HEADER RNA BINDING PROTEIN/RNA 30-AUG-12 4GV9 TITLE LASSA NUCLEOPROTEIN C-TERMINAL DOMAIN IN COMPLEX WITH TRIPHOSPHATED TITLE 2 DSRNA SOAKING FOR 5 MIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(GTP)P*GP*GP*C)-3'); COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: UNP RESIDUES 364-569; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*CP*GP*CP*CP*C)-3'); COMPND 8 CHAIN: F; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NUCLEOPROTEIN; COMPND 12 CHAIN: A; COMPND 13 SYNONYM: NUCLEOCAPSID PROTEIN, PROTEIN N; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRIPHOSPHATED DSRNA; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 ORGANISM_SCIENTIFIC: LASSA VIRUS; SOURCE 8 ORGANISM_COMMON: LASV; SOURCE 9 ORGANISM_TAXID: 11622; SOURCE 10 STRAIN: JOSIAH; SOURCE 11 GENE: N; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: ROSSETTA; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PLOU3 KEYWDS DEDDH FAMILY ENZYME, 3'-5' EXONUCLEASE, DSRNA, RNA BINDING PROTEIN- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.JIANG,Q.HUANG,W.WANG,H.DONG,H.LY,Y.LIANG,C.DONG REVDAT 4 28-FEB-24 4GV9 1 REMARK SEQADV LINK REVDAT 3 10-JUL-13 4GV9 1 JRNL REVDAT 2 15-MAY-13 4GV9 1 JRNL REVDAT 1 01-MAY-13 4GV9 0 JRNL AUTH X.JIANG,Q.HUANG,W.WANG,H.DONG,H.LY,Y.LIANG,C.DONG JRNL TITL STRUCTURES OF ARENAVIRAL NUCLEOPROTEINS WITH TRIPHOSPHATE JRNL TITL 2 DSRNA REVEAL A UNIQUE MECHANISM OF IMMUNE SUPPRESSION. JRNL REF J.BIOL.CHEM. V. 288 16949 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23615902 JRNL DOI 10.1074/JBC.M112.420521 REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8461 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 + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 423 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 598 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1564 REMARK 3 NUCLEIC ACID ATOMS : 201 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 32.71000 REMARK 3 B22 (A**2) : 32.71000 REMARK 3 B33 (A**2) : -65.42000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.295 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.681 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1813 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2492 ; 0.911 ; 1.914 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 195 ; 4.166 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 71 ;34.099 ;24.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 287 ;14.270 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;11.591 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 282 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1270 ; 0.002 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 397 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1813 ; 0.549 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 8 ;33.902 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1770 ;17.431 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 8 E 11 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9610 -10.5342 0.7624 REMARK 3 T TENSOR REMARK 3 T11: 0.3943 T22: 0.5313 REMARK 3 T33: 0.5852 T12: 0.0968 REMARK 3 T13: -0.0199 T23: 0.0396 REMARK 3 L TENSOR REMARK 3 L11: 20.8659 L22: 6.7816 REMARK 3 L33: 1.4512 L12: 10.9356 REMARK 3 L13: -5.3958 L23: -3.0645 REMARK 3 S TENSOR REMARK 3 S11: -0.5245 S12: 1.7055 S13: 0.1972 REMARK 3 S21: -0.4978 S22: 0.5847 S23: -0.0916 REMARK 3 S31: 0.1893 S32: -0.3756 S33: -0.0602 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 5 REMARK 3 ORIGIN FOR THE GROUP (A): 0.7510 -17.4742 -1.5076 REMARK 3 T TENSOR REMARK 3 T11: 0.5425 T22: 0.5782 REMARK 3 T33: 0.4897 T12: -0.0478 REMARK 3 T13: -0.0764 T23: -0.1384 REMARK 3 L TENSOR REMARK 3 L11: 18.5915 L22: 34.1705 REMARK 3 L33: 2.7537 L12: 3.3966 REMARK 3 L13: -3.3686 L23: 1.8582 REMARK 3 S TENSOR REMARK 3 S11: -0.7805 S12: 1.7009 S13: -1.3041 REMARK 3 S21: 0.8170 S22: -0.2125 S23: -0.0266 REMARK 3 S31: 0.2216 S32: -0.7690 S33: 0.9930 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 363 A 569 REMARK 3 ORIGIN FOR THE GROUP (A): 1.6253 -8.7070 18.5198 REMARK 3 T TENSOR REMARK 3 T11: 0.0496 T22: 0.0558 REMARK 3 T33: 0.6592 T12: 0.0314 REMARK 3 T13: -0.0445 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.8733 L22: 1.5050 REMARK 3 L33: 1.8204 L12: 0.5426 REMARK 3 L13: -0.4303 L23: -0.7465 REMARK 3 S TENSOR REMARK 3 S11: 0.0211 S12: 0.0324 S13: 0.0350 REMARK 3 S21: -0.1896 S22: -0.0209 S23: 0.0063 REMARK 3 S31: 0.1946 S32: 0.2750 S33: -0.0002 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4GV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000074675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : GRAPHIE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8461 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 73.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 2.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.78500 REMARK 200 R SYM FOR SHELL (I) : 0.75000 REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18.5% PEG MME 5000, 0.1 M SODIUM REMARK 280 CITRATE (PH4.5), AND 2.4% PEG MME350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 110.87000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.39000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.43500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.39000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 166.30500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.39000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.43500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.39000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.39000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 166.30500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 110.87000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 ALA A 357 REMARK 465 MET A 358 REMARK 465 ASP A 359 REMARK 465 HIS A 360 REMARK 465 VAL A 361 REMARK 465 GLU A 362 REMARK 465 LYS A 516 REMARK 465 LYS A 517 REMARK 465 LYS A 518 REMARK 465 ARG A 519 REMARK 465 GLY A 520 REMARK 465 GLY A 521 REMARK 465 THR A 562 REMARK 465 SER A 563 REMARK 465 THR A 564 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GTP E 8 O3' G E 9 P -0.157 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 GTP E 8 C3' - O3' - P ANGL. DEV. = -13.1 DEGREES REMARK 500 G E 9 O3' - P - OP2 ANGL. DEV. = 9.6 DEGREES REMARK 500 G E 9 C3' - O3' - P ANGL. DEV. = 15.3 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 SER A 430 -85.03 -137.81 REMARK 500 ARG A 476 63.34 -107.88 REMARK 500 VAL A 567 -15.09 -149.96 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 MN E 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 10 O3' REMARK 620 2 C E 11 OP1 60.5 REMARK 620 3 ASP A 389 OD1 153.4 94.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN E 103 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C E 11 OP1 REMARK 620 2 ASP A 389 OD2 100.6 REMARK 620 3 GLU A 391 OE2 125.0 87.3 REMARK 620 4 ASP A 533 OD2 128.8 78.5 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 399 OE2 REMARK 620 2 CYS A 506 SG 109.3 REMARK 620 3 HIS A 509 NE2 106.2 107.1 REMARK 620 4 CYS A 529 SG 110.4 122.7 99.5 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 MN E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MWP RELATED DB: PDB REMARK 900 DOMAIN REMARK 900 RELATED ID: 4GV6 RELATED DB: PDB REMARK 900 SOAKING WITH MN2+ FOR 1 MIN REMARK 900 RELATED ID: 4GV3 RELATED DB: PDB REMARK 900 SOAKING WITH MN2+ FOR 1.5 MIN DBREF 4GV9 A 364 569 UNP P13699 NCAP_LASSJ 364 569 DBREF 4GV9 E 8 11 PDB 4GV9 4GV9 8 11 DBREF 4GV9 F 1 5 PDB 4GV9 4GV9 1 5 SEQADV 4GV9 ALA A 357 UNP P13699 EXPRESSION TAG SEQADV 4GV9 MET A 358 UNP P13699 EXPRESSION TAG SEQADV 4GV9 ASP A 359 UNP P13699 EXPRESSION TAG SEQADV 4GV9 HIS A 360 UNP P13699 EXPRESSION TAG SEQADV 4GV9 VAL A 361 UNP P13699 EXPRESSION TAG SEQADV 4GV9 GLU A 362 UNP P13699 EXPRESSION TAG SEQADV 4GV9 PHE A 363 UNP P13699 EXPRESSION TAG SEQRES 1 E 4 GTP G G C SEQRES 1 F 5 C G C C C SEQRES 1 A 213 ALA MET ASP HIS VAL GLU PHE GLY LEU THR TYR SER GLN SEQRES 2 A 213 LEU MET THR LEU LYS ASP ALA MET LEU GLN LEU ASP PRO SEQRES 3 A 213 ASN ALA LYS THR TRP MET ASP ILE GLU GLY ARG PRO GLU SEQRES 4 A 213 ASP PRO VAL GLU ILE ALA LEU TYR GLN PRO SER SER GLY SEQRES 5 A 213 CYS TYR ILE HIS PHE PHE ARG GLU PRO THR ASP LEU LYS SEQRES 6 A 213 GLN PHE LYS GLN ASP ALA LYS TYR SER HIS GLY ILE ASP SEQRES 7 A 213 VAL THR ASP LEU PHE ALA THR GLN PRO GLY LEU THR SER SEQRES 8 A 213 ALA VAL ILE ASP ALA LEU PRO ARG ASN MET VAL ILE THR SEQRES 9 A 213 CYS GLN GLY SER ASP ASP ILE ARG LYS LEU LEU GLU SER SEQRES 10 A 213 GLN GLY ARG LYS ASP ILE LYS LEU ILE ASP ILE ALA LEU SEQRES 11 A 213 SER LYS THR ASP SER ARG LYS TYR GLU ASN ALA VAL TRP SEQRES 12 A 213 ASP GLN TYR LYS ASP LEU CYS HIS MET HIS THR GLY VAL SEQRES 13 A 213 VAL VAL GLU LYS LYS LYS ARG GLY GLY LYS GLU GLU ILE SEQRES 14 A 213 THR PRO HIS CYS ALA LEU MET ASP CYS ILE MET PHE ASP SEQRES 15 A 213 ALA ALA VAL SER GLY GLY LEU ASN THR SER VAL LEU ARG SEQRES 16 A 213 ALA VAL LEU PRO ARG ASP MET VAL PHE ARG THR SER THR SEQRES 17 A 213 PRO ARG VAL VAL LEU MODRES 4GV9 GTP E 8 G GUANOSINE-5'-TRIPHOSPHATE HET GTP E 8 32 HET MN E 101 1 HET MN E 102 1 HET MN E 103 1 HET ZN A 601 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 4 MN 3(MN 2+) FORMUL 7 ZN ZN 2+ FORMUL 8 HOH *9(H2 O) HELIX 1 1 THR A 366 MET A 377 1 12 HELIX 2 2 LEU A 378 LEU A 380 5 3 HELIX 3 3 ASP A 419 SER A 430 1 12 HELIX 4 4 ASP A 434 PHE A 439 5 6 HELIX 5 5 GLY A 444 LEU A 453 1 10 HELIX 6 6 GLY A 463 GLN A 474 1 12 HELIX 7 7 SER A 487 ARG A 492 1 6 HELIX 8 8 TYR A 494 LYS A 503 1 10 HELIX 9 9 ASP A 504 CYS A 506 5 3 HELIX 10 10 CYS A 529 GLY A 543 1 15 HELIX 11 11 PRO A 555 PHE A 560 1 6 SHEET 1 A 4 TRP A 387 ARG A 393 0 SHEET 2 A 4 ASP A 396 TYR A 403 -1 O TYR A 403 N TRP A 387 SHEET 3 A 4 CYS A 409 PHE A 414 -1 O PHE A 413 N ILE A 400 SHEET 4 A 4 ARG A 551 ALA A 552 1 O ARG A 551 N TYR A 410 SHEET 1 B 2 VAL A 458 CYS A 461 0 SHEET 2 B 2 LYS A 480 ASP A 483 1 O LYS A 480 N ILE A 459 SHEET 1 C 2 VAL A 513 VAL A 514 0 SHEET 2 C 2 GLU A 524 ILE A 525 -1 O ILE A 525 N VAL A 513 LINK O3' GTP E 8 P G E 9 1555 1555 1.45 LINK O3' G E 10 MN MN E 101 1555 1555 2.55 LINK OP1 C E 11 MN MN E 101 1555 1555 2.41 LINK OP1 C E 11 MN MN E 103 1555 1555 1.72 LINK MN MN E 101 OD1 ASP A 389 1555 1555 2.20 LINK MN MN E 103 OD2 ASP A 389 1555 1555 2.48 LINK MN MN E 103 OE2 GLU A 391 1555 1555 2.11 LINK MN MN E 103 OD2 ASP A 533 1555 1555 2.28 LINK OE2 GLU A 399 ZN ZN A 601 1555 1555 2.06 LINK SG CYS A 506 ZN ZN A 601 1555 1555 2.18 LINK NE2 HIS A 509 ZN ZN A 601 1555 1555 2.24 LINK SG CYS A 529 ZN ZN A 601 1555 1555 2.07 CISPEP 1 ARG A 566 VAL A 567 0 -11.01 SITE 1 AC1 4 ASP A 389 G E 10 C E 11 MN E 103 SITE 1 AC2 2 G E 9 C F 1 SITE 1 AC3 5 ASP A 389 GLU A 391 ASP A 533 C E 11 SITE 2 AC3 5 MN E 101 SITE 1 AC4 4 GLU A 399 CYS A 506 HIS A 509 CYS A 529 CRYST1 44.780 44.780 221.740 90.00 90.00 90.00 P 41 21 2 8 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 0.022331 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004510 0.00000 HETATM 1 PG GTP E 8 5.787 -12.051 -8.916 1.00150.63 P ANISOU 1 PG GTP E 8 18044 24400 14789 -2976 636 -989 P HETATM 2 O1G GTP E 8 4.934 -10.877 -9.335 1.00152.29 O ANISOU 2 O1G GTP E 8 17971 25606 14284 -3376 -38 61 O HETATM 3 O2G GTP E 8 6.373 -12.831 -10.068 1.00159.13 O ANISOU 3 O2G GTP E 8 19022 26061 15377 -3995 1380 -2265 O HETATM 4 O3G GTP E 8 5.177 -12.906 -7.829 1.00143.11 O ANISOU 4 O3G GTP E 8 17154 22393 14826 -2224 713 -1403 O HETATM 5 O3B GTP E 8 7.066 -11.364 -8.215 1.00146.79 O ANISOU 5 O3B GTP E 8 17791 23216 14765 -2335 452 -720 O HETATM 6 PB GTP E 8 8.101 -12.200 -7.304 1.00143.08 P ANISOU 6 PB GTP E 8 17351 21711 15301 -1690 879 -1266 P HETATM 7 O1B GTP E 8 7.773 -11.933 -5.853 1.00134.68 O ANISOU 7 O1B GTP E 8 16458 19716 14995 -694 396 -553 O HETATM 8 O2B GTP E 8 8.148 -13.624 -7.806 1.00147.98 O ANISOU 8 O2B GTP E 8 17900 22032 16292 -2060 1534 -2394 O HETATM 9 O3A GTP E 8 9.503 -11.499 -7.684 1.00143.02 O ANISOU 9 O3A GTP E 8 17268 21951 15120 -1721 852 -1211 O HETATM 10 PA GTP E 8 10.365 -10.631 -6.634 1.00134.03 P ANISOU 10 PA GTP E 8 16064 20273 14588 -730 753 -378 P HETATM 11 O1A GTP E 8 10.700 -11.510 -5.452 1.00130.11 O ANISOU 11 O1A GTP E 8 15832 18712 14889 -133 782 -732 O HETATM 12 O2A GTP E 8 11.477 -9.957 -7.402 1.00137.62 O ANISOU 12 O2A GTP E 8 16486 21196 14605 -1302 699 -227 O HETATM 13 O5' GTP E 8 9.336 -9.493 -6.141 1.00127.66 O ANISOU 13 O5' GTP E 8 15498 19400 13607 -858 -26 440 O HETATM 14 C5' GTP E 8 9.797 -8.451 -5.281 1.00119.22 C ANISOU 14 C5' GTP E 8 14152 18197 12949 -70 -98 1350 C HETATM 15 C4' GTP E 8 8.668 -7.514 -4.855 1.00114.00 C ANISOU 15 C4' GTP E 8 13600 17292 12420 -255 -710 2055 C HETATM 16 O4' GTP E 8 7.492 -7.670 -5.655 1.00115.12 O ANISOU 16 O4' GTP E 8 13571 18024 12144 -544 -632 2291 O HETATM 17 C3' GTP E 8 8.260 -7.764 -3.413 1.00106.95 C ANISOU 17 C3' GTP E 8 12719 15452 12464 439 -558 1860 C HETATM 18 O3' GTP E 8 8.731 -6.689 -2.592 1.00106.26 O ANISOU 18 O3' GTP E 8 12543 14882 12948 792 -549 2146 O HETATM 19 C2' GTP E 8 6.742 -7.831 -3.409 1.00105.20 C ANISOU 19 C2' GTP E 8 12650 15282 12039 448 -818 2088 C HETATM 20 O2' GTP E 8 6.177 -6.831 -2.555 1.00104.33 O ANISOU 20 O2' GTP E 8 12288 14583 12769 812 -875 2686 O HETATM 21 C1' GTP E 8 6.314 -7.581 -4.845 1.00109.97 C ANISOU 21 C1' GTP E 8 12947 16729 12105 -216 -1007 2534 C HETATM 22 N9 GTP E 8 5.300 -8.582 -5.274 1.00108.26 N ANISOU 22 N9 GTP E 8 12721 17080 11331 -336 -905 2114 N HETATM 23 C8 GTP E 8 5.505 -9.568 -6.168 1.00111.48 C ANISOU 23 C8 GTP E 8 13234 17950 11171 -940 -646 1365 C HETATM 24 N7 GTP E 8 4.387 -10.314 -6.349 1.00111.81 N ANISOU 24 N7 GTP E 8 13264 18222 10997 -1089 -572 1057 N HETATM 25 C5 GTP E 8 3.429 -9.805 -5.555 1.00107.01 C ANISOU 25 C5 GTP E 8 12648 17134 10875 -675 -1055 1705 C HETATM 26 C6 GTP E 8 2.008 -10.118 -5.262 1.00104.99 C ANISOU 26 C6 GTP E 8 12423 16747 10721 -510 -1270 1727 C HETATM 27 O6 GTP E 8 1.430 -11.072 -5.824 1.00106.81 O ANISOU 27 O6 GTP E 8 12709 17345 10529 -891 -1205 1217 O HETATM 28 N1 GTP E 8 1.364 -9.346 -4.374 1.00102.27 N ANISOU 28 N1 GTP E 8 11889 15902 11065 -31 -1505 2348 N HETATM 29 C2 GTP E 8 1.963 -8.307 -3.752 1.00101.16 C ANISOU 29 C2 GTP E 8 11656 15254 11526 398 -1514 2796 C HETATM 30 N2 GTP E 8 1.240 -7.577 -2.869 1.00 99.67 N ANISOU 30 N2 GTP E 8 11247 14461 12163 776 -1576 3269 N HETATM 31 N3 GTP E 8 3.262 -7.965 -3.973 1.00102.53 N ANISOU 31 N3 GTP E 8 11801 15541 11612 282 -1406 2835 N HETATM 32 C4 GTP E 8 4.032 -8.662 -4.849 1.00105.33 C ANISOU 32 C4 GTP E 8 12414 16396 11208 -134 -1193 2241 C