HEADER TRANSFERASE 29-AUG-16 5GUJ TITLE CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS DNAG RNA POLYMERASE DOMAIN, TITLE 2 NATURAL DEGRADATION OF FULL LENGTH DNAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 112-435; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: DNAG, DNAE, BSU25210; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHOU,Z.LIU,G.WANG REVDAT 2 08-NOV-23 5GUJ 1 REMARK REVDAT 1 19-APR-17 5GUJ 0 JRNL AUTH Y.ZHOU,H.LUO,Z.LIU,M.YANG,X.PANG,F.SUN,G.WANG JRNL TITL STRUCTURAL INSIGHT INTO THE SPECIFIC DNA TEMPLATE BINDING TO JRNL TITL 2 DNAG PRIMASE IN BACTERIA JRNL REF SCI REP V. 7 659 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28386108 JRNL DOI 10.1038/S41598-017-00767-8 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 13069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 606 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 29.2805 - 3.9640 1.00 3271 163 0.1678 0.1894 REMARK 3 2 3.9640 - 3.1476 1.00 3211 157 0.1856 0.2587 REMARK 3 3 3.1476 - 2.7500 1.00 3189 144 0.2269 0.3155 REMARK 3 4 2.7500 - 2.4987 0.88 2792 142 0.2156 0.2759 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 2651 REMARK 3 ANGLE : 0.897 3555 REMARK 3 CHIRALITY : 0.049 384 REMARK 3 PLANARITY : 0.005 456 REMARK 3 DIHEDRAL : 21.976 1607 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 5GUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.278 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 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: 4E2K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE TRIBASIC REMARK 280 DEHYDRATE, 0.1M TRIS HYDROCHLORIDE (PH 8.5) AND 30% (W/V) REMARK 280 POLYETHYLENE GLYCOL 400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.28600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.57200 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 24.42900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.71500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.14300 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 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: 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 OD1 ASP A 195 OG SER A 197 2.07 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 GLU A 194 -37.61 -39.18 REMARK 500 ALA A 220 -174.32 -170.45 REMARK 500 GLU A 283 40.65 -76.55 REMARK 500 ASP A 342 -143.01 64.47 REMARK 500 ILE A 362 -61.76 -104.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GUM RELATED DB: PDB DBREF 5GUJ A 112 435 UNP P05096 DNAG_BACSU 112 435 SEQRES 1 A 324 SER GLY GLU GLN LYS MET ALA GLU ALA HIS GLU LEU LEU SEQRES 2 A 324 LYS LYS PHE TYR HIS HIS LEU LEU ILE ASN THR LYS GLU SEQRES 3 A 324 GLY GLN GLU ALA LEU ASP TYR LEU LEU SER ARG GLY PHE SEQRES 4 A 324 THR LYS GLU LEU ILE ASN GLU PHE GLN ILE GLY TYR ALA SEQRES 5 A 324 LEU ASP SER TRP ASP PHE ILE THR LYS PHE LEU VAL LYS SEQRES 6 A 324 ARG GLY PHE SER GLU ALA GLN MET GLU LYS ALA GLY LEU SEQRES 7 A 324 LEU ILE ARG ARG GLU ASP GLY SER GLY TYR PHE ASP ARG SEQRES 8 A 324 PHE ARG ASN ARG VAL MET PHE PRO ILE HIS ASP HIS HIS SEQRES 9 A 324 GLY ALA VAL VAL ALA PHE SER GLY ARG ALA LEU GLY SER SEQRES 10 A 324 GLN GLN PRO LYS TYR MET ASN SER PRO GLU THR PRO LEU SEQRES 11 A 324 PHE HIS LYS SER LYS LEU LEU TYR ASN PHE TYR LYS ALA SEQRES 12 A 324 ARG LEU HIS ILE ARG LYS GLN GLU ARG ALA VAL LEU PHE SEQRES 13 A 324 GLU GLY PHE ALA ASP VAL ILE SER ALA VAL SER SER ASP SEQRES 14 A 324 VAL LYS GLU SER ILE ALA THR MET GLY THR SER LEU THR SEQRES 15 A 324 ASP ASP HIS VAL LYS ILE LEU ARG ARG ASN VAL GLU GLU SEQRES 16 A 324 ILE ILE LEU CYS TYR ASP SER ASP LYS ALA GLY TYR GLU SEQRES 17 A 324 ALA THR LEU LYS ALA SER GLU LEU LEU GLN LYS LYS GLY SEQRES 18 A 324 CYS LYS VAL ARG VAL ALA MET ILE PRO ASP GLY LEU ASP SEQRES 19 A 324 PRO ASP ASP TYR ILE LYS LYS PHE GLY GLY GLU LYS PHE SEQRES 20 A 324 LYS ASN ASP ILE ILE ASP ALA SER VAL THR VAL MET ALA SEQRES 21 A 324 PHE LYS MET GLN TYR PHE ARG LYS GLY LYS ASN LEU SER SEQRES 22 A 324 ASP GLU GLY ASP ARG LEU ALA TYR ILE LYS ASP VAL LEU SEQRES 23 A 324 LYS GLU ILE SER THR LEU SER GLY SER LEU GLU GLN GLU SEQRES 24 A 324 VAL TYR VAL LYS GLN LEU ALA SER GLU PHE SER LEU SER SEQRES 25 A 324 GLN GLU SER LEU THR GLU GLN LEU SER VAL PHE SER FORMUL 2 HOH *76(H2 O) HELIX 1 AA1 SER A 112 THR A 135 1 24 HELIX 2 AA2 GLU A 137 SER A 147 1 11 HELIX 3 AA3 THR A 151 GLN A 159 1 9 HELIX 4 AA4 ASP A 168 ARG A 177 1 10 HELIX 5 AA5 SER A 180 ALA A 187 1 8 HELIX 6 AA6 ASN A 250 GLU A 262 1 13 HELIX 7 AA7 GLY A 269 SER A 279 1 11 HELIX 8 AA8 THR A 293 VAL A 304 1 12 HELIX 9 AA9 ASP A 314 LYS A 331 1 18 HELIX 10 AB1 ASP A 345 GLY A 354 1 10 HELIX 11 AB2 GLY A 354 ILE A 362 1 9 HELIX 12 AB3 VAL A 369 PHE A 377 1 9 HELIX 13 AB4 ASP A 385 SER A 401 1 17 HELIX 14 AB5 GLY A 405 SER A 421 1 17 HELIX 15 AB6 SER A 423 SER A 435 1 13 SHEET 1 AA1 4 GLY A 161 ALA A 163 0 SHEET 2 AA1 4 ARG A 206 HIS A 212 -1 O MET A 208 N GLY A 161 SHEET 3 AA1 4 VAL A 218 ALA A 225 -1 O SER A 222 N PHE A 209 SHEET 4 AA1 4 TYR A 233 ASN A 235 -1 O MET A 234 N GLY A 223 SHEET 1 AA2 2 LEU A 190 ARG A 192 0 SHEET 2 AA2 2 TYR A 199 ASP A 201 -1 O PHE A 200 N ILE A 191 SHEET 1 AA3 5 SER A 284 THR A 287 0 SHEET 2 AA3 5 ARG A 263 GLU A 268 1 N PHE A 267 O ILE A 285 SHEET 3 AA3 5 GLU A 306 LEU A 309 1 O ILE A 308 N LEU A 266 SHEET 4 AA3 5 LYS A 334 VAL A 337 1 O LYS A 334 N ILE A 307 SHEET 5 AA3 5 VAL A 367 THR A 368 -1 O VAL A 367 N VAL A 337 CISPEP 1 GLN A 230 PRO A 231 0 -4.04 CRYST1 117.114 117.114 48.858 90.00 90.00 120.00 P 61 6 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 0.008539 0.004930 0.000000 0.00000 SCALE2 0.000000 0.009860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020467 0.00000