HEADER UNKNOWN FUNCTION 23-AUG-18 6M9M TITLE STREPTOCOCCUS MUTANS ALKD2 BOUND TO INOSINE-5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKD2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MUTANS; SOURCE 3 ORGANISM_TAXID: 1309; SOURCE 4 GENE: ALKD2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEAT-LIKE REPEAT, NUCLEOTIDE BINDING, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR B.F.EICHMAN,R.SHI REVDAT 4 11-OCT-23 6M9M 1 REMARK REVDAT 3 27-NOV-19 6M9M 1 REMARK REVDAT 2 31-OCT-18 6M9M 1 COMPND JRNL REVDAT 1 10-OCT-18 6M9M 0 JRNL AUTH R.SHI,X.X.SHEN,A.ROKAS,B.F.EICHMAN JRNL TITL STRUCTURAL BIOLOGY OF THE HEAT-LIKE REPEAT FAMILY OF DNA JRNL TITL 2 GLYCOSYLASES. JRNL REF BIOESSAYS V. 40 00133 2018 JRNL REFN ESSN 1521-1878 JRNL PMID 30264543 JRNL DOI 10.1002/BIES.201800133 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 48954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.4124 - 3.3737 0.96 3461 159 0.1548 0.2003 REMARK 3 2 3.3737 - 2.6785 1.00 3490 142 0.1419 0.1703 REMARK 3 3 2.6785 - 2.3401 1.00 3418 144 0.1349 0.1506 REMARK 3 4 2.3401 - 2.1262 0.90 3087 126 0.1355 0.1745 REMARK 3 5 2.1262 - 1.9738 1.00 3410 141 0.1355 0.1830 REMARK 3 6 1.9738 - 1.8575 0.99 3353 138 0.1521 0.1888 REMARK 3 7 1.8575 - 1.7645 1.00 3397 145 0.1267 0.1631 REMARK 3 8 1.7645 - 1.6877 1.00 3365 150 0.1156 0.1448 REMARK 3 9 1.6877 - 1.6227 0.99 3317 147 0.1019 0.1314 REMARK 3 10 1.6227 - 1.5667 1.00 3395 135 0.1062 0.1403 REMARK 3 11 1.5667 - 1.5177 0.99 3312 149 0.1057 0.1632 REMARK 3 12 1.5177 - 1.4744 0.99 3304 153 0.1113 0.1618 REMARK 3 13 1.4744 - 1.4356 0.99 3341 129 0.1190 0.1724 REMARK 3 14 1.4356 - 1.4005 0.99 3309 137 0.1339 0.1950 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6M9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49016 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4X8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (W/V) PEG 3350, 200 MM SODIUM REMARK 280 PHOSPHATE, PH 4.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.07600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.77300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.52050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.77300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.07600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.52050 REMARK 290 SMTRY3 4 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 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 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 PHE A 19 -3.76 -143.42 REMARK 500 TYR A 137 -59.04 74.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 831 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 832 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 833 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 834 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 835 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 836 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 837 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A 838 DISTANCE = 7.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 302 DBREF1 6M9M A 0 206 UNP A0A0M3KL00_STRMG DBREF2 6M9M A A0A0M3KL00 4 210 SEQRES 1 A 207 SER MET LYS GLN TYR VAL ALA ARG LEU GLU LYS ASP PHE SEQRES 2 A 207 SER LEU ILE GLU HIS GLY PHE LYS GLU GLU GLU GLN ARG SEQRES 3 A 207 ALA LEU THR ASP TYR LYS SER ASN ASP GLY GLU TYR ILE SEQRES 4 A 207 LYS LYS LEU ALA PHE LEU ALA TYR GLN SER ASP VAL TYR SEQRES 5 A 207 GLN VAL ARG MET TYR ALA VAL PHE LEU PHE GLY TYR LEU SEQRES 6 A 207 SER LYS ASP LYS GLU ILE LEU ILE PHE MET ARG ASP GLU SEQRES 7 A 207 VAL SER LYS ASP ASN ASN TRP ARG VAL GLN GLU VAL LEU SEQRES 8 A 207 ALA LYS ALA PHE ASP GLU PHE CYS LYS LYS ILE GLY TYR SEQRES 9 A 207 LYS LYS ALA LEU PRO ILE ILE ASP GLU TRP LEU LYS SER SEQRES 10 A 207 SER ASN LEU HIS THR ARG ARG ALA ALA THR GLU GLY LEU SEQRES 11 A 207 ARG ILE TRP THR ASN ARG PRO TYR PHE LYS GLU ASN PRO SEQRES 12 A 207 ASN GLU ALA ILE ARG ARG ILE ALA ASP LEU LYS GLU ASP SEQRES 13 A 207 VAL SER GLU TYR VAL ARG LYS SER VAL GLY ASN ALA LEU SEQRES 14 A 207 ARG ASP ILE SER LYS LYS PHE PRO ASP LEU VAL LYS ILE SEQRES 15 A 207 GLU LEU LYS ASN TRP LYS LEU GLU SER LYS GLU ILE ASN SEQRES 16 A 207 GLN VAL TYR LYS LEU ALA SER LYS PHE ILE ASP ALA HET IMP A 301 33 HET CL A 302 1 HETNAM IMP INOSINIC ACID HETNAM CL CHLORIDE ION FORMUL 2 IMP C10 H13 N4 O8 P FORMUL 3 CL CL 1- FORMUL 4 HOH *438(H2 O) HELIX 1 AA1 SER A 0 SER A 13 1 14 HELIX 2 AA2 PHE A 19 SER A 32 1 14 HELIX 3 AA3 ASP A 34 GLN A 47 1 14 HELIX 4 AA4 VAL A 50 SER A 65 1 16 HELIX 5 AA5 ASP A 67 GLU A 77 1 11 HELIX 6 AA6 VAL A 78 ASP A 81 5 4 HELIX 7 AA7 ASN A 83 GLY A 102 1 20 HELIX 8 AA8 ALA A 106 LYS A 115 1 10 HELIX 9 AA9 ASN A 118 LEU A 129 1 12 HELIX 10 AB1 ILE A 131 ARG A 135 5 5 HELIX 11 AB2 ASN A 141 ASP A 151 1 11 HELIX 12 AB3 SER A 157 PHE A 175 1 19 HELIX 13 AB4 PHE A 175 ASN A 185 1 11 HELIX 14 AB5 SER A 190 SER A 201 1 12 CISPEP 1 ARG A 130 ILE A 131 0 -7.03 SITE 1 AC1 8 HIS A 17 GLY A 18 TRP A 84 ARG A 85 SITE 2 AC1 8 HOH A 403 HOH A 413 HOH A 422 HOH A 507 SITE 1 AC2 5 ILE A 131 ASN A 134 ARG A 135 HOH A 700 SITE 2 AC2 5 HOH A 727 CRYST1 60.152 63.041 65.546 90.00 90.00 90.00 P 21 21 21 4 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 0.016625 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015256 0.00000