HEADER TRANSCRIPTION REGULATOR/DNA 24-AUG-15 5DDG TITLE THE STRUCTURE OF TRANSCRIPTIONAL FACTOR ARAR FROM BACTEROIDES TITLE 2 THETAIOTAOMICRON VPI IN COMPLEX WITH TARGET DOUBLE STRAND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL FACTOR ARAR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUDIX FAMILY HYDROLASE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (27-MER); COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (27-MER); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON (STRAIN ATCC 29148 SOURCE 3 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); SOURCE 4 ORGANISM_TAXID: 226186; SOURCE 5 STRAIN: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482; SOURCE 6 GENE: BT_0354; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG68; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 13 ORGANISM_TAXID: 226186; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON VPI-5482; SOURCE 17 ORGANISM_TAXID: 226186 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, MIDWEST CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, MCSG, ARAR, DNA BINDING, TRANSCRIPTIONAL REGULATOR, KEYWDS 3 BACTEROIDES THETAIOTAOMICRON, HELIX-TURN-HELIX MOTIF, NUDIX FOLD, KEYWDS 4 TRANSCRIPTION REGULATOR-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,C.TESAR,D.RODIONOV,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 4 06-NOV-24 5DDG 1 JRNL REMARK REVDAT 3 16-DEC-15 5DDG 1 JRNL REVDAT 2 21-OCT-15 5DDG 1 JRNL REVDAT 1 09-SEP-15 5DDG 0 JRNL AUTH C.CHANG,C.TESAR,X.LI,Y.KIM,D.A.RODIONOV,A.JOACHIMIAK JRNL TITL A NOVEL TRANSCRIPTIONAL REGULATOR OF L-ARABINOSE UTILIZATION JRNL TITL 2 IN HUMAN GUT BACTERIA. JRNL REF NUCLEIC ACIDS RES. V. 43 10546 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26438537 JRNL DOI 10.1093/NAR/GKV1005 REMARK 2 REMARK 2 RESOLUTION. 3.06 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 : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 25711 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1349 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) : 3.06 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1619 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3619 REMARK 3 NUCLEIC ACID ATOMS : 1107 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.529 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.310 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.797 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4953 ; 0.009 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 4169 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6902 ; 1.328 ; 1.766 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9648 ; 0.915 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 447 ; 6.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;37.559 ;24.426 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 620 ;14.882 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;11.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 684 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4846 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1119 ; 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): 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 : MASK 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 5DDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97903 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27538 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.11000 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) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.85100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM MAGNESIUM CHLORIDE, 50 MM MOPS, REMARK 280 55% TACSIMATE, 5MM HEXAMMINE COBALT CHLORIDE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 B 409 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MSE B 1 REMARK 465 LYS B 2 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 LYS A 2 CG CD CE NZ REMARK 470 LEU A 201 CG CD1 CD2 REMARK 470 ASN B 3 CG OD1 ND2 REMARK 470 SER B 203 OG REMARK 470 LYS B 222 CG CD CE NZ 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 ASP A 85 32.78 -99.95 REMARK 500 GLU A 123 44.47 -143.95 REMARK 500 PHE A 129 -135.44 52.93 REMARK 500 PRO A 221 67.85 -60.26 REMARK 500 GLU B 123 47.55 -106.14 REMARK 500 PHE B 129 -128.80 43.68 REMARK 500 ASP B 220 77.52 -162.17 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 MLA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLA B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DD4 RELATED DB: PDB REMARK 900 RELATED ID: MCSG-APC111381 RELATED DB: TARGETTRACK DBREF 5DDG A 1 225 UNP Q8AAV8 Q8AAV8_BACTN 1 225 DBREF 5DDG B 1 225 UNP Q8AAV8 Q8AAV8_BACTN 1 225 DBREF 5DDG C 1 27 PDB 5DDG 5DDG 1 27 DBREF 5DDG D 1 27 PDB 5DDG 5DDG 1 27 SEQADV 5DDG SER A -2 UNP Q8AAV8 EXPRESSION TAG SEQADV 5DDG ASN A -1 UNP Q8AAV8 EXPRESSION TAG SEQADV 5DDG ALA A 0 UNP Q8AAV8 EXPRESSION TAG SEQADV 5DDG SER B -2 UNP Q8AAV8 EXPRESSION TAG SEQADV 5DDG ASN B -1 UNP Q8AAV8 EXPRESSION TAG SEQADV 5DDG ALA B 0 UNP Q8AAV8 EXPRESSION TAG SEQRES 1 A 228 SER ASN ALA MSE LYS ASN TYR TYR SER SER ASN PRO THR SEQRES 2 A 228 PHE TYR LEU GLY ILE ASP CYS ILE ILE PHE GLY PHE ASN SEQRES 3 A 228 GLU GLY GLU ILE SER LEU LEU LEU LEU LYS ARG ASN PHE SEQRES 4 A 228 GLU PRO ALA MSE GLY GLU TRP SER LEU MSE GLY GLY PHE SEQRES 5 A 228 VAL GLN LYS ASP GLU SER VAL ASP ASP ALA ALA LYS ARG SEQRES 6 A 228 VAL LEU ALA GLU LEU THR GLY LEU GLU ASN VAL TYR MSE SEQRES 7 A 228 GLU GLN VAL GLY ALA PHE GLY ALA ILE ASP ARG ASP PRO SEQRES 8 A 228 GLY GLU ARG VAL VAL SER ILE ALA TYR TYR ALA LEU ILE SEQRES 9 A 228 ASN ILE ASN GLU TYR ASP ARG GLU LEU VAL GLN LYS HIS SEQRES 10 A 228 ASN ALA TYR TRP VAL ASN ILE ASN GLU LEU PRO ALA LEU SEQRES 11 A 228 ILE PHE ASP HIS PRO GLU MSE VAL ASP LYS ALA ARG GLU SEQRES 12 A 228 MSE MSE LYS GLN LYS ALA SER VAL GLU PRO ILE GLY PHE SEQRES 13 A 228 ASN LEU LEU PRO LYS LEU PHE THR LEU SER GLN LEU GLN SEQRES 14 A 228 SER LEU TYR GLU ALA ILE TYR GLY GLU PRO MSE ASP LYS SEQRES 15 A 228 ARG ASN PHE ARG LYS ARG VAL ALA GLU MSE ASP PHE ILE SEQRES 16 A 228 GLU LYS THR ASP LYS ILE ASP LYS LEU GLY SER LYS ARG SEQRES 17 A 228 GLY ALA ALA LEU TYR LYS PHE ASN GLY LYS ALA TYR ARG SEQRES 18 A 228 LYS ASP PRO LYS PHE LYS LEU SEQRES 1 B 228 SER ASN ALA MSE LYS ASN TYR TYR SER SER ASN PRO THR SEQRES 2 B 228 PHE TYR LEU GLY ILE ASP CYS ILE ILE PHE GLY PHE ASN SEQRES 3 B 228 GLU GLY GLU ILE SER LEU LEU LEU LEU LYS ARG ASN PHE SEQRES 4 B 228 GLU PRO ALA MSE GLY GLU TRP SER LEU MSE GLY GLY PHE SEQRES 5 B 228 VAL GLN LYS ASP GLU SER VAL ASP ASP ALA ALA LYS ARG SEQRES 6 B 228 VAL LEU ALA GLU LEU THR GLY LEU GLU ASN VAL TYR MSE SEQRES 7 B 228 GLU GLN VAL GLY ALA PHE GLY ALA ILE ASP ARG ASP PRO SEQRES 8 B 228 GLY GLU ARG VAL VAL SER ILE ALA TYR TYR ALA LEU ILE SEQRES 9 B 228 ASN ILE ASN GLU TYR ASP ARG GLU LEU VAL GLN LYS HIS SEQRES 10 B 228 ASN ALA TYR TRP VAL ASN ILE ASN GLU LEU PRO ALA LEU SEQRES 11 B 228 ILE PHE ASP HIS PRO GLU MSE VAL ASP LYS ALA ARG GLU SEQRES 12 B 228 MSE MSE LYS GLN LYS ALA SER VAL GLU PRO ILE GLY PHE SEQRES 13 B 228 ASN LEU LEU PRO LYS LEU PHE THR LEU SER GLN LEU GLN SEQRES 14 B 228 SER LEU TYR GLU ALA ILE TYR GLY GLU PRO MSE ASP LYS SEQRES 15 B 228 ARG ASN PHE ARG LYS ARG VAL ALA GLU MSE ASP PHE ILE SEQRES 16 B 228 GLU LYS THR ASP LYS ILE ASP LYS LEU GLY SER LYS ARG SEQRES 17 B 228 GLY ALA ALA LEU TYR LYS PHE ASN GLY LYS ALA TYR ARG SEQRES 18 B 228 LYS ASP PRO LYS PHE LYS LEU SEQRES 1 C 27 DG DC DA DA DA DA DG DT DG DT DT DA DC SEQRES 2 C 27 DT DT DT DT DA DC DA DC DC DC DA DT DG SEQRES 3 C 27 DC SEQRES 1 D 27 DG DC DA DT DG DG DG DT DG DT DA DA DA SEQRES 2 D 27 DA DG DT DA DA DC DA DC DT DT DT DT DG SEQRES 3 D 27 DC MODRES 5DDG MSE A 1 MET MODIFIED RESIDUE MODRES 5DDG MSE A 40 MET MODIFIED RESIDUE MODRES 5DDG MSE A 46 MET MODIFIED RESIDUE MODRES 5DDG MSE A 75 MET MODIFIED RESIDUE MODRES 5DDG MSE A 134 MET MODIFIED RESIDUE MODRES 5DDG MSE A 141 MET MODIFIED RESIDUE MODRES 5DDG MSE A 142 MET MODIFIED RESIDUE MODRES 5DDG MSE A 177 MET MODIFIED RESIDUE MODRES 5DDG MSE A 189 MET MODIFIED RESIDUE MODRES 5DDG MSE B 40 MET MODIFIED RESIDUE MODRES 5DDG MSE B 46 MET MODIFIED RESIDUE MODRES 5DDG MSE B 75 MET MODIFIED RESIDUE MODRES 5DDG MSE B 134 MET MODIFIED RESIDUE MODRES 5DDG MSE B 141 MET MODIFIED RESIDUE MODRES 5DDG MSE B 142 MET MODIFIED RESIDUE MODRES 5DDG MSE B 177 MET MODIFIED RESIDUE MODRES 5DDG MSE B 189 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 40 8 HET MSE A 46 8 HET MSE A 75 8 HET MSE A 134 8 HET MSE A 141 8 HET MSE A 142 8 HET MSE A 177 8 HET MSE A 189 8 HET MSE B 40 8 HET MSE B 46 8 HET MSE B 75 8 HET MSE B 134 8 HET MSE B 141 8 HET MSE B 142 8 HET MSE B 177 8 HET MSE B 189 8 HET MLA A 301 7 HET FMT A 302 3 HET FMT B 301 3 HET MLA B 302 7 HETNAM MSE SELENOMETHIONINE HETNAM MLA MALONIC ACID HETNAM FMT FORMIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 1 MSE 17(C5 H11 N O2 SE) FORMUL 5 MLA 2(C3 H4 O4) FORMUL 6 FMT 2(C H2 O2) FORMUL 9 HOH *16(H2 O) HELIX 1 AA1 MSE A 1 SER A 7 1 7 HELIX 2 AA2 SER A 55 GLY A 69 1 15 HELIX 3 AA3 ASP A 107 HIS A 114 1 8 HELIX 4 AA4 ASN A 122 LEU A 124 5 3 HELIX 5 AA5 ASP A 130 SER A 147 1 18 HELIX 6 AA6 ILE A 151 LEU A 156 5 6 HELIX 7 AA7 THR A 161 GLY A 174 1 14 HELIX 8 AA8 ASP A 178 MSE A 189 1 12 HELIX 9 AA9 ASN A 213 ASP A 220 1 8 HELIX 10 AB1 TYR B 4 ASN B 8 5 5 HELIX 11 AB2 SER B 55 GLY B 69 1 15 HELIX 12 AB3 ASP B 107 ASN B 115 1 9 HELIX 13 AB4 ASP B 130 GLU B 149 1 20 HELIX 14 AB5 ILE B 151 LEU B 156 5 6 HELIX 15 AB6 THR B 161 GLY B 174 1 14 HELIX 16 AB7 ASP B 178 MSE B 189 1 12 HELIX 17 AB8 ASN B 213 ASP B 220 1 8 SHEET 1 AA1 5 TRP A 43 SER A 44 0 SHEET 2 AA1 5 GLU A 26 LYS A 33 -1 N LEU A 32 O SER A 44 SHEET 3 AA1 5 TYR A 12 ASN A 23 -1 N ASN A 23 O GLU A 26 SHEET 4 AA1 5 VAL A 92 LEU A 100 1 O ALA A 99 N PHE A 20 SHEET 5 AA1 5 TYR A 74 PHE A 81 -1 N VAL A 78 O ALA A 96 SHEET 1 AA2 4 MSE A 46 PHE A 49 0 SHEET 2 AA2 4 TYR A 12 ASN A 23 -1 N CYS A 17 O MSE A 46 SHEET 3 AA2 4 GLU A 26 LYS A 33 -1 O GLU A 26 N ASN A 23 SHEET 4 AA2 4 ALA A 116 ASN A 120 -1 O VAL A 119 N LEU A 29 SHEET 1 AA3 2 ILE A 192 ASP A 199 0 SHEET 2 AA3 2 ALA A 207 PHE A 212 -1 O LEU A 209 N THR A 195 SHEET 1 AA4 5 TRP B 43 SER B 44 0 SHEET 2 AA4 5 GLU B 26 LYS B 33 -1 N LEU B 32 O SER B 44 SHEET 3 AA4 5 TYR B 12 ASN B 23 -1 N ASN B 23 O GLU B 26 SHEET 4 AA4 5 VAL B 92 LEU B 100 1 O ALA B 99 N PHE B 20 SHEET 5 AA4 5 TYR B 74 PHE B 81 -1 N VAL B 78 O ALA B 96 SHEET 1 AA5 4 MSE B 46 PHE B 49 0 SHEET 2 AA5 4 TYR B 12 ASN B 23 -1 N CYS B 17 O MSE B 46 SHEET 3 AA5 4 GLU B 26 LYS B 33 -1 O GLU B 26 N ASN B 23 SHEET 4 AA5 4 ALA B 116 ASN B 120 -1 O TYR B 117 N LEU B 31 SHEET 1 AA6 2 ILE B 192 ASP B 199 0 SHEET 2 AA6 2 ALA B 207 PHE B 212 -1 O ALA B 207 N ASP B 199 LINK C ALA A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ALA A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N GLY A 41 1555 1555 1.32 LINK C LEU A 45 N MSE A 46 1555 1555 1.32 LINK C MSE A 46 N GLY A 47 1555 1555 1.33 LINK C TYR A 74 N MSE A 75 1555 1555 1.34 LINK C MSE A 75 N GLU A 76 1555 1555 1.33 LINK C GLU A 133 N MSE A 134 1555 1555 1.33 LINK C MSE A 134 N VAL A 135 1555 1555 1.32 LINK C GLU A 140 N MSE A 141 1555 1555 1.32 LINK C MSE A 141 N MSE A 142 1555 1555 1.32 LINK C MSE A 142 N LYS A 143 1555 1555 1.32 LINK C PRO A 176 N MSE A 177 1555 1555 1.32 LINK C MSE A 177 N ASP A 178 1555 1555 1.32 LINK C GLU A 188 N MSE A 189 1555 1555 1.32 LINK C MSE A 189 N ASP A 190 1555 1555 1.32 LINK C ALA B 39 N MSE B 40 1555 1555 1.33 LINK C MSE B 40 N GLY B 41 1555 1555 1.32 LINK C LEU B 45 N MSE B 46 1555 1555 1.32 LINK C MSE B 46 N GLY B 47 1555 1555 1.32 LINK C TYR B 74 N MSE B 75 1555 1555 1.33 LINK C MSE B 75 N GLU B 76 1555 1555 1.33 LINK C GLU B 133 N MSE B 134 1555 1555 1.34 LINK C MSE B 134 N VAL B 135 1555 1555 1.32 LINK C GLU B 140 N MSE B 141 1555 1555 1.32 LINK C MSE B 141 N MSE B 142 1555 1555 1.32 LINK C MSE B 142 N LYS B 143 1555 1555 1.33 LINK C PRO B 176 N MSE B 177 1555 1555 1.33 LINK C MSE B 177 N ASP B 178 1555 1555 1.33 LINK C GLU B 188 N MSE B 189 1555 1555 1.33 LINK C MSE B 189 N ASP B 190 1555 1555 1.33 CISPEP 1 GLU A 37 PRO A 38 0 -1.98 CISPEP 2 GLU B 37 PRO B 38 0 -0.15 SITE 1 AC1 5 ASP A 16 ARG A 86 ASP A 87 VAL A 92 SITE 2 AC1 5 HIS A 131 SITE 1 AC2 1 LYS A 137 SITE 1 AC3 2 ASP A 57 LYS B 137 SITE 1 AC4 5 ASP B 16 ARG B 86 ASP B 87 VAL B 92 SITE 2 AC4 5 HIS B 131 CRYST1 163.017 163.017 163.017 90.00 90.00 90.00 P 2 3 24 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 0.006134 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006134 0.00000 CONECT 3 6 CONECT 6 3 7 CONECT 7 6 8 10 CONECT 8 7 9 14 CONECT 9 8 CONECT 10 7 11 CONECT 11 10 12 CONECT 12 11 13 CONECT 13 12 CONECT 14 8 CONECT 317 320 CONECT 320 317 321 CONECT 321 320 322 324 CONECT 322 321 323 328 CONECT 323 322 CONECT 324 321 325 CONECT 325 324 326 CONECT 326 325 327 CONECT 327 326 CONECT 328 322 CONECT 363 369 CONECT 369 363 370 CONECT 370 369 371 373 CONECT 371 370 372 377 CONECT 372 371 CONECT 373 370 374 CONECT 374 373 375 CONECT 375 374 376 CONECT 376 375 CONECT 377 371 CONECT 579 589 CONECT 589 579 590 CONECT 590 589 591 593 CONECT 591 590 592 597 CONECT 592 591 CONECT 593 590 594 CONECT 594 593 595 CONECT 595 594 596 CONECT 596 595 CONECT 597 591 CONECT 1064 1071 CONECT 1071 1064 1072 CONECT 1072 1071 1073 1075 CONECT 1073 1072 1074 1079 CONECT 1074 1073 CONECT 1075 1072 1076 CONECT 1076 1075 1077 CONECT 1077 1076 1078 CONECT 1078 1077 CONECT 1079 1073 CONECT 1121 1128 CONECT 1128 1121 1129 CONECT 1129 1128 1130 1132 CONECT 1130 1129 1131 1136 CONECT 1131 1130 CONECT 1132 1129 1133 CONECT 1133 1132 1134 CONECT 1134 1133 1135 CONECT 1135 1134 CONECT 1136 1130 1137 CONECT 1137 1136 1138 1140 CONECT 1138 1137 1139 1144 CONECT 1139 1138 CONECT 1140 1137 1141 CONECT 1141 1140 1142 CONECT 1142 1141 1143 CONECT 1143 1142 CONECT 1144 1138 CONECT 1409 1414 CONECT 1414 1409 1415 CONECT 1415 1414 1416 1418 CONECT 1416 1415 1417 1422 CONECT 1417 1416 CONECT 1418 1415 1419 CONECT 1419 1418 1420 CONECT 1420 1419 1421 CONECT 1421 1420 CONECT 1422 1416 CONECT 1514 1521 CONECT 1521 1514 1522 CONECT 1522 1521 1523 1525 CONECT 1523 1522 1524 1529 CONECT 1524 1523 CONECT 1525 1522 1526 CONECT 1526 1525 1527 CONECT 1527 1526 1528 CONECT 1528 1527 CONECT 1529 1523 CONECT 2118 2121 CONECT 2121 2118 2122 CONECT 2122 2121 2123 2125 CONECT 2123 2122 2124 2129 CONECT 2124 2123 CONECT 2125 2122 2126 CONECT 2126 2125 2127 CONECT 2127 2126 2128 CONECT 2128 2127 CONECT 2129 2123 CONECT 2164 2170 CONECT 2170 2164 2171 CONECT 2171 2170 2172 2174 CONECT 2172 2171 2173 2178 CONECT 2173 2172 CONECT 2174 2171 2175 CONECT 2175 2174 2176 CONECT 2176 2175 2177 CONECT 2177 2176 CONECT 2178 2172 CONECT 2380 2390 CONECT 2390 2380 2391 CONECT 2391 2390 2392 2394 CONECT 2392 2391 2393 2398 CONECT 2393 2392 CONECT 2394 2391 2395 CONECT 2395 2394 2396 CONECT 2396 2395 2397 CONECT 2397 2396 CONECT 2398 2392 CONECT 2865 2872 CONECT 2872 2865 2873 CONECT 2873 2872 2874 2876 CONECT 2874 2873 2875 2880 CONECT 2875 2874 CONECT 2876 2873 2877 CONECT 2877 2876 2878 CONECT 2878 2877 2879 CONECT 2879 2878 CONECT 2880 2874 CONECT 2922 2929 CONECT 2929 2922 2930 CONECT 2930 2929 2931 2933 CONECT 2931 2930 2932 2937 CONECT 2932 2931 CONECT 2933 2930 2934 CONECT 2934 2933 2935 CONECT 2935 2934 2936 CONECT 2936 2935 CONECT 2937 2931 2938 CONECT 2938 2937 2939 2941 CONECT 2939 2938 2940 2945 CONECT 2940 2939 CONECT 2941 2938 2942 CONECT 2942 2941 2943 CONECT 2943 2942 2944 CONECT 2944 2943 CONECT 2945 2939 CONECT 3210 3215 CONECT 3215 3210 3216 CONECT 3216 3215 3217 3219 CONECT 3217 3216 3218 3223 CONECT 3218 3217 CONECT 3219 3216 3220 CONECT 3220 3219 3221 CONECT 3221 3220 3222 CONECT 3222 3221 CONECT 3223 3217 CONECT 3315 3322 CONECT 3322 3315 3323 CONECT 3323 3322 3324 3326 CONECT 3324 3323 3325 3330 CONECT 3325 3324 CONECT 3326 3323 3327 CONECT 3327 3326 3328 CONECT 3328 3327 3329 CONECT 3329 3328 CONECT 3330 3324 CONECT 4731 4732 4733 4734 CONECT 4732 4731 CONECT 4733 4731 CONECT 4734 4731 4735 CONECT 4735 4734 4736 4737 CONECT 4736 4735 CONECT 4737 4735 CONECT 4738 4739 4740 CONECT 4739 4738 CONECT 4740 4738 CONECT 4741 4742 4743 CONECT 4742 4741 CONECT 4743 4741 CONECT 4744 4745 4746 4747 CONECT 4745 4744 CONECT 4746 4744 CONECT 4747 4744 4748 CONECT 4748 4747 4749 4750 CONECT 4749 4748 CONECT 4750 4748 MASTER 345 0 21 17 22 0 6 6 4762 4 186 42 END