HEADER REPLICATION/DNA/RNA 28-NOV-15 5F0S TITLE CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF THE HUMAN DNA PRIMASE LARGE TITLE 2 SUBUNIT WITH BOUND DNA TEMPLATE/RNA PRIMER AND MANGANESE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PRIMASE LARGE SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 266-456; COMPND 5 SYNONYM: DNA PRIMASE 58 KDA SUBUNIT,P58; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3'); COMPND 10 CHAIN: C, E; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: CONTAINS 5'-TRIPHOSPHATE; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3'); COMPND 15 CHAIN: D, F; COMPND 16 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: PRIM2, PRIM2A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS TRANFERASE-DNA-RNA COMPLEX, DNA PRIMASE, LARGE SUBUNIT, IRON-SULFUR KEYWDS 2 CLUSTER, RNA, DNA, PRIMER, TEMPLATE, TRIPHOSPHATE, INITIATION SITE, KEYWDS 3 MANGANESE, REPLICATION-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,A.G.BARANOVSKIY,N.D.BABAYEVA REVDAT 6 04-DEC-19 5F0S 1 REMARK REVDAT 5 01-NOV-17 5F0S 1 REMARK REVDAT 4 20-SEP-17 5F0S 1 JRNL REMARK REVDAT 3 01-JUN-16 5F0S 1 JRNL REVDAT 2 30-MAR-16 5F0S 1 JRNL REVDAT 1 23-MAR-16 5F0S 0 JRNL AUTH A.G.BARANOVSKIY,N.D.BABAYEVA,Y.ZHANG,J.GU,Y.SUWA,Y.I.PAVLOV, JRNL AUTH 2 T.H.TAHIROV JRNL TITL MECHANISM OF CONCERTED RNA-DNA PRIMER SYNTHESIS BY THE HUMAN JRNL TITL 2 PRIMOSOME. JRNL REF J.BIOL.CHEM. V. 291 10006 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26975377 JRNL DOI 10.1074/JBC.M116.717405 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4333058.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 11818 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 SET) : 0.232 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 607 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1576 REMARK 3 BIN R VALUE (WORKING SET) : 0.3980 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 74 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3034 REMARK 3 NUCLEIC ACID ATOMS : 721 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : -0.82000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.91 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.85 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.810 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.720 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.28 REMARK 3 BSOL : 13.61 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : SF4.PAR REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : SF4.TOP REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5F0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 FR-E DW 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11834 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: 5F0Q REMARK 200 REMARK 200 REMARK: NEEDLE-LIKE PRISMS WITH A SQUARE IN CROSS-SECTION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION CONTAINE 0.18 M REMARK 280 LITHIUM SULFATE, 50 MM SODIUM CITRATE, 2 MM TCEP, 0.1 M SODIUM REMARK 280 MALONATE, 0.1 M HEPES-NAOH (PH 7.0), 19.7% PEG 8,000 AND 0.02 M REMARK 280 MAGNESIUM CHLORIDE. TO EXCHANGE MG TO MN CRYSTALS WERE SOAKED REMARK 280 FOR 5 MIN IN A RESERVOIR SOLUTION CONTAINING 2 MM MANGANESE REMARK 280 CHLORIDE INSTEAD OF MAGNESIUM CHLORIDE., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 41.84500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.84500 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 61.37650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.80650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 61.37650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.80650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.84500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 61.37650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.80650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.84500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 61.37650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.80650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: TRIMER ACCORDING TO ELECTROPHORESIS 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E, F 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 266 REMARK 465 ASN A 267 REMARK 465 VAL A 268 REMARK 465 GLY A 269 REMARK 465 GLY B 266 REMARK 465 ASN B 267 REMARK 465 VAL B 268 REMARK 465 GLY B 269 REMARK 465 LYS B 270 REMARK 465 ASN B 456 REMARK 465 DT F 11 REMARK 465 DA F 12 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 LYS A 397 OG SER A 400 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 DC D 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 11 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 DC F 3 O4' - C1' - N1 ANGL. DEV. = 2.8 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 274 26.76 -71.81 REMARK 500 LYS A 343 -71.71 -55.87 REMARK 500 ARG A 359 70.98 66.23 REMARK 500 ASN A 374 60.51 31.12 REMARK 500 PRO A 405 -15.03 -43.51 REMARK 500 ASN A 442 13.06 -158.85 REMARK 500 HIS B 300 147.84 -177.46 REMARK 500 GLN B 329 -39.38 -39.57 REMARK 500 LYS B 335 12.18 57.95 REMARK 500 ARG B 359 63.81 61.23 REMARK 500 SER B 377 -168.65 -126.95 REMARK 500 HIS B 419 49.80 -102.13 REMARK 500 ASN B 442 16.75 -156.31 REMARK 500 HIS B 443 116.09 -161.84 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 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 367 SG REMARK 620 2 SF4 A 501 S2 114.0 REMARK 620 3 SF4 A 501 S3 136.3 86.6 REMARK 620 4 SF4 A 501 S4 118.0 91.5 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 384 SG REMARK 620 2 SF4 A 501 S1 124.5 REMARK 620 3 SF4 A 501 S3 95.6 85.8 REMARK 620 4 SF4 A 501 S4 142.4 91.6 97.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 424 SG REMARK 620 2 SF4 A 501 S1 107.8 REMARK 620 3 SF4 A 501 S2 155.3 81.2 REMARK 620 4 SF4 A 501 S4 108.6 92.8 93.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 287 SG REMARK 620 2 SF4 B 501 S1 145.8 REMARK 620 3 SF4 B 501 S2 103.4 85.0 REMARK 620 4 SF4 B 501 S3 124.0 88.3 91.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 367 SG REMARK 620 2 SF4 B 501 S2 118.1 REMARK 620 3 SF4 B 501 S3 145.2 87.4 REMARK 620 4 SF4 B 501 S4 103.3 94.2 97.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 384 SG REMARK 620 2 SF4 B 501 S1 113.5 REMARK 620 3 SF4 B 501 S3 100.0 83.3 REMARK 620 4 SF4 B 501 S4 152.3 90.5 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 B 501 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 424 SG REMARK 620 2 SF4 B 501 S1 123.4 REMARK 620 3 SF4 B 501 S2 138.7 81.7 REMARK 620 4 SF4 B 501 S4 114.0 92.0 95.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP C 1 O2G REMARK 620 2 GTP C 1 O2A 75.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN E 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP E 1 O1G REMARK 620 2 GTP E 1 O1B 60.1 REMARK 620 N 1 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP E 1 and G E 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F0Q RELATED DB: PDB REMARK 900 CONTAINS MG INSTEAD OF MN DBREF 5F0S A 266 456 UNP P49643 PRI2_HUMAN 266 456 DBREF 5F0S B 266 456 UNP P49643 PRI2_HUMAN 266 456 DBREF 5F0S C 1 6 PDB 5F0S 5F0S 1 6 DBREF 5F0S D 1 12 PDB 5F0S 5F0S 1 12 DBREF 5F0S E 1 6 PDB 5F0S 5F0S 1 6 DBREF 5F0S F 1 12 PDB 5F0S 5F0S 1 12 SEQRES 1 A 191 GLY ASN VAL GLY LYS ILE SER LEU ASP GLN ILE ASP LEU SEQRES 2 A 191 LEU SER THR LYS SER PHE PRO PRO CYS MET ARG GLN LEU SEQRES 3 A 191 HIS LYS ALA LEU ARG GLU ASN HIS HIS LEU ARG HIS GLY SEQRES 4 A 191 GLY ARG MET GLN TYR GLY LEU PHE LEU LYS GLY ILE GLY SEQRES 5 A 191 LEU THR LEU GLU GLN ALA LEU GLN PHE TRP LYS GLN GLU SEQRES 6 A 191 PHE ILE LYS GLY LYS MET ASP PRO ASP LYS PHE ASP LYS SEQRES 7 A 191 GLY TYR SER TYR ASN ILE ARG HIS SER PHE GLY LYS GLU SEQRES 8 A 191 GLY LYS ARG THR ASP TYR THR PRO PHE SER CYS LEU LYS SEQRES 9 A 191 ILE ILE LEU SER ASN PRO PRO SER GLN GLY ASP TYR HIS SEQRES 10 A 191 GLY CYS PRO PHE ARG HIS SER ASP PRO GLU LEU LEU LYS SEQRES 11 A 191 GLN LYS LEU GLN SER TYR LYS ILE SER PRO GLY GLY ILE SEQRES 12 A 191 SER GLN ILE LEU ASP LEU VAL LYS GLY THR HIS TYR GLN SEQRES 13 A 191 VAL ALA CYS GLN LYS TYR PHE GLU MET ILE HIS ASN VAL SEQRES 14 A 191 ASP ASP CYS GLY PHE SER LEU ASN HIS PRO ASN GLN PHE SEQRES 15 A 191 PHE CYS GLU SER GLN ARG ILE LEU ASN SEQRES 1 B 191 GLY ASN VAL GLY LYS ILE SER LEU ASP GLN ILE ASP LEU SEQRES 2 B 191 LEU SER THR LYS SER PHE PRO PRO CYS MET ARG GLN LEU SEQRES 3 B 191 HIS LYS ALA LEU ARG GLU ASN HIS HIS LEU ARG HIS GLY SEQRES 4 B 191 GLY ARG MET GLN TYR GLY LEU PHE LEU LYS GLY ILE GLY SEQRES 5 B 191 LEU THR LEU GLU GLN ALA LEU GLN PHE TRP LYS GLN GLU SEQRES 6 B 191 PHE ILE LYS GLY LYS MET ASP PRO ASP LYS PHE ASP LYS SEQRES 7 B 191 GLY TYR SER TYR ASN ILE ARG HIS SER PHE GLY LYS GLU SEQRES 8 B 191 GLY LYS ARG THR ASP TYR THR PRO PHE SER CYS LEU LYS SEQRES 9 B 191 ILE ILE LEU SER ASN PRO PRO SER GLN GLY ASP TYR HIS SEQRES 10 B 191 GLY CYS PRO PHE ARG HIS SER ASP PRO GLU LEU LEU LYS SEQRES 11 B 191 GLN LYS LEU GLN SER TYR LYS ILE SER PRO GLY GLY ILE SEQRES 12 B 191 SER GLN ILE LEU ASP LEU VAL LYS GLY THR HIS TYR GLN SEQRES 13 B 191 VAL ALA CYS GLN LYS TYR PHE GLU MET ILE HIS ASN VAL SEQRES 14 B 191 ASP ASP CYS GLY PHE SER LEU ASN HIS PRO ASN GLN PHE SEQRES 15 B 191 PHE CYS GLU SER GLN ARG ILE LEU ASN SEQRES 1 C 6 GTP G C G G C SEQRES 1 D 12 DG DC DC DG DC DC DA DA DC DA DT DA SEQRES 1 E 6 GTP G C G G C SEQRES 1 F 12 DG DC DC DG DC DC DA DA DC DA DT DA HET GTP C 1 32 HET GTP E 1 32 HET SF4 A 501 8 HET SF4 B 501 8 HET MN C 101 1 HET MN E 101 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MN MANGANESE (II) ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 7 SF4 2(FE4 S4) FORMUL 9 MN 2(MN 2+) HELIX 1 AA1 SER A 272 ASP A 274 5 3 HELIX 2 AA2 GLN A 275 SER A 283 1 9 HELIX 3 AA3 PRO A 285 HIS A 299 1 15 HELIX 4 AA4 ARG A 302 GLY A 317 1 16 HELIX 5 AA5 THR A 319 LYS A 333 1 15 HELIX 6 AA6 ASP A 337 GLY A 344 1 8 HELIX 7 AA7 GLY A 344 PHE A 353 1 10 HELIX 8 AA8 SER A 366 SER A 373 1 8 HELIX 9 AA9 CYS A 384 SER A 389 1 6 HELIX 10 AB1 ASP A 390 TYR A 401 1 12 HELIX 11 AB2 SER A 404 GLY A 417 1 14 HELIX 12 AB3 HIS A 419 HIS A 432 1 14 HELIX 13 AB4 HIS A 443 ASN A 456 1 14 HELIX 14 AB5 SER B 272 ASP B 274 5 3 HELIX 15 AB6 GLN B 275 SER B 283 1 9 HELIX 16 AB7 PRO B 285 HIS B 299 1 15 HELIX 17 AB8 ARG B 302 ILE B 316 1 15 HELIX 18 AB9 THR B 319 LYS B 333 1 15 HELIX 19 AC1 ASP B 337 GLY B 344 1 8 HELIX 20 AC2 GLY B 344 PHE B 353 1 10 HELIX 21 AC3 SER B 366 SER B 373 1 8 HELIX 22 AC4 CYS B 384 SER B 389 1 6 HELIX 23 AC5 ASP B 390 TYR B 401 1 12 HELIX 24 AC6 SER B 404 GLY B 417 1 14 HELIX 25 AC7 HIS B 419 HIS B 432 1 14 HELIX 26 AC8 HIS B 443 LEU B 455 1 13 LINK SG CYS A 367 FE1 SF4 A 501 1555 1555 2.37 LINK SG CYS A 384 FE2 SF4 A 501 1555 1555 2.48 LINK SG CYS A 424 FE3 SF4 A 501 1555 1555 2.48 LINK SG CYS B 287 FE4 SF4 B 501 1555 1555 2.51 LINK SG CYS B 367 FE1 SF4 B 501 1555 1555 2.48 LINK SG CYS B 384 FE2 SF4 B 501 1555 1555 2.57 LINK SG CYS B 424 FE3 SF4 B 501 1555 1555 2.50 LINK O2G GTP C 1 MN MN C 101 1555 1555 2.24 LINK O2A GTP C 1 MN MN C 101 1555 1555 2.28 LINK O3' GTP C 1 P G C 2 1555 1555 1.60 LINK O1G GTP E 1 MN MN E 101 1555 1555 1.86 LINK O1B GTP E 1 MN MN E 101 1555 1555 2.66 LINK O3' GTP E 1 P G E 2 1555 1555 1.61 SITE 1 AC1 6 PRO A 286 CYS A 287 CYS A 367 CYS A 384 SITE 2 AC1 6 CYS A 424 LEU A 441 SITE 1 AC2 8 PRO B 285 PRO B 286 CYS B 287 CYS B 367 SITE 2 AC2 8 CYS B 384 PHE B 386 CYS B 424 PRO B 444 SITE 1 AC3 1 GTP C 1 SITE 1 AC4 2 TYR B 345 GTP E 1 SITE 1 AC5 10 HIS B 300 ARG B 302 HIS B 303 ARG B 306 SITE 2 AC5 10 TYR B 345 C E 3 MN E 101 DC F 5 SITE 3 AC5 10 DC F 6 DA F 7 CRYST1 122.753 125.613 83.690 90.00 90.00 90.00 C 2 2 21 16 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 0.008146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011949 0.00000 MASTER 444 0 6 26 0 0 9 6 0 0 0 34 END