2 A 247 ILE ASP MSE ARG THR GLY GLU VAL LEU ALA ALA GLU ALA SEQRES 3 A 247 LEU VAL ARG TRP GLU HIS PRO THR ARG GLY LEU LEU SER SEQRES 4 A 247 PRO ASP SER PHE ILE GLY VAL ALA GLU SER ILE ASN LEU SEQRES 5 A 247 ALA GLY GLU LEU GLY ARG TRP VAL LEU ARG THR ALA CYS SEQRES 6 A 247 ALA GLU PHE SER ARG TRP ARG ALA ASN GLY VAL GLY ARG SEQRES 7 A 247 ASN ILE VAL LEU ARG ILE ASN VAL SER PRO VAL GLN LEU SEQRES 8 A 247 VAL THR ASP GLY PHE VAL GLU SER VAL ALA GLY ILE MSE SEQRES 9 A 247 LYS GLU PHE GLY LEU PRO ARG GLY SER VAL CYS LEU GLU SEQRES 10 A 247 ILE THR GLU SER VAL VAL VAL GLN ASP ILE GLU THR THR SEQRES 11 A 247 ARG THR THR LEU THR GLY LEU HIS ASN VAL GLY VAL GLN SEQRES 12 A 247 VAL ALA ILE ASP ASP PHE GLY THR GLY TYR SER VAL LEU SEQRES 13 A 247 SER LEU LEU LYS SER LEU PRO VAL ASP THR LEU LYS ILE SEQRES 14 A 247 ASP ARG SER PHE VAL ALA GLU LEU GLY SER ASN PRO GLY SEQRES 15 A 247 ASP LEU PRO ILE VAL ARG ALA VAL ILE ALA LEU ALA GLY SEQRES 16 A 247 ALA PHE GLY LEU GLN LEU VAL ALA GLU GLY VAL GLU THR SEQRES 17 A 247 GLU ARG ALA ALA LEU THR LEU LEU ARG HIS GLY CYS TYR SEQRES 18 A 247 ARG ALA GLN GLY PHE LEU LEU SER LYS PRO ILE LEU GLY SEQRES 19 A 247 SER GLU MSE GLN THR LEU LEU ALA LYS GLY ARG VAL PRO SEQRES 1 B 247 ILE GLU GLY GLY ALA LEU VAL LEU HIS TYR LEU PRO GLU SEQRES 2 B 247 ILE ASP MSE ARG THR GLY GLU VAL LEU ALA ALA GLU ALA SEQRES 3 B 247 LEU VAL ARG TRP GLU HIS PRO THR ARG GLY LEU LEU SER SEQRES 4 B 247 PRO ASP SER PHE ILE GLY VAL ALA GLU SER ILE ASN LEU SEQRES 5 B 247 ALA GLY GLU LEU GLY ARG TRP VAL LEU ARG THR ALA CYS SEQRES 6 B 247 ALA GLU PHE SER ARG TRP ARG ALA ASN GLY VAL GLY ARG SEQRES 7 B 247 ASN ILE VAL LEU ARG ILE ASN VAL SER PRO VAL GLN LEU SEQRES 8 B 247 VAL THR ASP GLY PHE VAL GLU SER VAL ALA GLY ILE MSE SEQRES 9 B 247 LYS GLU PHE GLY LEU PRO ARG GLY SER VAL CYS LEU GLU SEQRES 10 B 247 ILE THR GLU SER VAL VAL VAL GLN ASP ILE GLU THR THR SEQRES 11 B 247 ARG THR THR LEU THR GLY LEU HIS ASN VAL GLY VAL GLN SEQRES 12 B 247 VAL ALA ILE ASP ASP PHE GLY THR GLY TYR SER VAL LEU SEQRES 13 B 247 SER LEU LEU LYS SER LEU PRO VAL ASP THR LEU LYS ILE SEQRES 14 B 247 ASP ARG SER PHE VAL ALA GLU LEU GLY SER ASN PRO GLY SEQRES 15 B 247 ASP LEU PRO ILE VAL ARG ALA VAL ILE ALA LEU ALA GLY SEQRES 16 B 247 ALA PHE GLY LEU GLN LEU VAL ALA GLU GLY VAL GLU THR SEQRES 17 B 247 GLU ARG ALA ALA LEU THR LEU LEU ARG HIS GLY CYS TYR SEQRES 18 B 247 ARG ALA GLN GLY PHE LEU LEU SER LYS PRO ILE LEU GLY SEQRES 19 B 247 SER GLU MSE GLN THR LEU LEU ALA LYS GLY ARG VAL PRO MODRES 5YRP MSE A 375 MET MODIFIED RESIDUE MODRES 5YRP MSE A 463 MET MODIFIED RESIDUE MODRES 5YRP MSE A 596 MET MODIFIED RESIDUE MODRES 5YRP MSE B 375 MET MODIFIED RESIDUE MODRES 5YRP MSE B 463 MET MODIFIED RESIDUE MODRES 5YRP MSE B 596 MET MODIFIED RESIDUE HET MSE A 375 8 HET MSE A 463 8 HET MSE A 596 8 HET MSE B 375 8 HET MSE B 463 8 HET MSE B 596 8 HET MG A 701 1 HET MG B 701 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *29(H2 O) HELIX 1 AA1 ASN A 410 ASN A 433 1 24 HELIX 2 AA2 GLY A 454 PHE A 466 1 13 HELIX 3 AA3 THR A 488 GLY A 500 1 13 HELIX 4 AA4 VAL A 514 LYS A 519 1 6 HELIX 5 AA5 ASP A 529 GLU A 535 1 7 HELIX 6 AA6 GLY A 541 GLY A 557 1 17 HELIX 7 AA7 THR A 567 GLY A 578 1 12 HELIX 8 AA8 LEU A 592 GLY A 603 1 12 HELIX 9 AA9 GLY B 416 ASN B 433 1 18 HELIX 10 AB1 GLY B 454 PHE B 466 1 13 HELIX 11 AB2 ASP B 485 VAL B 499 1 15 HELIX 12 AB3 SER B 513 LEU B 521 1 9 HELIX 13 AB4 ASP B 529 GLU B 535 1 7 HELIX 14 AB5 GLY B 541 PHE B 556 1 16 HELIX 15 AB6 THR B 567 HIS B 577 1 11 HELIX 16 AB7 GLY B 593 GLY B 603 1 11 SHEET 1 AA1 9 VAL A 366 ASP A 374 0 SHEET 2 AA1 9 VAL A 380 ARG A 388 -1 O LEU A 386 N HIS A 368 SHEET 3 AA1 9 VAL A 440 VAL A 445 1 O ARG A 442 N ALA A 385 SHEET 4 AA1 9 VAL A 473 THR A 478 1 O GLU A 476 N VAL A 445 SHEET 5 AA1 9 VAL A 501 PHE A 508 1 O GLN A 502 N VAL A 473 SHEET 6 AA1 9 THR A 525 ILE A 528 1 O LYS A 527 N ILE A 505 SHEET 7 AA1 9 GLN A 559 ALA A 562 1 O GLN A 559 N LEU A 526 SHEET 8 AA1 9 ARG A 581 ALA A 582 1 O ARG A 581 N ALA A 562 SHEET 9 AA1 9 VAL A 366 ASP A 374 -1 N ILE A 373 O ALA A 582 SHEET 1 AA210 ILE B 591 LEU B 592 0 SHEET 2 AA210 HIS B 368 ASP B 374 -1 N TYR B 369 O ILE B 591 SHEET 3 AA210 ARG B 581 GLN B 583 -1 O ALA B 582 N ILE B 373 SHEET 4 AA210 GLN B 559 GLU B 563 1 N ALA B 562 O GLN B 583 SHEET 5 AA210 THR B 525 ILE B 528 1 N LEU B 526 O GLN B 559 SHEET 6 AA210 GLN B 502 PHE B 508 1 N PHE B 508 O LYS B 527 SHEET 7 AA210 VAL B 473 THR B 478 1 N ILE B 477 O ALA B 504 SHEET 8 AA210 VAL B 440 VAL B 445 1 N VAL B 445 O GLU B 476 SHEET 9 AA210 VAL B 380 LEU B 386 1 N ALA B 385 O ARG B 442 SHEET 10 AA210 HIS B 368 ASP B 374 -1 N GLU B 372 O ALA B 382 LINK C ASP A 374 N MSE A 375 1555 1555 1.33 LINK C MSE A 375 N ARG A 376 1555 1555 1.33 LINK C ILE A 462 N MSE A 463 1555 1555 1.33 LINK C MSE A 463 N LYS A 464 1555 1555 1.33 LINK C GLU A 595 N MSE A 596 1555 1555 1.33 LINK C MSE A 596 N GLN A 597 1555 1555 1.33 LINK C ASP B 374 N MSE B 375 1555 1555 1.32 LINK C MSE B 375 N ARG B 376 1555 1555 1.33 LINK C ILE B 462 N MSE B 463 1555 1555 1.33 LINK C MSE B 463 N LYS B 464 1555 1555 1.33 LINK C GLU B 595 N MSE B 596 1555 1555 1.33 LINK C MSE B 596 N GLN B 597 1555 1555 1.33 LINK OE2 GLU A 384 MG MG A 701 1555 1555 2.42 LINK OD1 ASN A 444 MG MG A 701 1555 1555 2.67 LINK OE2 GLU A 476 MG MG A 701 1555 1555 2.27 LINK OD1 ASP A 506 MG MG A 701 1555 1555 2.31 LINK OD2 ASP A 506 MG MG A 701 1555 1555 2.69 LINK MG MG A 701 O HOH A 804 1555 1555 2.62 LINK OE1 GLU B 384 MG MG B 701 1555 1555 2.77 LINK OE2 GLU B 384 MG MG B 701 1555 1555 2.10 LINK OE2 GLU B 476 MG MG B 701 1555 1555 2.82 LINK OD1 ASP B 506 MG MG B 701 1555 1555 2.82 LINK OD2 ASP B 506 MG MG B 701 1555 1555 2.54 LINK MG MG B 701 O HOH B 809 1555 1555 2.60 SITE 1 AC1 5 GLU A 384 ASN A 444 GLU A 476 ASP A 506 SITE 2 AC1 5 HOH A 804 SITE 1 AC2 6 GLU B 384 ASN B 444 GLU B 476 ASP B 506 SITE 2 AC2 6 GLU B 563 HOH B 809 CRYST1 129.053 129.053 165.535 90.00 90.00 90.00 I 4 2 2 32 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 0.007749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006041 0.00000