HEADER TRANSFERASE 02-JUL-13 4LIM TITLE CRYSTAL STRUCTURE OF THE CATALYTIC SUBUNIT OF YEAST PRIMASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE SMALL SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 8-396; COMPND 5 SYNONYM: DNA POLYMERASE ALPHA:PRIMASE COMPLEX P48 SUBUNIT, DNA COMPND 6 POLYMERASE-PRIMASE COMPLEX P48 SUBUNIT, POL ALPHA-PRIMASE COMPLEX P48 COMPND 7 SUBUNIT, DNA PRIMASE 48 KDA SUBUNIT; COMPND 8 EC: 2.7.7.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: PRI1, PRIM1, YIB8C, YIR008C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRIM FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.VAITHIYALINGAM,W.J.CHAZIN,J.M.BERGER,J.CORN,S.STEPHENSON REVDAT 3 28-FEB-24 4LIM 1 REMARK SEQADV REVDAT 2 05-FEB-14 4LIM 1 JRNL REVDAT 1 18-DEC-13 4LIM 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. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 50009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2554 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 19.8304 - 4.2585 0.96 2656 155 0.1451 0.1621 REMARK 3 2 4.2585 - 3.3856 0.98 2707 128 0.1356 0.1661 REMARK 3 3 3.3856 - 2.9592 0.98 2758 148 0.1584 0.1924 REMARK 3 4 2.9592 - 2.6894 0.97 2656 155 0.1638 0.2060 REMARK 3 5 2.6894 - 2.4970 0.97 2712 150 0.1609 0.2179 REMARK 3 6 2.4970 - 2.3500 0.97 2656 141 0.1629 0.2199 REMARK 3 7 2.3500 - 2.2325 0.96 2703 133 0.1548 0.2019 REMARK 3 8 2.2325 - 2.1355 0.96 2687 127 0.1532 0.1900 REMARK 3 9 2.1355 - 2.0533 0.96 2648 152 0.1515 0.1714 REMARK 3 10 2.0533 - 1.9825 0.96 2650 133 0.1506 0.1866 REMARK 3 11 1.9825 - 1.9206 0.96 2662 164 0.1641 0.1902 REMARK 3 12 1.9206 - 1.8658 0.95 2618 138 0.1634 0.1895 REMARK 3 13 1.8658 - 1.8167 0.95 2640 144 0.1619 0.2111 REMARK 3 14 1.8167 - 1.7724 0.95 2604 135 0.1611 0.1873 REMARK 3 15 1.7724 - 1.7321 0.95 2621 160 0.1746 0.1971 REMARK 3 16 1.7321 - 1.6953 0.93 2575 137 0.1783 0.2169 REMARK 3 17 1.6953 - 1.6614 0.92 2534 135 0.1853 0.2246 REMARK 3 18 1.6614 - 1.6300 0.84 2368 119 0.1912 0.1983 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.360 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 : 0.019 3233 REMARK 3 ANGLE : 1.840 4374 REMARK 3 CHIRALITY : 0.123 463 REMARK 3 PLANARITY : 0.012 567 REMARK 3 DIHEDRAL : 13.729 1242 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6993 10.7605 45.4126 REMARK 3 T TENSOR REMARK 3 T11: 0.1119 T22: 0.1167 REMARK 3 T33: 0.0846 T12: 0.0050 REMARK 3 T13: -0.0165 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.4165 L22: 2.7954 REMARK 3 L33: 1.7289 L12: 0.3706 REMARK 3 L13: 0.2260 L23: 0.0252 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: 0.1253 S13: 0.0918 REMARK 3 S21: -0.2493 S22: 0.0251 S23: 0.1272 REMARK 3 S31: -0.0115 S32: -0.0785 S33: -0.0184 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 191 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0631 10.6310 63.7935 REMARK 3 T TENSOR REMARK 3 T11: 0.0731 T22: 0.1153 REMARK 3 T33: 0.1282 T12: 0.0246 REMARK 3 T13: 0.0116 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 1.0025 L22: 1.7061 REMARK 3 L33: 1.6658 L12: 0.3045 REMARK 3 L13: 0.5151 L23: 0.0496 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: -0.0668 S13: 0.0408 REMARK 3 S21: 0.0711 S22: -0.0039 S23: -0.0697 REMARK 3 S31: 0.0440 S32: 0.0183 S33: 0.0082 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 192 THROUGH 251 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7484 -0.1400 83.3226 REMARK 3 T TENSOR REMARK 3 T11: 0.2689 T22: 0.3167 REMARK 3 T33: 0.1238 T12: -0.0419 REMARK 3 T13: 0.0128 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.8344 L22: 4.6488 REMARK 3 L33: 2.6744 L12: -0.5678 REMARK 3 L13: 1.0708 L23: -1.4722 REMARK 3 S TENSOR REMARK 3 S11: 0.1085 S12: -0.1868 S13: -0.0555 REMARK 3 S21: 0.0515 S22: -0.1468 S23: -0.3466 REMARK 3 S31: 0.2578 S32: -0.0840 S33: 0.0276 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 252 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9025 -11.1335 95.5791 REMARK 3 T TENSOR REMARK 3 T11: 0.5790 T22: 0.4476 REMARK 3 T33: 0.2628 T12: -0.0545 REMARK 3 T13: -0.0970 T23: 0.1117 REMARK 3 L TENSOR REMARK 3 L11: 2.3214 L22: 3.7159 REMARK 3 L33: 2.7027 L12: 0.6685 REMARK 3 L13: 0.6593 L23: 0.5972 REMARK 3 S TENSOR REMARK 3 S11: 0.3340 S12: -0.3828 S13: -0.2799 REMARK 3 S21: 0.7416 S22: -0.0288 S23: -0.2482 REMARK 3 S31: 1.0052 S32: -0.2391 S33: -0.2886 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 290 THROUGH 347 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6951 4.8496 71.9175 REMARK 3 T TENSOR REMARK 3 T11: 0.1256 T22: 0.1733 REMARK 3 T33: 0.1391 T12: 0.0159 REMARK 3 T13: 0.0184 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.2583 L22: 0.9119 REMARK 3 L33: 2.6373 L12: 0.1040 REMARK 3 L13: 0.2769 L23: -0.3635 REMARK 3 S TENSOR REMARK 3 S11: 0.0481 S12: -0.1218 S13: 0.0280 REMARK 3 S21: 0.1768 S22: -0.0930 S23: -0.0474 REMARK 3 S31: 0.0783 S32: 0.1670 S33: 0.0452 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 348 THROUGH 393) REMARK 3 ORIGIN FOR THE GROUP (A): -3.1589 7.9461 55.7910 REMARK 3 T TENSOR REMARK 3 T11: 0.0750 T22: 0.1903 REMARK 3 T33: 0.1744 T12: 0.0054 REMARK 3 T13: 0.0262 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 1.7010 L22: 2.9518 REMARK 3 L33: 2.0570 L12: -1.4563 REMARK 3 L13: 0.2302 L23: -0.3407 REMARK 3 S TENSOR REMARK 3 S11: 0.1021 S12: -0.0642 S13: 0.0486 REMARK 3 S21: 0.0247 S22: 0.0308 S23: -0.1021 REMARK 3 S31: -0.0206 S32: -0.2505 S33: -0.0963 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 4LIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UNKNOWN REMARK 200 DATA SCALING SOFTWARE : UNKNOWN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: UNKNOWN REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 ARG A 93 REMARK 465 ASP A 94 REMARK 465 THR A 95 REMARK 465 LEU A 96 REMARK 465 LEU A 97 REMARK 465 LYS A 98 REMARK 465 SER A 99 REMARK 465 VAL A 394 REMARK 465 LYS A 395 REMARK 465 ARG A 396 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 801 O HOH A 806 2.04 REMARK 500 O HOH A 705 O HOH A 846 2.08 REMARK 500 O HOH A 781 O HOH A 916 2.11 REMARK 500 O HOH A 866 O HOH A 983 2.11 REMARK 500 O HOH A 909 O HOH A 938 2.11 REMARK 500 O HOH A 722 O HOH A 782 2.11 REMARK 500 O HOH A 668 O HOH A 888 2.12 REMARK 500 O HOH A 549 O HOH A 933 2.15 REMARK 500 O HOH A 837 O HOH A 969 2.16 REMARK 500 O HOH A 849 O HOH A 914 2.18 REMARK 500 OD1 ASN A 364 O HOH A 639 2.19 REMARK 500 O HOH A 683 O HOH A 788 2.19 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 653 O HOH A 781 1455 2.16 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 PHE A 68 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 185 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ARG A 164 -64.51 -130.76 REMARK 500 ARG A 165 44.02 -156.15 REMARK 500 ALA A 204 57.98 38.82 REMARK 500 ASN A 364 87.31 -150.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 45 0.07 SIDE CHAIN 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 123 SG REMARK 620 2 CYS A 124 SG 122.6 REMARK 620 3 CYS A 130 SG 103.7 102.4 REMARK 620 4 CYS A 133 SG 101.6 111.1 116.0 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 401 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 DBREF 4LIM A 8 396 UNP P10363 PRI1_YEAST 8 396 SEQADV 4LIM GLY A 6 UNP P10363 EXPRESSION TAG SEQADV 4LIM ALA A 7 UNP P10363 EXPRESSION TAG SEQRES 1 A 391 GLY ALA ASN GLY PRO SER SER SER ASP MET GLU TYR TYR SEQRES 2 A 391 TYR LYS SER LEU TYR PRO PHE LYS HIS ILE PHE ASN TRP SEQRES 3 A 391 LEU ASN HIS SER PRO LYS PRO SER ARG ASP MET ILE ASN SEQRES 4 A 391 ARG GLU PHE ALA MET ALA PHE ARG SER GLY ALA TYR LYS SEQRES 5 A 391 ARG TYR ASN SER PHE ASN SER VAL GLN ASP PHE LYS ALA SEQRES 6 A 391 GLN ILE GLU LYS ALA ASN PRO ASP ARG PHE GLU ILE GLY SEQRES 7 A 391 ALA ILE TYR ASN LYS PRO PRO ARG GLU ARG ASP THR LEU SEQRES 8 A 391 LEU LYS SER GLU LEU LYS ALA LEU GLU LYS GLU LEU VAL SEQRES 9 A 391 PHE ASP ILE ASP MET ASP ASP TYR ASP ALA PHE ARG THR SEQRES 10 A 391 CYS CYS SER GLY ALA GLN VAL CYS SER LYS CYS TRP LYS SEQRES 11 A 391 PHE ILE SER LEU ALA MET LYS ILE THR ASN THR ALA LEU SEQRES 12 A 391 ARG GLU ASP PHE GLY TYR LYS ASP PHE ILE TRP VAL PHE SEQRES 13 A 391 SER GLY ARG ARG GLY ALA HIS CYS TRP VAL SER ASP LYS SEQRES 14 A 391 ARG ALA ARG ALA LEU THR ASP VAL GLN ARG ARG ASN VAL SEQRES 15 A 391 LEU ASP TYR VAL ASN VAL ILE ARG ASP ARG ASN THR ASP SEQRES 16 A 391 LYS ARG LEU ALA LEU LYS ARG PRO TYR HIS PRO HIS LEU SEQRES 17 A 391 ALA ARG SER LEU GLU GLN LEU LYS PRO PHE PHE VAL SER SEQRES 18 A 391 ILE MET LEU GLU GLU GLN ASN PRO TRP GLU ASP ASP GLN SEQRES 19 A 391 HIS ALA ILE GLN THR LEU LEU PRO ALA LEU TYR ASP LYS SEQRES 20 A 391 GLN LEU ILE ASP SER LEU LYS LYS TYR TRP LEU ASP ASN SEQRES 21 A 391 PRO ARG ARG SER SER LYS GLU LYS TRP ASN ASP ILE ASP SEQRES 22 A 391 GLN ILE ALA THR SER LEU PHE LYS GLY PRO LYS GLN ASP SEQRES 23 A 391 SER HIS ILE ILE LYS LEU ARG GLU CYS LYS GLU ASP LEU SEQRES 24 A 391 VAL LEU MET THR LEU TYR PRO LYS LEU ASP VAL GLU VAL SEQRES 25 A 391 THR LYS GLN THR ILE HIS LEU LEU LYS ALA PRO PHE CYS SEQRES 26 A 391 ILE HIS PRO ALA THR GLY ASN VAL CYS VAL PRO ILE ASP SEQRES 27 A 391 GLU SER PHE ALA PRO GLU LYS ALA PRO LYS LEU ILE ASP SEQRES 28 A 391 LEU GLN THR GLU MET GLU LYS ASN ASN ASP VAL SER LEU SEQRES 29 A 391 THR ALA LEU GLN PRO PHE ILE ASN GLN PHE GLN ALA TYR SEQRES 30 A 391 VAL SER SER LEU LEU LYS ASN GLU LEU GLY SER VAL LYS SEQRES 31 A 391 ARG HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *492(H2 O) HELIX 1 1 SER A 11 LEU A 22 1 12 HELIX 2 2 PRO A 24 HIS A 34 1 11 HELIX 3 3 SER A 39 ASN A 44 1 6 HELIX 4 4 SER A 64 ASN A 76 1 13 HELIX 5 5 ASP A 115 ARG A 121 5 7 HELIX 6 6 CYS A 130 ASP A 151 1 22 HELIX 7 7 ASP A 173 ALA A 178 1 6 HELIX 8 8 THR A 180 ASN A 192 1 13 HELIX 9 9 HIS A 210 MET A 228 1 19 HELIX 10 10 ASP A 237 LEU A 245 1 9 HELIX 11 11 LEU A 246 LEU A 249 5 4 HELIX 12 12 ASP A 251 ASN A 265 1 15 HELIX 13 13 SER A 269 PHE A 285 1 17 HELIX 14 14 LYS A 289 TYR A 310 1 22 HELIX 15 15 ASP A 314 GLN A 320 5 7 HELIX 16 16 ALA A 347 ALA A 351 5 5 HELIX 17 17 LYS A 353 ASN A 364 1 12 HELIX 18 18 ASP A 366 THR A 370 5 5 HELIX 19 19 LEU A 372 GLY A 392 1 21 SHEET 1 A 4 TYR A 56 ASN A 60 0 SHEET 2 A 4 ARG A 45 ALA A 50 -1 N MET A 49 O LYS A 57 SHEET 3 A 4 ARG A 79 TYR A 86 -1 O GLY A 83 N GLU A 46 SHEET 4 A 4 ALA A 103 GLU A 105 -1 O LEU A 104 N ILE A 85 SHEET 1 B 4 TYR A 56 ASN A 60 0 SHEET 2 B 4 ARG A 45 ALA A 50 -1 N MET A 49 O LYS A 57 SHEET 3 B 4 ARG A 79 TYR A 86 -1 O GLY A 83 N GLU A 46 SHEET 4 B 4 LEU A 325 LYS A 326 -1 O LEU A 325 N ILE A 82 SHEET 1 C 4 LEU A 108 ASP A 113 0 SHEET 2 C 4 GLY A 166 VAL A 171 -1 O VAL A 171 N LEU A 108 SHEET 3 C 4 PHE A 157 PHE A 161 -1 N VAL A 160 O HIS A 168 SHEET 4 C 4 PRO A 341 ILE A 342 -1 O ILE A 342 N TRP A 159 LINK SG CYS A 123 ZN ZN A 401 1555 1555 2.24 LINK SG CYS A 124 ZN ZN A 401 1555 1555 2.26 LINK SG CYS A 130 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 133 ZN ZN A 401 1555 1555 2.31 CISPEP 1 ARG A 207 PRO A 208 0 -3.22 SITE 1 AC1 4 CYS A 123 CYS A 124 CYS A 130 CYS A 133 CRYST1 37.166 43.624 69.383 83.11 83.25 78.00 P 1 1 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 0.026906 -0.005719 -0.002635 0.00000 SCALE2 0.000000 0.023435 -0.002316 0.00000 SCALE3 0.000000 0.000000 0.014584 0.00000