PDB Short entry for 5JAJ HEADER RNA BINDING PROTEIN 12-APR-16 5JAJ TITLE STRUCTURE OF CHICKEN LGP2 WITHA 5'P 10-MER DSRNA AND ADP-ALF4-MG. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LGP2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3'); COMPND 8 CHAIN: X; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: RNA (5'-R(P*GP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3'); COMPND 12 CHAIN: Y; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETM11SUMO; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS INNATE IMMUNE PATTERN RECOGNITION RECEPTOR, RIG-I LIKE HELCASE, DSRNA KEYWDS 2 BINDING, DSRNA-DEPENDENT ATPASE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.CUSACK,E.UCHIKAWA REVDAT 3 10-JAN-24 5JAJ 1 LINK REVDAT 2 20-FEB-19 5JAJ 1 SOURCE REVDAT 1 01-JUN-16 5JAJ 0 JRNL AUTH E.UCHIKAWA,M.LETHIER,H.MALET,J.BRUNEL,D.GERLIER,S.CUSACK JRNL TITL STRUCTURAL ANALYSIS OF DSRNA BINDING TO ANTI-VIRAL PATTERN JRNL TITL 2 RECOGNITION RECEPTORS LGP2 AND MDA5. JRNL REF MOL.CELL V. 62 586 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 27203181 JRNL DOI 10.1016/J.MOLCEL.2016.04.021 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 126226 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) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6681 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9206 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 514 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5228 REMARK 3 NUCLEIC ACID ATOMS : 448 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 563 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00000 REMARK 3 B22 (A**2) : -0.62000 REMARK 3 B33 (A**2) : -0.38000 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): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.413 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6254 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5670 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8612 ; 1.510 ; 1.887 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13039 ; 1.014 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 721 ; 5.826 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 287 ;33.296 ;23.693 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1021 ;13.321 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;18.634 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 944 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6950 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1536 ; 0.002 ; 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): 2791 ; 2.990 ; 2.561 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2790 ; 2.991 ; 2.559 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3543 ; 3.658 ; 3.840 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3544 ; 3.657 ; 3.843 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3463 ; 4.252 ; 2.983 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3463 ; 4.252 ; 2.983 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5070 ; 4.929 ; 4.308 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7800 ; 5.578 ;22.338 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7562 ; 5.276 ;21.866 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11924 ; 2.681 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 170 ;36.294 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 12138 ;14.583 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5JAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 132907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 76.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.250 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.27 REMARK 200 R MERGE FOR SHELL (I) : 0.74600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.310 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3TMI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5PRIME MONOPHOSPHATE 10-MER REMARK 280 DSRNA:ADP:ALF4:MG COMPLEX WAS MIXED WITH RESERVOIR BUFFER (0.1 M REMARK 280 TRI-SODIUM CITRATE DIHYDRATE PH 6.1, 0.04-0.08 M AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE) IN A 2:1 RATIO., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 34.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.26000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.26000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.52500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, Y 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 -6 REMARK 465 ALA A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 GLU A 202 REMARK 465 HIS A 203 REMARK 465 ALA A 204 REMARK 465 GLN A 205 REMARK 465 HIS A 206 REMARK 465 LEU A 207 REMARK 465 GLN A 208 REMARK 465 SER A 209 REMARK 465 HIS A 210 REMARK 465 VAL A 211 REMARK 465 PRO A 212 REMARK 465 LYS A 313 REMARK 465 ARG A 314 REMARK 465 ASP A 315 REMARK 465 THR A 316 REMARK 465 PRO A 362 REMARK 465 PRO A 363 REMARK 465 GLU A 672 REMARK 465 SER A 673 REMARK 465 LEU A 674 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 213 CG CD OE1 NE2 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 O2B ADP A 702 AL ALF A 703 1.95 REMARK 500 AL ALF A 703 O HOH A 836 1.95 REMARK 500 O HOH A 1190 O HOH X 127 2.13 REMARK 500 O HOH A 865 O HOH A 1255 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 G X 1 P G X 1 OP3 -0.119 REMARK 500 G X 1 P G X 1 OP3 -0.112 REMARK 500 G Y 1 P G Y 1 OP3 -0.114 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 ARG A 503 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 503 NE - CZ - NH2 ANGL. DEV. = -4.9 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 GLU A 67 -61.71 -133.76 REMARK 500 LYS A 138 -136.37 57.81 REMARK 500 LYS A 138 -136.37 59.16 REMARK 500 SER A 169 85.15 -159.50 REMARK 500 VAL A 297 -138.90 -130.37 REMARK 500 ALA A 410 118.89 -166.03 REMARK 500 MET A 573 -48.84 -136.49 REMARK 500 ARG A 624 -117.45 48.92 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 G X 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1289 DISTANCE = 7.32 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 554 SG REMARK 620 2 CYS A 557 SG 111.0 REMARK 620 3 CYS A 610 SG 110.4 110.3 REMARK 620 4 CYS A 613 SG 103.5 112.2 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 704 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 702 O3B REMARK 620 2 HOH A 851 O 171.8 REMARK 620 3 HOH A 922 O 88.8 85.3 REMARK 620 4 HOH A 990 O 91.3 95.2 98.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MGF Y 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH X 126 O REMARK 620 2 MGF Y 101 F1 107.3 REMARK 620 3 MGF Y 101 F2 101.2 114.3 REMARK 620 4 MGF Y 101 F3 107.6 121.9 102.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ALF A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MGF Y 101 DBREF 5JAJ A 2 674 UNP G0YYQ5 G0YYQ5_CHICK 2 674 DBREF 5JAJ X 1 11 PDB 5JAJ 5JAJ 1 11 DBREF 5JAJ Y 1 10 PDB 5JAJ 5JAJ 1 10 SEQADV 5JAJ GLY A -6 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ ALA A -5 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ MET A -4 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ GLY A -3 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ GLY A -2 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ GLY A -1 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ GLY A 0 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JAJ SER A 1 UNP G0YYQ5 EXPRESSION TAG SEQRES 1 A 681 GLY ALA MET GLY GLY GLY GLY SER GLU LEU HIS GLY TYR SEQRES 2 A 681 GLN LEU GLU ALA VAL ALA PRO ALA LEU ARG GLY ARG ASN SEQRES 3 A 681 SER ILE VAL TRP LEU PRO THR GLY ALA GLY LYS THR ARG SEQRES 4 A 681 ALA ALA VAL HIS VAL CYS ARG ARG HIS LEU GLU GLY ARG SEQRES 5 A 681 ARG GLY GLY ARG VAL ALA VAL LEU VAL ASN LYS VAL HIS SEQRES 6 A 681 LEU VAL GLN GLN HIS LEU GLU LYS GLU PHE HIS VAL LEU SEQRES 7 A 681 ARG ASP ALA PHE LYS VAL THR ALA VAL SER GLY ASP SER SEQRES 8 A 681 SER HIS LYS CYS PHE PHE GLY GLN LEU ALA LYS GLY SER SEQRES 9 A 681 ASP VAL VAL ILE CYS THR ALA GLN ILE LEU GLN ASN ALA SEQRES 10 A 681 LEU LEU SER GLY GLU GLU GLU ALA ARG VAL GLU LEU THR SEQRES 11 A 681 ASP PHE SER LEU LEU VAL ILE ASP GLU CYS HIS HIS THR SEQRES 12 A 681 GLN LYS GLU ALA VAL TYR ASN LYS ILE MET LEU SER TYR SEQRES 13 A 681 LEU GLN LYS LYS LEU SER GLY GLN ARG ASP LEU PRO GLN SEQRES 14 A 681 ILE LEU GLY LEU THR ALA SER PRO GLY THR GLY GLY GLU SEQRES 15 A 681 THR SER PHE GLU GLY ALA VAL GLU HIS ILE LEU GLN ILE SEQRES 16 A 681 CYS ALA ASN LEU ASP THR GLU VAL ILE ALA SER ALA GLN SEQRES 17 A 681 GLU HIS ALA GLN HIS LEU GLN SER HIS VAL PRO GLN PRO SEQRES 18 A 681 THR LYS GLN TYR ASP LEU CYS GLN GLU ARG GLU GLN ASP SEQRES 19 A 681 PRO PHE GLY GLN ARG LEU LYS LYS ILE MET ALA GLN ILE SEQRES 20 A 681 GLN GLU HIS MET GLU MET PRO GLU LEU PRO GLN ASN PHE SEQRES 21 A 681 GLY THR GLN VAL TYR GLU GLN ARG ILE VAL GLU LEU GLU SEQRES 22 A 681 ASN ARG ALA ALA GLU ARG PHE CYS ARG LYS THR ARG VAL SEQRES 23 A 681 CYS ALA LEU HIS LEU ARG ARG TYR ASN ASP ALA LEU LEU SEQRES 24 A 681 ILE ASN ASP THR VAL ARG MET MET ASP ALA PHE GLN CYS SEQRES 25 A 681 LEU GLN GLN PHE TYR ALA ASP LYS ARG ASP THR LYS ASP SEQRES 26 A 681 PRO THR GLU ARG PHE LEU ALA THR THR PHE GLU GLU ASN SEQRES 27 A 681 ARG ALA THR LEU GLN ALA LEU ALA GLY ASP GLN ARG TYR SEQRES 28 A 681 GLU ASN PRO ARG LEU SER LYS LEU GLU GLU ILE LEU GLN SEQRES 29 A 681 GLU HIS PHE GLN PRO PRO GLY SER SER ARG GLY ILE VAL SEQRES 30 A 681 PHE THR LYS THR ARG GLN SER ALA HIS SER LEU LEU SER SEQRES 31 A 681 TRP LEU GLN ASP THR ALA GLY LEU CYS GLY GLN HIS ILE SEQRES 32 A 681 ARG ALA ALA VAL LEU THR GLY SER GLY HIS SER ASN GLN SEQRES 33 A 681 ALA LYS GLY MET THR GLN ASN GLU GLN GLN ASP VAL ILE SEQRES 34 A 681 THR LEU PHE ARG TYR GLY GLU LEU ASN LEU LEU PHE SER SEQRES 35 A 681 THR SER VAL ALA GLU GLU GLY LEU ASP ILE PRO GLU CYS SEQRES 36 A 681 ASN ILE VAL VAL ARG TYR GLY LEU MET THR ASN GLU ILE SEQRES 37 A 681 ALA MET VAL GLN ALA GLN GLY ARG ALA ARG ALA GLN ASN SEQRES 38 A 681 SER MET TYR SER VAL LEU ALA LYS ALA ASN SER ARG GLU SEQRES 39 A 681 VAL TYR ARG GLU GLN LEU ASN GLU SER LEU VAL GLY LEU SEQRES 40 A 681 MET GLU ARG ALA ILE ARG ALA VAL GLN ALA MET PRO GLU SEQRES 41 A 681 ARG LYS TYR ARG LEU LYS ILE VAL GLU LEU GLN ARG ASN SEQRES 42 A 681 ALA VAL LEU SER TRP GLN VAL LYS GLU ALA ARG SER SER SEQRES 43 A 681 GLU ARG ARG GLN LEU HIS ASP PRO ASP ASP VAL TYR PHE SEQRES 44 A 681 HIS CYS VAL ASN CYS ASN VAL ALA VAL CYS ARG GLY SER SEQRES 45 A 681 ASP ILE ARG THR VAL GLU ALA MET HIS HIS VAL ASN ILE SEQRES 46 A 681 ASN PRO ASN PHE ARG PHE TYR TYR THR VAL SER SER GLY SEQRES 47 A 681 LYS ILE HIS PHE GLU ARG THR PHE ARG ASP TRP GLU PRO SEQRES 48 A 681 GLY CYS ARG ILE VAL CYS SER GLU CYS ARG GLN GLU TRP SEQRES 49 A 681 GLY MET GLU MET ILE TYR ARG ASN VAL THR LEU PRO ILE SEQRES 50 A 681 LEU SER ILE LYS ASN PHE VAL VAL VAL THR PRO ASP GLU SEQRES 51 A 681 LYS LYS LYS TYR LYS LYS TRP SER THR VAL THR PHE PRO SEQRES 52 A 681 ILE GLU GLU PHE SER TYR LEU GLU TYR CYS SER SER THR SEQRES 53 A 681 GLN ASP GLU SER LEU SEQRES 1 X 11 G G U A C G U A C C C SEQRES 1 Y 10 G G U A C G U A C C HET ZN A 701 1 HET ADP A 702 27 HET ALF A 703 5 HET MG A 704 1 HET EDO A 705 4 HET EDO A 706 4 HET EDO A 707 4 HET MGF Y 101 4 HETNAM ZN ZINC ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM MGF TRIFLUOROMAGNESATE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ZN ZN 2+ FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 ALF AL F4 1- FORMUL 7 MG MG 2+ FORMUL 8 EDO 3(C2 H6 O2) FORMUL 11 MGF F3 MG 1- FORMUL 12 HOH *563(H2 O) HELIX 1 AA1 HIS A 4 ARG A 16 1 13 HELIX 2 AA2 GLY A 29 GLY A 44 1 16 HELIX 3 AA3 LYS A 56 GLU A 67 1 12 HELIX 4 AA4 PHE A 68 ALA A 74 5 7 HELIX 5 AA5 PHE A 89 GLY A 96 1 8 HELIX 6 AA6 ALA A 104 SER A 113 1 10 HELIX 7 AA7 GLU A 121 PHE A 125 5 5 HELIX 8 AA8 GLU A 132 THR A 136 5 5 HELIX 9 AA9 ALA A 140 SER A 155 1 16 HELIX 10 AB1 SER A 177 LEU A 192 1 16 HELIX 11 AB2 ASP A 227 GLU A 245 1 19 HELIX 12 AB3 THR A 255 ARG A 272 1 18 HELIX 13 AB4 CYS A 274 VAL A 297 1 24 HELIX 14 AB5 ARG A 298 ASP A 312 1 15 HELIX 15 AB6 ASP A 318 GLY A 340 1 23 HELIX 16 AB7 ASP A 341 GLU A 345 5 5 HELIX 17 AB8 ASN A 346 PHE A 360 1 15 HELIX 18 AB9 THR A 374 ASP A 387 1 14 HELIX 19 AC1 THR A 414 TYR A 427 1 14 HELIX 20 AC2 SER A 437 GLU A 440 5 4 HELIX 21 AC3 ASN A 459 GLY A 468 1 10 HELIX 22 AC4 SER A 485 MET A 511 1 27 HELIX 23 AC5 PRO A 512 GLN A 543 1 32 HELIX 24 AC6 ASP A 546 ASP A 549 5 4 HELIX 25 AC7 ASN A 581 PHE A 584 5 4 HELIX 26 AC8 LYS A 649 VAL A 653 5 5 HELIX 27 AC9 SER A 661 ASP A 671 1 11 SHEET 1 AA1 7 VAL A 77 VAL A 80 0 SHEET 2 AA1 7 VAL A 99 THR A 103 1 O VAL A 99 N THR A 78 SHEET 3 AA1 7 VAL A 50 VAL A 54 1 N VAL A 52 O VAL A 100 SHEET 4 AA1 7 LEU A 127 ILE A 130 1 O VAL A 129 N LEU A 53 SHEET 5 AA1 7 GLN A 162 THR A 167 1 O GLN A 162 N LEU A 128 SHEET 6 AA1 7 SER A 20 TRP A 23 1 N VAL A 22 O GLY A 165 SHEET 7 AA1 7 VAL A 196 ALA A 198 1 O ALA A 198 N ILE A 21 SHEET 1 AA2 6 THR A 215 CYS A 221 0 SHEET 2 AA2 6 MET A 476 LYS A 482 1 O VAL A 479 N ASP A 219 SHEET 3 AA2 6 ILE A 450 TYR A 454 1 N ARG A 453 O SER A 478 SHEET 4 AA2 6 GLY A 368 PHE A 371 1 N PHE A 371 O VAL A 452 SHEET 5 AA2 6 LEU A 432 SER A 435 1 O LEU A 433 N VAL A 370 SHEET 6 AA2 6 ALA A 398 LEU A 401 1 N LEU A 401 O PHE A 434 SHEET 1 AA3 4 ALA A 560 ARG A 563 0 SHEET 2 AA3 4 TYR A 551 CYS A 554 -1 N PHE A 552 O VAL A 561 SHEET 3 AA3 4 PHE A 636 VAL A 639 -1 O VAL A 639 N TYR A 551 SHEET 4 AA3 4 LYS A 644 LYS A 645 -1 O LYS A 645 N VAL A 638 SHEET 1 AA4 3 HIS A 574 ASN A 577 0 SHEET 2 AA4 3 ILE A 567 VAL A 570 -1 N VAL A 570 O HIS A 574 SHEET 3 AA4 3 GLU A 658 GLU A 659 1 O GLU A 658 N THR A 569 SHEET 1 AA5 4 TYR A 586 LYS A 592 0 SHEET 2 AA5 4 TRP A 602 CYS A 610 -1 O VAL A 609 N THR A 587 SHEET 3 AA5 4 GLU A 616 TYR A 623 -1 O ILE A 622 N GLU A 603 SHEET 4 AA5 4 VAL A 626 LEU A 631 -1 O ILE A 630 N MET A 619 LINK SG CYS A 554 ZN ZN A 701 1555 1555 2.35 LINK SG CYS A 557 ZN ZN A 701 1555 1555 2.34 LINK SG CYS A 610 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 613 ZN ZN A 701 1555 1555 2.29 LINK O3B ADP A 702 MG MG A 704 1555 1555 2.03 LINK MG MG A 704 O HOH A 851 1555 1555 2.04 LINK MG MG A 704 O HOH A 922 1555 1555 2.00 LINK MG MG A 704 O HOH A 990 1555 1555 2.10 LINK O HOH X 126 MG MGF Y 101 1555 1555 1.90 SITE 1 AC1 4 CYS A 554 CYS A 557 CYS A 610 CYS A 613 SITE 1 AC2 21 GLU A 2 LEU A 3 HIS A 4 GLN A 7 SITE 2 AC2 21 GLY A 27 ALA A 28 GLY A 29 LYS A 30 SITE 3 AC2 21 THR A 31 ARG A 32 GLU A 67 ASP A 444 SITE 4 AC2 21 ARG A 471 ALF A 703 MG A 704 EDO A 705 SITE 5 AC2 21 HOH A 853 HOH A 887 HOH A 922 HOH A 990 SITE 6 AC2 21 HOH A1044 SITE 1 AC3 15 THR A 26 GLY A 27 LYS A 30 GLU A 132 SITE 2 AC3 15 ALA A 168 GLY A 442 ARG A 469 ARG A 471 SITE 3 AC3 15 ADP A 702 MG A 704 HOH A 836 HOH A 851 SITE 4 AC3 15 HOH A 872 HOH A 990 HOH A1059 SITE 1 AC4 5 ADP A 702 ALF A 703 HOH A 851 HOH A 922 SITE 2 AC4 5 HOH A 990 SITE 1 AC5 6 THR A 31 GLN A 62 HIS A 63 GLU A 67 SITE 2 AC5 6 ASP A 444 ADP A 702 SITE 1 AC6 5 LYS A 138 ASN A 143 LEU A 147 TRP A 531 SITE 2 AC6 5 HOH A 892 SITE 1 AC7 5 VAL A 196 ILE A 197 VAL A 508 GLN A 509 SITE 2 AC7 5 HOH A 945 SITE 1 AC8 7 LYS A 56 HOH A 987 HOH A1235 G X 6 SITE 2 AC8 7 HOH X 126 G Y 6 U Y 7 CRYST1 69.590 97.050 122.520 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014370 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008162 0.00000