HEADER TRANFERASE/DNA/RNA 28-NOV-15 5F0Q TITLE CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF THE HUMAN DNA PRIMASE LARGE TITLE 2 SUBUNIT WITH BOUND DNA TEMPLATE/RNA PRIMER 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: CONTAIN 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 EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TAHIROV,A.G.BARANOVSKIY,N.D.BABAYEVA REVDAT 7 27-SEP-23 5F0Q 1 REMARK REVDAT 6 04-DEC-19 5F0Q 1 REMARK REVDAT 5 01-NOV-17 5F0Q 1 REMARK REVDAT 4 20-SEP-17 5F0Q 1 JRNL REMARK REVDAT 3 01-JUN-16 5F0Q 1 JRNL REVDAT 2 30-MAR-16 5F0Q 1 JRNL REVDAT 1 23-MAR-16 5F0Q 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. 2.21 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 92148.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 30821 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) : 0.223 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1532 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3246 REMARK 3 BIN R VALUE (WORKING SET) : 0.4090 REMARK 3 BIN FREE R VALUE : 0.4550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 178 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.034 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 : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.81000 REMARK 3 B22 (A**2) : 7.28000 REMARK 3 B33 (A**2) : -16.09000 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.800 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) : 3.190 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.550 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 56.48 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 5F0Q 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_1000215805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 95.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.550 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: 4RR2 REMARK 200 REMARK 200 REMARK: NEEDLE-LIKE PRISMS WITH A SQUARE IN CROSS-SECTION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.18 M LITHIUM SULFATE, 50 MM SODIUM REMARK 280 CITRATE, 2 MM TCEP, 0.1 M SODIUM MALONATE, 0.1 M HEPES-NAOH (PH REMARK 280 7.0), 19.7% PEG 8,000 AND 0.02 M MAGNESIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, 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 41.97100 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 41.97100 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 61.25350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.00100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 61.25350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.00100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.97100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 61.25350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.00100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.97100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 61.25350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.00100 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: 3360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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: 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. = 3.2 DEGREES REMARK 500 DT D 11 N1 - C1' - C2' ANGL. DEV. = 10.0 DEGREES REMARK 500 DC F 3 O4' - C1' - N1 ANGL. DEV. = 2.4 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 26.41 -72.78 REMARK 500 LYS A 343 -72.12 -55.89 REMARK 500 ARG A 359 70.93 64.72 REMARK 500 ASN A 374 62.63 28.18 REMARK 500 HIS A 382 -178.00 -68.81 REMARK 500 PRO A 391 -42.13 -29.37 REMARK 500 PRO A 405 -18.01 -45.09 REMARK 500 ASN A 442 16.57 -153.73 REMARK 500 LYS B 335 12.06 58.29 REMARK 500 HIS B 419 49.98 -101.07 REMARK 500 ASN B 442 13.62 -155.17 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 DC D 3 0.07 SIDE CHAIN REMARK 500 DA D 8 0.05 SIDE CHAIN REMARK 500 DC F 3 0.06 SIDE CHAIN REMARK 500 DA F 8 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 SF4 A 501 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 287 SG REMARK 620 2 SF4 A 501 S1 116.6 REMARK 620 3 SF4 A 501 S2 131.2 84.1 REMARK 620 4 SF4 A 501 S3 131.1 90.2 89.0 REMARK 620 N 1 2 3 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 115.7 REMARK 620 3 SF4 A 501 S3 125.7 85.2 REMARK 620 4 SF4 A 501 S4 129.0 91.5 97.2 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 127.7 REMARK 620 3 SF4 A 501 S3 121.8 86.6 REMARK 620 4 SF4 A 501 S4 121.2 92.8 97.8 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 129.6 REMARK 620 3 SF4 A 501 S2 128.6 82.2 REMARK 620 4 SF4 A 501 S4 118.6 94.2 92.8 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 119.4 REMARK 620 3 SF4 B 501 S2 129.8 85.0 REMARK 620 4 SF4 B 501 S3 130.3 90.6 88.2 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 116.4 REMARK 620 3 SF4 B 501 S3 131.1 84.8 REMARK 620 4 SF4 B 501 S4 124.2 91.1 96.7 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 121.1 REMARK 620 3 SF4 B 501 S3 120.2 87.2 REMARK 620 4 SF4 B 501 S4 127.8 93.7 97.0 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 134.1 REMARK 620 3 SF4 B 501 S2 123.5 83.1 REMARK 620 4 SF4 B 501 S4 117.7 94.5 92.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP C 1 O2G REMARK 620 2 GTP C 1 O1B 61.7 REMARK 620 3 GTP C 1 O2A 71.2 49.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP E 1 O1G REMARK 620 2 GTP E 1 O1B 82.9 REMARK 620 3 GTP E 1 O1A 93.9 65.9 REMARK 620 N 1 2 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 MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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: 5F0S RELATED DB: PDB DBREF 5F0Q A 266 456 UNP P49643 PRI2_HUMAN 266 456 DBREF 5F0Q B 266 456 UNP P49643 PRI2_HUMAN 266 456 DBREF 5F0Q C 1 6 PDB 5F0Q 5F0Q 1 6 DBREF 5F0Q D 1 12 PDB 5F0Q 5F0Q 1 12 DBREF 5F0Q E 1 6 PDB 5F0Q 5F0Q 1 6 DBREF 5F0Q F 1 12 PDB 5F0Q 5F0Q 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 MG C 101 1 HET MG E 101 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM MG MAGNESIUM ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 7 SF4 2(FE4 S4) FORMUL 9 MG 2(MG 2+) FORMUL 11 HOH *65(H2 O) 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 O3' GTP C 1 P G C 2 1555 1555 1.61 LINK O3' GTP E 1 P G E 2 1555 1555 1.60 LINK SG CYS A 287 FE4 SF4 A 501 1555 1555 2.32 LINK SG CYS A 367 FE1 SF4 A 501 1555 1555 2.33 LINK SG CYS A 384 FE2 SF4 A 501 1555 1555 2.47 LINK SG CYS A 424 FE3 SF4 A 501 1555 1555 2.33 LINK SG CYS B 287 FE4 SF4 B 501 1555 1555 2.22 LINK SG CYS B 367 FE1 SF4 B 501 1555 1555 2.21 LINK SG CYS B 384 FE2 SF4 B 501 1555 1555 2.32 LINK SG CYS B 424 FE3 SF4 B 501 1555 1555 2.51 LINK O2G GTP C 1 MG MG C 101 1555 1555 2.38 LINK O1B GTP C 1 MG MG C 101 1555 1555 2.88 LINK O2A GTP C 1 MG MG C 101 1555 1555 2.78 LINK O1G GTP E 1 MG MG E 101 1555 1555 1.85 LINK O1B GTP E 1 MG MG E 101 1555 1555 2.47 LINK O1A GTP E 1 MG MG E 101 1555 1555 2.21 SITE 1 AC1 4 CYS A 287 CYS A 367 CYS A 384 CYS A 424 SITE 1 AC2 5 PRO B 285 CYS B 287 CYS B 367 CYS B 384 SITE 2 AC2 5 CYS B 424 SITE 1 AC3 1 GTP C 1 SITE 1 AC4 1 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 MG E 101 DC F 5 SITE 3 AC5 10 DC F 6 DA F 7 CRYST1 122.507 126.002 83.942 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 0.008163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011913 0.00000