HEADER HYDROLASE 29-OCT-18 6IOA TITLE THE STRUCTURE OF UDGX IN COMPLEX WITH URACIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE SPO1 DNA POLYMERASE-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 7-215; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 GENE: MSMEI_0259; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS URACIL DNA GLYCOSYLASE, DNA REPAIR, IRON-SULFUR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,J.TU REVDAT 2 22-NOV-23 6IOA 1 REMARK REVDAT 1 24-JUL-19 6IOA 0 JRNL AUTH J.TU,R.CHEN,Y.YANG,W.CAO,W.XIE JRNL TITL SUICIDE INACTIVATION OF THE URACIL DNA GLYCOSYLASE UDGX BY JRNL TITL 2 COVALENT COMPLEX FORMATION. JRNL REF NAT.CHEM.BIOL. V. 15 615 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31101915 JRNL DOI 10.1038/S41589-019-0290-X REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 10151 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 500 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.1610 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.2060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : 0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.245 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.076 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1572 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1503 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2138 ; 2.116 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3436 ; 1.922 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 206 ; 6.352 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 65 ;32.333 ;22.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 235 ;13.715 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;14.366 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 247 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1794 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 344 ; 0.015 ; 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): 827 ; 1.365 ; 1.233 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 826 ; 1.366 ; 1.231 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1032 ; 2.261 ; 1.841 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1033 ; 2.261 ; 1.843 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 745 ; 1.850 ; 1.342 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 742 ; 1.836 ; 1.330 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1089 ; 2.930 ; 1.949 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1752 ; 4.588 ;10.071 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1753 ; 4.634 ;10.076 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 6IOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10655 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 24.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6IO9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MES PH 5.6, 2.45M (NH4)2SO4 AND REMARK 280 0.1M MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.72400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ARG A 208 REMARK 465 PRO A 209 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 MET A 1 CG SD CE REMARK 470 HIS A 10 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ASP A 166 CG OD1 OD2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 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 O HOH A 475 O HOH A 505 2255 2.19 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 ASP A 83 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = 3.4 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 ASP A 166 -15.68 -48.08 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 SF4 A 301 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 24 SG REMARK 620 2 SF4 A 301 S1 123.4 REMARK 620 3 SF4 A 301 S3 118.5 97.4 REMARK 620 4 SF4 A 301 S4 111.0 102.2 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 27 SG REMARK 620 2 SF4 A 301 S1 124.7 REMARK 620 3 SF4 A 301 S2 106.9 99.2 REMARK 620 4 SF4 A 301 S3 123.0 98.1 100.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 SF4 A 301 S1 112.3 REMARK 620 3 SF4 A 301 S2 124.3 100.0 REMARK 620 4 SF4 A 301 S4 114.9 101.6 100.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 301 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 SF4 A 301 S2 122.6 REMARK 620 3 SF4 A 301 S3 115.1 98.0 REMARK 620 4 SF4 A 301 S4 119.8 97.6 99.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue URA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 DBREF 6IOA A 1 209 UNP I7F541 I7F541_MYCS2 7 215 SEQADV 6IOA MET A -19 UNP I7F541 INITIATING METHIONINE SEQADV 6IOA GLY A -18 UNP I7F541 EXPRESSION TAG SEQADV 6IOA SER A -17 UNP I7F541 EXPRESSION TAG SEQADV 6IOA SER A -16 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -15 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -14 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -13 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -12 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -11 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A -10 UNP I7F541 EXPRESSION TAG SEQADV 6IOA SER A -9 UNP I7F541 EXPRESSION TAG SEQADV 6IOA SER A -8 UNP I7F541 EXPRESSION TAG SEQADV 6IOA GLY A -7 UNP I7F541 EXPRESSION TAG SEQADV 6IOA LEU A -6 UNP I7F541 EXPRESSION TAG SEQADV 6IOA VAL A -5 UNP I7F541 EXPRESSION TAG SEQADV 6IOA PRO A -4 UNP I7F541 EXPRESSION TAG SEQADV 6IOA ARG A -3 UNP I7F541 EXPRESSION TAG SEQADV 6IOA GLY A -2 UNP I7F541 EXPRESSION TAG SEQADV 6IOA SER A -1 UNP I7F541 EXPRESSION TAG SEQADV 6IOA HIS A 0 UNP I7F541 EXPRESSION TAG SEQRES 1 A 229 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 229 LEU VAL PRO ARG GLY SER HIS MET ALA GLY ALA GLN ASP SEQRES 3 A 229 PHE VAL PRO HIS THR ALA ASP LEU ALA GLU LEU ALA ALA SEQRES 4 A 229 ALA ALA GLY GLU CYS ARG GLY CYS GLY LEU TYR ARG ASP SEQRES 5 A 229 ALA THR GLN ALA VAL PHE GLY ALA GLY GLY ARG SER ALA SEQRES 6 A 229 ARG ILE MET MET ILE GLY GLU GLN PRO GLY ASP LYS GLU SEQRES 7 A 229 ASP LEU ALA GLY LEU PRO PHE VAL GLY PRO ALA GLY ARG SEQRES 8 A 229 LEU LEU ASP ARG ALA LEU GLU ALA ALA ASP ILE ASP ARG SEQRES 9 A 229 ASP ALA LEU TYR VAL THR ASN ALA VAL LYS HIS PHE LYS SEQRES 10 A 229 PHE THR ARG ALA ALA GLY GLY LYS ARG ARG ILE HIS LYS SEQRES 11 A 229 THR PRO SER ARG THR GLU VAL VAL ALA CYS ARG PRO TRP SEQRES 12 A 229 LEU ILE ALA GLU MET THR SER VAL GLU PRO ASP VAL VAL SEQRES 13 A 229 VAL LEU LEU GLY ALA THR ALA ALA LYS ALA LEU LEU GLY SEQRES 14 A 229 ASN ASP PHE ARG VAL THR GLN HIS ARG GLY GLU VAL LEU SEQRES 15 A 229 HIS VAL ASP ASP VAL PRO GLY ASP PRO ALA LEU VAL ALA SEQRES 16 A 229 THR VAL HIS PRO SER SER LEU LEU ARG GLY PRO LYS GLU SEQRES 17 A 229 GLU ARG GLU SER ALA PHE ALA GLY LEU VAL ASP ASP LEU SEQRES 18 A 229 ARG VAL ALA ALA ASP VAL ARG PRO HET SF4 A 301 8 HET URA A 302 8 HET SO4 A 303 5 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM URA URACIL HETNAM SO4 SULFATE ION FORMUL 2 SF4 FE4 S4 FORMUL 3 URA C4 H4 N2 O2 FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *115(H2 O) HELIX 1 AA1 ALA A 2 VAL A 8 5 7 HELIX 2 AA2 ASP A 13 GLU A 23 1 11 HELIX 3 AA3 CYS A 27 ARG A 31 5 5 HELIX 4 AA4 GLY A 55 GLY A 62 1 8 HELIX 5 AA5 GLY A 67 ALA A 80 1 14 HELIX 6 AA6 ASP A 83 LEU A 87 5 5 HELIX 7 AA7 SER A 113 GLU A 132 1 20 HELIX 8 AA8 GLY A 140 GLY A 149 1 10 HELIX 9 AA9 ARG A 153 HIS A 157 5 5 HELIX 10 AB1 HIS A 178 LEU A 183 5 6 HELIX 11 AB2 PRO A 186 ASP A 206 1 21 SHEET 1 AA1 4 TYR A 88 ASN A 91 0 SHEET 2 AA1 4 ILE A 47 GLY A 51 1 N MET A 49 O THR A 90 SHEET 3 AA1 4 VAL A 135 LEU A 139 1 O VAL A 137 N MET A 48 SHEET 4 AA1 4 ALA A 172 THR A 176 1 O VAL A 174 N LEU A 138 SHEET 1 AA2 2 PHE A 98 THR A 99 0 SHEET 2 AA2 2 ILE A 108 HIS A 109 -1 O ILE A 108 N THR A 99 LINK SG CYS A 24 FE2 SF4 A 301 1555 1555 2.30 LINK SG CYS A 27 FE4 SF4 A 301 1555 1555 2.29 LINK ND1 HIS A 95 FE3 SF4 A 301 1555 1555 1.90 LINK SG CYS A 120 FE1 SF4 A 301 1555 1555 2.24 SITE 1 AC1 5 CYS A 24 GLY A 26 CYS A 27 HIS A 95 SITE 2 AC1 5 CYS A 120 SITE 1 AC2 9 GLU A 52 GLN A 53 GLU A 58 PRO A 64 SITE 2 AC2 9 PHE A 65 ASN A 91 HIS A 178 SO4 A 303 SITE 3 AC2 9 HOH A 455 SITE 1 AC3 9 PRO A 68 ALA A 69 SER A 180 LEU A 183 SITE 2 AC3 9 URA A 302 HOH A 403 HOH A 432 HOH A 452 SITE 3 AC3 9 HOH A 455 CRYST1 36.407 51.448 55.430 90.00 105.48 90.00 P 1 21 1 2 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 0.027467 0.000000 0.007606 0.00000 SCALE2 0.000000 0.019437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018720 0.00000