HEADER DNA BINDING PROTEIN/DNA 04-APR-18 5ZMN TITLE SULFUR BINDING DOMAIN AND SRA DOMAIN OF SCOMCRA COMPLEXED WITH TITLE 2 PHOSPHOROTHIOATED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN MCRA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SBD-SRA DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3'); COMPND 8 CHAIN: B, C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR (STRAIN ATCC BAA-471 / SOURCE 3 A3(2) / M145); SOURCE 4 ORGANISM_TAXID: 100226; SOURCE 5 STRAIN: ATCC BAA-471 / A3(2) / M145; SOURCE 6 GENE: SCO4631; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS; SOURCE 12 ORGANISM_TAXID: 1916 KEYWDS TYPE IV RESTRICTION ENDONUCLEASE, DNA PHOSPHOROTHIOATION, DNA BINDING KEYWDS 2 PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.LIU,W.FU,Z.ZHANG,Y.HE,H.YU,Y.ZHAO,Z.DENG,G.WU,X.HE REVDAT 3 27-MAR-24 5ZMN 1 REMARK REVDAT 2 28-NOV-18 5ZMN 1 JRNL REVDAT 1 26-SEP-18 5ZMN 0 JRNL AUTH G.LIU,W.FU,Z.ZHANG,Y.HE,H.YU,Y.WANG,X.WANG,Y.ZHAO,Z.DENG, JRNL AUTH 2 G.WU,X.HE JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF SULFUR IN JRNL TITL 2 PHOSPHOROTHIOATED DNA. JRNL REF NAT COMMUN V. 9 4689 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30409991 JRNL DOI 10.1038/S41467-018-07093-1 REMARK 2 REMARK 2 RESOLUTION. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 3.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 113.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17670 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) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 943 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) : 3.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1243 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2523 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.78000 REMARK 3 B22 (A**2) : 3.78000 REMARK 3 B33 (A**2) : -7.55000 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): 0.595 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.394 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.331 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.896 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.821 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3061 ; 0.018 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2581 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4253 ; 1.792 ; 1.828 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5953 ; 1.216 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 7.320 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;32.935 ;22.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 388 ;22.935 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.702 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3196 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 689 ; 0.003 ; 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5ZMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300007352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34877 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.290 REMARK 200 RESOLUTION RANGE LOW (A) : 113.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.1M CAPS REMARK 280 BUFFER, PH 10.5, 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z 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 61.17000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.17000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 156.84550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.42275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.17000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 235.26825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 235.26825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.17000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 78.42275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 61.17000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 156.84550 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 61.17000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 61.17000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 156.84550 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 61.17000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 235.26825 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 78.42275 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.17000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 78.42275 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 235.26825 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 61.17000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 61.17000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 156.84550 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A 89 REMARK 465 SER A 90 REMARK 465 ARG A 91 REMARK 465 GLU A 92 REMARK 465 ALA A 93 REMARK 465 PRO A 94 REMARK 465 ARG A 419 REMARK 465 PRO A 420 REMARK 465 SER A 421 REMARK 465 ASP A 422 REMARK 465 LEU A 423 REMARK 465 ALA A 424 REMARK 465 LEU A 425 REMARK 465 THR A 426 REMARK 465 PRO A 427 REMARK 465 GLY A 428 REMARK 465 ALA A 429 REMARK 465 PRO A 430 REMARK 465 ASP A 431 REMARK 465 GLY A 432 REMARK 465 THR A 433 REMARK 465 GLU A 434 REMARK 465 SER A 435 REMARK 465 ASP A 436 REMARK 465 ASP A 437 REMARK 465 GLU A 438 REMARK 465 ALA A 439 REMARK 465 TYR A 440 REMARK 465 ARG A 441 REMARK 465 ARG A 442 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 ARG A 191 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 211 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 229 CG1 CG2 CD1 REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 PHE A 244 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 246 CG CD1 CD2 REMARK 470 ARG A 253 CG CD NE CZ NH1 NH2 REMARK 470 MET A 281 CG SD CE REMARK 470 ARG A 366 CG CD NE CZ NH1 NH2 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 LEU A 197 O VAL A 200 2.17 REMARK 500 OG SER A 187 N7 GS B 5 2.19 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 THR A 96 N THR A 96 CA 0.181 REMARK 500 THR A 96 CA THR A 96 CB 0.185 REMARK 500 THR A 96 CB THR A 96 OG1 0.122 REMARK 500 THR A 96 CB THR A 96 CG2 0.258 REMARK 500 THR A 96 C THR A 96 O 0.136 REMARK 500 GS C 5 O3' DC C 6 P -0.079 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 DG B 8 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DG B 10 C1' - O4' - C4' ANGL. DEV. = -6.9 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 130 24.83 -79.56 REMARK 500 GLN A 154 44.88 31.66 REMARK 500 ARG A 188 -137.21 63.65 REMARK 500 ASP A 201 74.78 -118.21 REMARK 500 PHE A 233 -76.73 -111.77 REMARK 500 HIS A 234 -6.26 71.70 REMARK 500 LEU A 246 -45.69 146.22 REMARK 500 MET A 281 -141.58 160.69 REMARK 500 ASP A 289 -8.59 -58.85 REMARK 500 SER A 321 -17.86 -140.35 REMARK 500 ASP A 323 127.48 -35.37 REMARK 500 LEU A 326 78.63 -69.37 REMARK 500 ASP A 328 -115.07 43.22 REMARK 500 PHE A 350 111.67 135.00 REMARK 500 LYS A 375 23.89 84.05 REMARK 500 ASP A 417 -12.49 -141.45 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DG C 4 and GS C 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GS C 5 and DC C 6 DBREF 5ZMN A 91 442 UNP Q9L0M9 Q9L0M9_STRCO 91 442 DBREF 5ZMN B 1 10 PDB 5ZMN 5ZMN 1 10 DBREF 5ZMN C 1 10 PDB 5ZMN 5ZMN 1 10 SEQADV 5ZMN GLY A 89 UNP Q9L0M9 EXPRESSION TAG SEQADV 5ZMN SER A 90 UNP Q9L0M9 EXPRESSION TAG SEQRES 1 A 354 GLY SER ARG GLU ALA PRO LYS THR PHE HIS ARG ARG VAL SEQRES 2 A 354 GLY ASP VAL ARG PRO ALA ARG ARG ALA MET GLY PRO ALA SEQRES 3 A 354 LEU HIS ARG PRO VAL LEU LEU LEU TRP ALA ILE GLY GLN SEQRES 4 A 354 ALA VAL ALA ARG ALA PRO ARG LEU GLN PRO TRP SER THR SEQRES 5 A 354 THR ARG ASP ALA VAL ALA PRO LEU MET GLU LYS TYR GLY SEQRES 6 A 354 GLN VAL GLU ASP GLY VAL ASP GLY VAL ARG TYR PRO PHE SEQRES 7 A 354 TRP ALA LEU VAL ARG ASP ASP LEU TRP CYS VAL GLU GLN SEQRES 8 A 354 ALA GLU GLU LEU THR LEU THR SER ARG GLY ARG ARG PRO SEQRES 9 A 354 THR LEU GLU SER LEU ASN ALA VAL ASP PRO SER ALA GLY SEQRES 10 A 354 LEU ARG GLU ASP ASP TYR ASN LEU LEU ARG SER GLN PRO SEQRES 11 A 354 GLU ALA ALA ALA SER ALA ALA ALA GLY LEU ILE ALA ARG SEQRES 12 A 354 TYR PHE HIS LEU LEU PRO ALA GLY LEU LEU GLU ASP PHE SEQRES 13 A 354 GLY LEU HIS GLU LEU LEU ALA GLY ARG TRP PRO ASP ALA SEQRES 14 A 354 LEU ARG PRO LEU LEU GLY GLU THR PHE LYS ASP ARG ASP SEQRES 15 A 354 ALA ILE TRP ARG ALA TYR GLY GLY GLN LYS MET ALA GLY SEQRES 16 A 354 ILE GLY CYS LEU ALA ASP GLY ILE LEU SER ALA PHE SER SEQRES 17 A 354 ASP ASP LYS GLY PRO TYR ALA ASP GLY ARG ILE PRO ASP SEQRES 18 A 354 THR THR TRP ILE ALA TYR VAL GLY ASP GLY LEU SER GLY SEQRES 19 A 354 ASP GLN LYS LEU THR ASP GLY ASN GLU LEU MET ALA GLU SEQRES 20 A 354 HIS GLN ALA VAL GLY ARG ALA LEU ARG TYR TRP HIS LYS SEQRES 21 A 354 PRO PHE GLN GLY GLN TRP SER PHE GLU THR TRP ALA VAL SEQRES 22 A 354 ILE VAL GLN ARG ARG LEU ARG TRP GLY LEU GLY GLU ASP SEQRES 23 A 354 LYS LEU PRO ARG ARG GLU PHE LEU TRP VAL LEU ALA PRO SEQRES 24 A 354 VAL PRO SER PRO GLU ARG GLU THR TRP PRO PRO GLU VAL SEQRES 25 A 354 LEU GLU ALA LEU GLU ALA ASP THR GLY GLU LEU HIS ASP SEQRES 26 A 354 ASP THR GLY ASP TYR ARG PRO SER ASP LEU ALA LEU THR SEQRES 27 A 354 PRO GLY ALA PRO ASP GLY THR GLU SER ASP ASP GLU ALA SEQRES 28 A 354 TYR ARG ARG SEQRES 1 B 10 DC DC DC DG GS DC DC DG DG DG SEQRES 1 C 10 DC DC DC DG GS DC DC DG DG DG HET GS B 5 22 HET GS C 5 22 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HETNAM GS GUANOSINE-5'-THIO-MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 GS 2(C10 H14 N5 O6 P S) FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 HOH *3(H2 O) HELIX 1 AA1 THR A 96 VAL A 104 1 9 HELIX 2 AA2 LEU A 115 ALA A 130 1 16 HELIX 3 AA3 TRP A 138 GLY A 153 1 16 HELIX 4 AA4 ASP A 157 VAL A 162 1 6 HELIX 5 AA5 VAL A 162 LEU A 169 1 8 HELIX 6 AA6 THR A 193 VAL A 200 1 8 HELIX 7 AA7 ARG A 207 GLN A 217 1 11 HELIX 8 AA8 GLN A 217 PHE A 233 1 17 HELIX 9 AA9 PRO A 237 GLY A 245 1 9 HELIX 10 AB1 LEU A 246 ALA A 251 1 6 HELIX 11 AB2 ARG A 253 LEU A 258 5 6 HELIX 12 AB3 ASP A 268 GLY A 277 1 10 HELIX 13 AB4 ASP A 328 GLY A 340 1 13 HELIX 14 AB5 GLU A 392 TRP A 396 5 5 HELIX 15 AB6 PRO A 397 ASP A 407 1 11 SHEET 1 AA1 3 LEU A 135 PRO A 137 0 SHEET 2 AA1 3 SER A 203 LEU A 206 -1 O ALA A 204 N GLN A 136 SHEET 3 AA1 3 TRP A 175 VAL A 177 -1 N CYS A 176 O GLY A 205 SHEET 1 AA2 4 THR A 265 PHE A 266 0 SHEET 2 AA2 4 TRP A 354 LEU A 371 -1 O TRP A 354 N PHE A 266 SHEET 3 AA2 4 PRO A 377 VAL A 388 -1 O GLU A 380 N ARG A 368 SHEET 4 AA2 4 ILE A 313 VAL A 316 -1 N ILE A 313 O LEU A 385 SHEET 1 AA3 5 ILE A 284 CYS A 286 0 SHEET 2 AA3 5 LEU A 292 ASP A 297 -1 O SER A 293 N GLY A 285 SHEET 3 AA3 5 ALA A 342 LYS A 348 1 O TRP A 346 N ALA A 294 SHEET 4 AA3 5 TRP A 354 LEU A 371 -1 O THR A 358 N TYR A 345 SHEET 5 AA3 5 HIS A 412 ASP A 413 1 O HIS A 412 N LEU A 367 LINK O3' DG B 4 P GS B 5 1555 1555 1.59 LINK O3' GS B 5 P DC B 6 1555 1555 1.60 LINK O3' DG C 4 P GS C 5 1555 1555 1.55 LINK O3' GS C 5 P DC C 6 1555 1555 1.53 CISPEP 1 GLY A 245 LEU A 246 0 21.45 CISPEP 2 ARG A 259 PRO A 260 0 3.50 SITE 1 AC1 4 LYS A 267 ASP A 268 ARG A 269 TRP A 354 SITE 1 AC2 4 ARG A 108 THR A 327 ASP A 328 GLU A 331 SITE 1 AC3 3 GLN A 279 GLY A 285 CYS A 286 SITE 1 AC4 5 ARG A 105 PRO A 106 ALA A 107 ARG A 117 SITE 2 AC4 5 DG C 4 SITE 1 AC5 12 ALA A 114 HIS A 116 ARG A 117 TYR A 164 SITE 2 AC5 12 ARG A 171 ARG A 190 SO4 A 504 DC B 6 SITE 3 AC5 12 DC B 7 DG B 8 DC C 3 DC C 6 SITE 1 AC6 12 ARG A 109 ALA A 114 HIS A 116 ARG A 117 SITE 2 AC6 12 TYR A 164 ARG A 190 DG B 4 GS B 5 SITE 3 AC6 12 DC B 6 DC B 7 DG C 4 DC C 7 CRYST1 122.340 122.340 313.691 90.00 90.00 90.00 I 41 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 0.008174 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003188 0.00000