PDB Short entry for 4LIK HEADER TRANSFERASE 02-JUL-13 4LIK TITLE CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF HUMAN PRIMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE SMALL SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC SUBUNIT P48, UNP RESIDUES 1-390 (DELTA 360-379); COMPND 5 SYNONYM: DNA PRIMASE 49 KDA SUBUNIT, P49; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRIM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRIM FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.VAITHIYALINGAM,B.F.EICHMAN,W.J.CHAZIN REVDAT 2 05-FEB-14 4LIK 1 JRNL REVDAT 1 11-DEC-13 4LIK 0 JRNL AUTH S.VAITHIYALINGAM,D.R.ARNETT,A.AGGARWAL,B.F.EICHMAN, JRNL AUTH 2 E.FANNING,W.J.CHAZIN JRNL TITL INSIGHTS INTO EUKARYOTIC PRIMER SYNTHESIS FROM STRUCTURES OF JRNL TITL 2 THE P48 SUBUNIT OF HUMAN DNA PRIMASE. JRNL REF J.MOL.BIOL. V. 426 558 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 24239947 JRNL DOI 10.1016/J.JMB.2013.11.007 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 56577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2865 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 30.4039 - 4.6000 0.97 2713 153 0.1919 0.2159 REMARK 3 2 4.6000 - 3.6531 0.99 2713 152 0.1471 0.1520 REMARK 3 3 3.6531 - 3.1919 0.99 2760 132 0.1622 0.1962 REMARK 3 4 3.1919 - 2.9003 1.00 2734 144 0.1789 0.1947 REMARK 3 5 2.9003 - 2.6926 1.00 2709 154 0.1759 0.1881 REMARK 3 6 2.6926 - 2.5339 1.00 2748 145 0.1818 0.2026 REMARK 3 7 2.5339 - 2.4071 1.00 2685 159 0.1761 0.1991 REMARK 3 8 2.4071 - 2.3023 1.00 2755 111 0.1715 0.2068 REMARK 3 9 2.3023 - 2.2137 1.00 2750 132 0.1682 0.1882 REMARK 3 10 2.2137 - 2.1373 1.00 2718 156 0.1722 0.2057 REMARK 3 11 2.1373 - 2.0705 1.00 2679 149 0.1711 0.2335 REMARK 3 12 2.0705 - 2.0114 1.00 2711 151 0.1758 0.1983 REMARK 3 13 2.0114 - 1.9584 1.00 2714 151 0.1859 0.2102 REMARK 3 14 1.9584 - 1.9106 1.00 2731 148 0.1829 0.2180 REMARK 3 15 1.9106 - 1.8672 1.00 2707 159 0.1870 0.2249 REMARK 3 16 1.8672 - 1.8275 1.00 2668 152 0.1854 0.2186 REMARK 3 17 1.8275 - 1.7909 1.00 2725 131 0.1985 0.2630 REMARK 3 18 1.7909 - 1.7571 0.99 2693 135 0.2093 0.2306 REMARK 3 19 1.7571 - 1.7258 0.93 2525 125 0.2219 0.2335 REMARK 3 20 1.7258 - 1.7000 0.83 2274 126 0.2306 0.2589 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.120 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 : 0.009 3261 REMARK 3 ANGLE : 1.235 4423 REMARK 3 CHIRALITY : 0.088 469 REMARK 3 PLANARITY : 0.006 566 REMARK 3 DIHEDRAL : 14.352 1271 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain 'A' and (resid 1 through 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.2154 11.0953 64.4321 REMARK 3 T TENSOR REMARK 3 T11: 0.3053 T22: 0.2130 REMARK 3 T33: 0.1506 T12: 0.0853 REMARK 3 T13: -0.0485 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.0416 L22: 0.3152 REMARK 3 L33: 0.0965 L12: -0.0481 REMARK 3 L13: -0.0147 L23: 0.1702 REMARK 3 S TENSOR REMARK 3 S11: 0.1664 S12: 0.0800 S13: -0.0086 REMARK 3 S21: -0.5268 S22: -0.1168 S23: 0.0051 REMARK 3 S31: -0.2628 S32: -0.2574 S33: -0.0041 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain 'A' and (resid 20 through 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.2689 2.6937 72.3087 REMARK 3 T TENSOR REMARK 3 T11: 0.1348 T22: 0.0983 REMARK 3 T33: 0.1191 T12: -0.0219 REMARK 3 T13: 0.0091 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.4944 L22: 0.6533 REMARK 3 L33: 0.2784 L12: -0.2987 REMARK 3 L13: -0.3132 L23: 0.1239 REMARK 3 S TENSOR REMARK 3 S11: 0.0243 S12: 0.0253 S13: -0.0313 REMARK 3 S21: -0.2851 S22: 0.0071 S23: -0.1263 REMARK 3 S31: -0.0589 S32: -0.0005 S33: 0.0012 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: chain 'A' and (resid 94 through 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.7013 -5.3777 84.8462 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.1631 REMARK 3 T33: 0.1495 T12: -0.0787 REMARK 3 T13: 0.0718 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 0.8661 L22: 0.1110 REMARK 3 L33: -0.1021 L12: -0.1166 REMARK 3 L13: -0.1731 L23: -0.1484 REMARK 3 S TENSOR REMARK 3 S11: -0.5281 S12: -0.6272 S13: -0.1899 REMARK 3 S21: 0.0011 S22: 0.2336 S23: -0.0262 REMARK 3 S31: 0.3721 S32: -0.1582 S33: -0.1394 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: chain 'A' and (resid 119 through 148 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0919 4.4652 91.3725 REMARK 3 T TENSOR REMARK 3 T11: 0.1355 T22: 0.2983 REMARK 3 T33: 0.1656 T12: -0.0116 REMARK 3 T13: 0.0196 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.1247 L22: 0.0745 REMARK 3 L33: 0.3128 L12: 0.0515 REMARK 3 L13: -0.2259 L23: -0.1179 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: -0.1678 S13: 0.1746 REMARK 3 S21: 0.0718 S22: 0.0428 S23: 0.1328 REMARK 3 S31: -0.0564 S32: -0.3610 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: chain 'A' and (resid 149 through 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6614 1.4402 91.1382 REMARK 3 T TENSOR REMARK 3 T11: 0.1350 T22: 0.1476 REMARK 3 T33: 0.1096 T12: -0.0126 REMARK 3 T13: -0.0008 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.2743 L22: 0.3670 REMARK 3 L33: 0.4376 L12: 0.0777 REMARK 3 L13: -0.3095 L23: -0.2852 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: 0.0025 S13: -0.0552 REMARK 3 S21: 0.0289 S22: 0.0211 S23: 0.0028 REMARK 3 S31: 0.1040 S32: -0.0126 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: chain 'A' and (resid 190 through 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.3186 -2.4811 102.2067 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.3428 REMARK 3 T33: 0.1490 T12: -0.0779 REMARK 3 T13: 0.0473 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 1.5200 L22: 2.3465 REMARK 3 L33: 2.3346 L12: 0.9573 REMARK 3 L13: 0.4923 L23: -0.3580 REMARK 3 S TENSOR REMARK 3 S11: 0.0042 S12: -0.3833 S13: 0.1746 REMARK 3 S21: 0.2505 S22: 0.0409 S23: 0.1696 REMARK 3 S31: -0.1665 S32: -0.6224 S33: -0.0434 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: chain 'A' and (resid 228 through 276 ) REMARK 3 ORIGIN FOR THE GROUP (A): -48.4614 -3.8917 103.5126 REMARK 3 T TENSOR REMARK 3 T11: 0.7219 T22: 1.4517 REMARK 3 T33: 1.0815 T12: -0.3666 REMARK 3 T13: 0.4596 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 2.0993 L22: 1.8789 REMARK 3 L33: 1.4435 L12: -0.8752 REMARK 3 L13: 0.2372 L23: 0.4439 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: -0.5126 S13: -0.6395 REMARK 3 S21: 1.2684 S22: -0.2585 S23: 1.9256 REMARK 3 S31: 0.9540 S32: -1.8189 S33: -0.1568 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: chain 'A' and (resid 292 through 321 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.6408 -3.6839 92.2230 REMARK 3 T TENSOR REMARK 3 T11: 0.1225 T22: 0.1970 REMARK 3 T33: 0.1382 T12: -0.0759 REMARK 3 T13: 0.0011 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.1476 L22: 0.0755 REMARK 3 L33: 0.2752 L12: -0.0182 REMARK 3 L13: 0.2292 L23: -0.0336 REMARK 3 S TENSOR REMARK 3 S11: 0.0319 S12: -0.0965 S13: -0.0961 REMARK 3 S21: -0.0472 S22: -0.0383 S23: -0.0217 REMARK 3 S31: 0.1769 S32: -0.2101 S33: 0.0044 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: chain 'A' and (resid 322 through 388 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0790 15.7846 75.4887 REMARK 3 T TENSOR REMARK 3 T11: 0.1976 T22: 0.1366 REMARK 3 T33: 0.1612 T12: 0.0570 REMARK 3 T13: -0.0129 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.4559 L22: 0.3752 REMARK 3 L33: 0.2203 L12: -0.2835 REMARK 3 L13: 0.3302 L23: -0.3107 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: -0.0761 S13: 0.0113 REMARK 3 S21: -0.0057 S22: 0.0320 S23: 0.0765 REMARK 3 S31: -0.2011 S32: -0.2030 S33: 0.0128 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: chain 'A' and (resid 389 through 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5440 17.0037 85.8501 REMARK 3 T TENSOR REMARK 3 T11: 0.2153 T22: 0.1156 REMARK 3 T33: 0.1972 T12: -0.0189 REMARK 3 T13: -0.0254 T23: -0.0881 REMARK 3 L TENSOR REMARK 3 L11: -0.0046 L22: 0.0827 REMARK 3 L33: 0.3776 L12: 0.0101 REMARK 3 L13: 0.0517 L23: -0.1226 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: -0.1421 S13: 0.4808 REMARK 3 S21: -0.2061 S22: -0.1674 S23: -0.0464 REMARK 3 S31: -0.6033 S32: 0.2206 S33: -0.0438 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 4LIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB080674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 REMARK 200 MONOCHROMATOR : 0.990 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 56.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM SODIUM CITRATE AND 20% PEG3350, REMARK 280 PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 50.90600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.95800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.90600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.95800 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 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 -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 SER A 205 REMARK 465 GLU A 206 REMARK 465 LYS A 207 REMARK 465 SER A 277 REMARK 465 ARG A 278 REMARK 465 TYR A 279 REMARK 465 GLN A 280 REMARK 465 ASN A 281 REMARK 465 ASN A 282 REMARK 465 ILE A 283 REMARK 465 LYS A 284 REMARK 465 ASN A 285 REMARK 465 ASP A 286 REMARK 465 LYS A 287 REMARK 465 TYR A 288 REMARK 465 GLY A 289 REMARK 465 PRO A 290 REMARK 465 TRP A 291 REMARK 465 GLY A 408 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 242 CG CD CE NZ REMARK 470 ASP A 253 CG OD1 OD2 REMARK 470 LEU A 255 CG CD1 CD2 REMARK 470 GLN A 256 CG CD OE1 NE2 REMARK 470 GLN A 257 CG CD OE1 NE2 REMARK 470 PHE A 259 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 260 CG CD OE1 NE2 REMARK 470 SER A 262 OG REMARK 470 LYS A 273 CG CD CE NZ REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 LYS A 311 CG CD CE NZ 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 HOH A 655 O HOH A 767 2.03 REMARK 500 NZ LYS A 318 O5 CIT A 502 2.04 REMARK 500 O HOH A 909 O HOH A 910 2.06 REMARK 500 NZ LYS A 14 O HOH A 913 2.16 REMARK 500 OD1 ASP A 65 O HOH A 802 2.17 REMARK 500 OH TYR A 54 O HOH A 649 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 856 O HOH A 877 4547 2.01 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 ARG A 56 -168.61 -126.25 REMARK 500 ASN A 62 -177.22 -171.01 REMARK 500 ARG A 162 -72.33 -139.71 REMARK 500 ILE A 233 11.20 -69.04 REMARK 500 LEU A 234 25.43 -145.18 REMARK 500 ASN A 236 -167.27 -161.56 REMARK 500 GLU A 249 -36.55 -34.79 REMARK 500 ASP A 253 -71.01 -54.93 REMARK 500 SER A 262 158.37 -45.38 REMARK 500 LEU A 305 -72.07 -84.88 REMARK 500 ASP A 306 84.87 104.90 REMARK 500 LYS A 385 50.16 -108.04 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 915 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 916 DISTANCE = 6.92 ANGSTROMS 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 128 SG REMARK 620 2 CYS A 122 SG 107.3 REMARK 620 3 CYS A 121 SG 101.3 119.3 REMARK 620 4 CYS A 131 SG 113.7 110.8 104.4 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4LIK RELATED DB: PDB REMARK 900 CATALYTIC SUBUNIT OF HUMAN PRIMASE REMARK 900 RELATED ID: 4LIL RELATED DB: PDB REMARK 900 CATALYTIC SUBUNIT OF HUMAN PRIMASE BOUND TO MN AND UTP REMARK 900 RELATED ID: 4LIM RELATED DB: PDB REMARK 900 CATALYTIC SUBUNIT OF HUMAN PRIMASE BOUND TO ZN DBREF 4LIK A 1 408 UNP P49642 PRI1_HUMAN 1 408 SEQADV 4LIK GLY A -3 UNP P49642 EXPRESSION TAG SEQADV 4LIK PRO A -2 UNP P49642 EXPRESSION TAG SEQADV 4LIK GLY A -1 UNP P49642 EXPRESSION TAG SEQADV 4LIK SER A 0 UNP P49642 EXPRESSION TAG SEQADV 4LIK A UNP P49642 ILE 360 DELETION SEQADV 4LIK A UNP P49642 SER 361 DELETION SEQADV 4LIK A UNP P49642 THR 362 DELETION SEQADV 4LIK A UNP P49642 ASN 363 DELETION SEQADV 4LIK A UNP P49642 GLU 364 DELETION SEQADV 4LIK A UNP P49642 GLU 365 DELETION SEQADV 4LIK A UNP P49642 GLU 366 DELETION SEQADV 4LIK A UNP P49642 LYS 367 DELETION SEQADV 4LIK A UNP P49642 GLU 368 DELETION SEQADV 4LIK A UNP P49642 GLU 369 DELETION SEQADV 4LIK A UNP P49642 ASN 370 DELETION SEQADV 4LIK A UNP P49642 GLU 371 DELETION SEQADV 4LIK A UNP P49642 ALA 372 DELETION SEQADV 4LIK A UNP P49642 GLU 373 DELETION SEQADV 4LIK A UNP P49642 SER 374 DELETION SEQADV 4LIK A UNP P49642 ASP 375 DELETION SEQADV 4LIK A UNP P49642 VAL 376 DELETION SEQADV 4LIK A UNP P49642 LYS 377 DELETION SEQADV 4LIK A UNP P49642 HIS 378 DELETION SEQADV 4LIK A UNP P49642 ARG 379 DELETION SEQRES 1 A 392 GLY PRO GLY SER MET GLU THR PHE ASP PRO THR GLU LEU SEQRES 2 A 392 PRO GLU LEU LEU LYS LEU TYR TYR ARG ARG LEU PHE PRO SEQRES 3 A 392 TYR SER GLN TYR TYR ARG TRP LEU ASN TYR GLY GLY VAL SEQRES 4 A 392 ILE LYS ASN TYR PHE GLN HIS ARG GLU PHE SER PHE THR SEQRES 5 A 392 LEU LYS ASP ASP ILE TYR ILE ARG TYR GLN SER PHE ASN SEQRES 6 A 392 ASN GLN SER ASP LEU GLU LYS GLU MET GLN LYS MET ASN SEQRES 7 A 392 PRO TYR LYS ILE ASP ILE GLY ALA VAL TYR SER HIS ARG SEQRES 8 A 392 PRO ASN GLN HIS ASN THR VAL LYS LEU GLY ALA PHE GLN SEQRES 9 A 392 ALA GLN GLU LYS GLU LEU VAL PHE ASP ILE ASP MET THR SEQRES 10 A 392 ASP TYR ASP ASP VAL ARG ARG CYS CYS SER SER ALA ASP SEQRES 11 A 392 ILE CYS PRO LYS CYS TRP THR LEU MET THR MET ALA ILE SEQRES 12 A 392 ARG ILE ILE ASP ARG ALA LEU LYS GLU ASP PHE GLY PHE SEQRES 13 A 392 LYS HIS ARG LEU TRP VAL TYR SER GLY ARG ARG GLY VAL SEQRES 14 A 392 HIS CYS TRP VAL CYS ASP GLU SER VAL ARG LYS LEU SER SEQRES 15 A 392 SER ALA VAL ARG SER GLY ILE VAL GLU TYR LEU SER LEU SEQRES 16 A 392 VAL LYS GLY GLY GLN ASP VAL LYS LYS LYS VAL HIS LEU SEQRES 17 A 392 SER GLU LYS ILE HIS PRO PHE ILE ARG LYS SER ILE ASN SEQRES 18 A 392 ILE ILE LYS LYS TYR PHE GLU GLU TYR ALA LEU VAL ASN SEQRES 19 A 392 GLN ASP ILE LEU GLU ASN LYS GLU SER TRP ASP LYS ILE SEQRES 20 A 392 LEU ALA LEU VAL PRO GLU THR ILE HIS ASP GLU LEU GLN SEQRES 21 A 392 GLN SER PHE GLN LYS SER HIS ASN SER LEU GLN ARG TRP SEQRES 22 A 392 GLU HIS LEU LYS LYS VAL ALA SER ARG TYR GLN ASN ASN SEQRES 23 A 392 ILE LYS ASN ASP LYS TYR GLY PRO TRP LEU GLU TRP GLU SEQRES 24 A 392 ILE MET LEU GLN TYR CYS PHE PRO ARG LEU ASP ILE ASN SEQRES 25 A 392 VAL SER LYS GLY ILE ASN HIS LEU LEU LYS SER PRO PHE SEQRES 26 A 392 SER VAL HIS PRO LYS THR GLY ARG ILE SER VAL PRO ILE SEQRES 27 A 392 ASP LEU GLN LYS VAL ASP GLN PHE ASP PRO PHE THR VAL SEQRES 28 A 392 PRO THR ILE SER PHE ILE CYS ARG GLU LEU ASP ALA THR SEQRES 29 A 392 ARG ASP TYR LYS LYS THR SER LEU ALA PRO TYR VAL LYS SEQRES 30 A 392 VAL PHE GLU HIS PHE LEU GLU ASN LEU ASP LYS SER ARG SEQRES 31 A 392 LYS GLY HET ZN A 501 1 HET CIT A 502 18 HET CIT A 503 18 HET CIT A 504 18 HETNAM ZN ZINC ION HETNAM CIT CITRIC ACID FORMUL 2 ZN ZN 2+ FORMUL 3 CIT 3(C6 H8 O7) FORMUL 6 HOH *322(H2 O) HELIX 1 1 ASP A 5 THR A 7 5 3 HELIX 2 2 GLU A 8 LEU A 20 1 13 HELIX 3 3 PRO A 22 ASN A 31 1 10 HELIX 4 4 TYR A 32 VAL A 35 5 4 HELIX 5 5 LYS A 50 ASP A 52 5 3 HELIX 6 6 ASN A 62 ASN A 74 1 13 HELIX 7 7 ARG A 87 VAL A 94 5 8 HELIX 8 8 THR A 113 ARG A 119 5 7 HELIX 9 9 TRP A 132 ASP A 149 1 18 HELIX 10 10 ASP A 171 LYS A 176 1 6 HELIX 11 11 SER A 178 SER A 190 1 13 HELIX 12 12 HIS A 209 LYS A 220 1 12 HELIX 13 13 TYR A 222 LEU A 228 1 7 HELIX 14 14 ASN A 236 ALA A 245 1 10 HELIX 15 15 ILE A 251 SER A 262 1 12 HELIX 16 16 ASN A 264 ALA A 276 1 13 HELIX 17 17 GLU A 293 PHE A 302 1 10 HELIX 18 18 ASP A 306 GLY A 312 1 7 HELIX 19 19 ASP A 335 PHE A 342 5 8 HELIX 20 20 ASP A 343 VAL A 347 5 5 HELIX 21 21 THR A 349 ARG A 381 1 13 HELIX 22 22 ASP A 382 THR A 386 5 5 HELIX 23 23 LEU A 388 LYS A 407 1 20 SHEET 1 A 4 TYR A 54 GLN A 58 0 SHEET 2 A 4 ARG A 43 THR A 48 -1 N PHE A 47 O ILE A 55 SHEET 3 A 4 LYS A 77 TYR A 84 -1 O GLY A 81 N GLU A 44 SHEET 4 A 4 ALA A 101 GLU A 103 -1 O GLU A 103 N VAL A 83 SHEET 1 B 4 TYR A 54 GLN A 58 0 SHEET 2 B 4 ARG A 43 THR A 48 -1 N PHE A 47 O ILE A 55 SHEET 3 B 4 LYS A 77 TYR A 84 -1 O GLY A 81 N GLU A 44 SHEET 4 B 4 LEU A 317 LYS A 318 -1 O LEU A 317 N ILE A 80 SHEET 1 C 3 LEU A 106 ASP A 111 0 SHEET 2 C 3 GLY A 164 VAL A 169 -1 O VAL A 169 N LEU A 106 SHEET 3 C 3 ARG A 155 TYR A 159 -1 N VAL A 158 O HIS A 166 LINK SG CYS A 128 ZN ZN A 501 1555 1555 2.01 LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.28 LINK SG CYS A 121 ZN ZN A 501 1555 1555 2.33 LINK SG CYS A 131 ZN ZN A 501 1555 1555 2.42 SITE 1 AC1 4 CYS A 121 CYS A 122 CYS A 128 CYS A 131 SITE 1 AC2 11 SER A 160 ARG A 162 LYS A 318 HIS A 324 SITE 2 AC2 11 HOH A 667 HOH A 719 HOH A 752 HOH A 781 SITE 3 AC2 11 HOH A 822 HOH A 906 HOH A 907 SITE 1 AC3 10 PRO A 88 ASN A 89 GLN A 90 HIS A 91 SITE 2 AC3 10 ASN A 92 HOH A 628 HOH A 700 HOH A 835 SITE 3 AC3 10 HOH A 864 HOH A 901 SITE 1 AC4 5 LYS A 147 GLY A 151 LYS A 153 HOH A 841 SITE 2 AC4 5 HOH A 921 CRYST1 101.812 71.916 84.797 90.00 122.04 90.00 C 1 2 1 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 0.009822 0.000000 0.006148 0.00000 SCALE2 0.000000 0.013905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013912 0.00000