HEADER IMMUNE SYSTEM 13-APR-16 5JB2 TITLE CRYSTAL STRUCTURE OF CHICKEN LGP2 WITH 5'PPP 10-MER DSRNA AND ADP- TITLE 2 ALF4-MG2+ AT 2.2 A RESOLUTION. 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(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*CP*C)-3'); COMPND 8 CHAIN: X; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 OTHER_DETAILS: SYNTHETIC RNA WITH 5' TRIPHOSPHATE; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: RNA (5'-R(*GPPP*GP*UP*AP*CP*GP*UP*AP*CP*C)-3'); COMPND 14 CHAIN: Y; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 OTHER_DETAILS: SYNTHETIC RNA WITH 5' TRIPHOSPHATE 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS INNATE IMMUNE PATTERN RECOGNITION RECEPTOR, RIG-I LIKE HELICASE, KEYWDS 2 DSRNA DEPENDENT ATPASE, ZINC-CONTAINING CTD DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.CUSACK,E.UCHIKAWA REVDAT 2 10-JAN-24 5JB2 1 LINK REVDAT 1 01-JUN-16 5JB2 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 40943 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2114 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2959 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5364 REMARK 3 NUCLEIC ACID ATOMS : 464 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : -1.20000 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): 0.275 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.877 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6291 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5699 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8654 ; 1.365 ; 1.910 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13112 ; 0.959 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 728 ; 6.124 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 294 ;34.402 ;23.844 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1035 ;15.072 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 53 ;17.321 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 942 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7005 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1538 ; 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): 2831 ; 1.926 ; 3.247 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2830 ; 1.926 ; 3.244 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3586 ; 3.316 ; 4.850 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3587 ; 3.316 ; 4.853 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3460 ; 2.126 ; 3.487 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3459 ; 2.127 ; 3.488 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5068 ; 3.708 ; 5.119 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7220 ; 6.333 ;25.552 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7109 ; 6.274 ;25.460 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 5JB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 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 : 43057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 75.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.640 REMARK 200 R MERGE (I) : 0.16900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7300 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) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.83500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.870 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: 5JAJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CHLGP2, DIRECTLY AFTER SIZE EXCLUSION REMARK 280 CHROMATOGRAPHY, WAS MIXED WITH DSRNA IN A 1:1 RATIO AND REMARK 280 INCUBATED FOR 30 MINUTES ON ICE. THE COMPLEX WAS CONCENTRATED REMARK 280 WITH AN AMICON ULTRA CONCENTRATOR TO AROUND 10 MG/ML AND THEN 2 REMARK 280 MM ADP:ALF4 AND 2 MM MGCL2 WERE ADDED. 5 PRIME TRIPHOSPHATE 10- REMARK 280 MER DSRNA:ADP:ALF4 COMPLEX WAS MIXED WITH RESERVOIR BUFFER (0.1 REMARK 280 M MG FORMATE, 20% PEG3350M) IN A 2:1 RATIO., PH 8, VAPOR REMARK 280 DIFFUSION, SITTING 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 35.07000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.43000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.29000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 -5 REMARK 465 ALA A -4 REMARK 465 MET A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 ARG A 314 REMARK 465 ASP A 315 REMARK 465 THR A 316 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 SER A 1 CB OG 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 AL ALF A 703 O HOH A 817 1.96 REMARK 500 O2B ADP A 702 AL ALF A 703 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 429 O VAL A 561 3549 2.19 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 -63.96 -129.95 REMARK 500 SER A 85 -51.94 -23.09 REMARK 500 LYS A 138 -132.14 54.77 REMARK 500 LYS A 138 -132.14 54.76 REMARK 500 SER A 169 84.49 -156.25 REMARK 500 HIS A 210 -55.45 -169.18 REMARK 500 VAL A 297 -138.55 -130.35 REMARK 500 PRO A 363 -36.91 -30.00 REMARK 500 ASP A 387 40.40 -103.29 REMARK 500 CYS A 392 94.27 -68.40 REMARK 500 GLN A 473 -82.64 -28.29 REMARK 500 ASN A 474 72.92 -104.16 REMARK 500 MET A 573 -54.61 -142.79 REMARK 500 ARG A 624 -109.69 56.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 554 SG REMARK 620 2 CYS A 557 SG 110.3 REMARK 620 3 CYS A 610 SG 113.1 108.5 REMARK 620 4 CYS A 613 SG 101.3 112.5 111.1 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 819 O 157.7 REMARK 620 3 HOH A 828 O 82.5 76.5 REMARK 620 4 HOH A 934 O 95.5 94.3 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG X 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 812 O REMARK 620 2 GTP X 1 O1B 90.3 REMARK 620 3 GTP X 1 O2A 85.3 81.6 REMARK 620 4 G X 2 OP2 174.4 93.7 91.4 REMARK 620 5 HOH X 215 O 89.2 178.7 99.5 86.8 REMARK 620 6 HOH X 224 O 91.4 92.0 172.8 92.4 86.8 REMARK 620 N 1 2 3 4 5 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 MG X 101 DBREF 5JB2 A 2 674 UNP G0YYQ5 G0YYQ5_CHICK 2 674 DBREF 5JB2 X 1 11 PDB 5JB2 5JB2 1 11 DBREF 5JB2 Y 1 10 PDB 5JB2 5JB2 1 10 SEQADV 5JB2 GLY A -5 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 ALA A -4 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 MET A -3 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 GLY A -2 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 GLY A -1 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 GLY A 0 UNP G0YYQ5 EXPRESSION TAG SEQADV 5JB2 SER A 1 UNP G0YYQ5 EXPRESSION TAG SEQRES 1 A 680 GLY ALA MET GLY GLY GLY SER GLU LEU HIS GLY TYR GLN SEQRES 2 A 680 LEU GLU ALA VAL ALA PRO ALA LEU ARG GLY ARG ASN SER SEQRES 3 A 680 ILE VAL TRP LEU PRO THR GLY ALA GLY LYS THR ARG ALA SEQRES 4 A 680 ALA VAL HIS VAL CYS ARG ARG HIS LEU GLU GLY ARG ARG SEQRES 5 A 680 GLY GLY ARG VAL ALA VAL LEU VAL ASN LYS VAL HIS LEU SEQRES 6 A 680 VAL GLN GLN HIS LEU GLU LYS GLU PHE HIS VAL LEU ARG SEQRES 7 A 680 ASP ALA PHE LYS VAL THR ALA VAL SER GLY ASP SER SER SEQRES 8 A 680 HIS LYS CYS PHE PHE GLY GLN LEU ALA LYS GLY SER ASP SEQRES 9 A 680 VAL VAL ILE CYS THR ALA GLN ILE LEU GLN ASN ALA LEU SEQRES 10 A 680 LEU SER GLY GLU GLU GLU ALA ARG VAL GLU LEU THR ASP SEQRES 11 A 680 PHE SER LEU LEU VAL ILE ASP GLU CYS HIS HIS THR GLN SEQRES 12 A 680 LYS GLU ALA VAL TYR ASN LYS ILE MET LEU SER TYR LEU SEQRES 13 A 680 GLN LYS LYS LEU SER GLY GLN ARG ASP LEU PRO GLN ILE SEQRES 14 A 680 LEU GLY LEU THR ALA SER PRO GLY THR GLY GLY GLU THR SEQRES 15 A 680 SER PHE GLU GLY ALA VAL GLU HIS ILE LEU GLN ILE CYS SEQRES 16 A 680 ALA ASN LEU ASP THR GLU VAL ILE ALA SER ALA GLN GLU SEQRES 17 A 680 HIS ALA GLN HIS LEU GLN SER HIS VAL PRO GLN PRO THR SEQRES 18 A 680 LYS GLN TYR ASP LEU CYS GLN GLU ARG GLU GLN ASP PRO SEQRES 19 A 680 PHE GLY GLN ARG LEU LYS LYS ILE MET ALA GLN ILE GLN SEQRES 20 A 680 GLU HIS MET GLU MET PRO GLU LEU PRO GLN ASN PHE GLY SEQRES 21 A 680 THR GLN VAL TYR GLU GLN ARG ILE VAL GLU LEU GLU ASN SEQRES 22 A 680 ARG ALA ALA GLU ARG PHE CYS ARG LYS THR ARG VAL CYS SEQRES 23 A 680 ALA LEU HIS LEU ARG ARG TYR ASN ASP ALA LEU LEU ILE SEQRES 24 A 680 ASN ASP THR VAL ARG MET MET ASP ALA PHE GLN CYS LEU SEQRES 25 A 680 GLN GLN PHE TYR ALA ASP LYS ARG ASP THR LYS ASP PRO SEQRES 26 A 680 THR GLU ARG PHE LEU ALA THR THR PHE GLU GLU ASN ARG SEQRES 27 A 680 ALA THR LEU GLN ALA LEU ALA GLY ASP GLN ARG TYR GLU SEQRES 28 A 680 ASN PRO ARG LEU SER LYS LEU GLU GLU ILE LEU GLN GLU SEQRES 29 A 680 HIS PHE GLN PRO PRO GLY SER SER ARG GLY ILE VAL PHE SEQRES 30 A 680 THR LYS THR ARG GLN SER ALA HIS SER LEU LEU SER TRP SEQRES 31 A 680 LEU GLN ASP THR ALA GLY LEU CYS GLY GLN HIS ILE ARG SEQRES 32 A 680 ALA ALA VAL LEU THR GLY SER GLY HIS SER ASN GLN ALA SEQRES 33 A 680 LYS GLY MET THR GLN ASN GLU GLN GLN ASP VAL ILE THR SEQRES 34 A 680 LEU PHE ARG TYR GLY GLU LEU ASN LEU LEU PHE SER THR SEQRES 35 A 680 SER VAL ALA GLU GLU GLY LEU ASP ILE PRO GLU CYS ASN SEQRES 36 A 680 ILE VAL VAL ARG TYR GLY LEU MET THR ASN GLU ILE ALA SEQRES 37 A 680 MET VAL GLN ALA GLN GLY ARG ALA ARG ALA GLN ASN SER SEQRES 38 A 680 MET TYR SER VAL LEU ALA LYS ALA ASN SER ARG GLU VAL SEQRES 39 A 680 TYR ARG GLU GLN LEU ASN GLU SER LEU VAL GLY LEU MET SEQRES 40 A 680 GLU ARG ALA ILE ARG ALA VAL GLN ALA MET PRO GLU ARG SEQRES 41 A 680 LYS TYR ARG LEU LYS ILE VAL GLU LEU GLN ARG ASN ALA SEQRES 42 A 680 VAL LEU SER TRP GLN VAL LYS GLU ALA ARG SER SER GLU SEQRES 43 A 680 ARG ARG GLN LEU HIS ASP PRO ASP ASP VAL TYR PHE HIS SEQRES 44 A 680 CYS VAL ASN CYS ASN VAL ALA VAL CYS ARG GLY SER ASP SEQRES 45 A 680 ILE ARG THR VAL GLU ALA MET HIS HIS VAL ASN ILE ASN SEQRES 46 A 680 PRO ASN PHE ARG PHE TYR TYR THR VAL SER SER GLY LYS SEQRES 47 A 680 ILE HIS PHE GLU ARG THR PHE ARG ASP TRP GLU PRO GLY SEQRES 48 A 680 CYS ARG ILE VAL CYS SER GLU CYS ARG GLN GLU TRP GLY SEQRES 49 A 680 MET GLU MET ILE TYR ARG ASN VAL THR LEU PRO ILE LEU SEQRES 50 A 680 SER ILE LYS ASN PHE VAL VAL VAL THR PRO ASP GLU LYS SEQRES 51 A 680 LYS LYS TYR LYS LYS TRP SER THR VAL THR PHE PRO ILE SEQRES 52 A 680 GLU GLU PHE SER TYR LEU GLU TYR CYS SER SER THR GLN SEQRES 53 A 680 ASP GLU SER LEU SEQRES 1 X 11 GTP G U A C G U A C C C SEQRES 1 Y 10 GTP G U A C G U A C C HET GTP X 1 32 HET GTP Y 1 32 HET ZN A 701 1 HET ADP A 702 27 HET ALF A 703 5 HET MG A 704 1 HET MG X 101 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM MG MAGNESIUM ION FORMUL 2 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 ZN ZN 2+ FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 ALF AL F4 1- FORMUL 7 MG 2(MG 2+) FORMUL 9 HOH *344(H2 O) HELIX 1 AA1 HIS A 4 VAL A 11 1 8 HELIX 2 AA2 VAL A 11 ARG A 16 1 6 HELIX 3 AA3 GLY A 29 GLY A 44 1 16 HELIX 4 AA4 VAL A 57 GLU A 67 1 11 HELIX 5 AA5 PHE A 68 ALA A 74 5 7 HELIX 6 AA6 SER A 84 CYS A 88 5 5 HELIX 7 AA7 PHE A 89 GLY A 96 1 8 HELIX 8 AA8 ALA A 104 SER A 113 1 10 HELIX 9 AA9 GLU A 121 PHE A 125 5 5 HELIX 10 AB1 GLU A 132 THR A 136 5 5 HELIX 11 AB2 ALA A 140 SER A 155 1 16 HELIX 12 AB3 SER A 177 LEU A 192 1 16 HELIX 13 AB4 HIS A 203 SER A 209 1 7 HELIX 14 AB5 ASP A 227 GLU A 245 1 19 HELIX 15 AB6 THR A 255 ARG A 272 1 18 HELIX 16 AB7 CYS A 274 VAL A 297 1 24 HELIX 17 AB8 ARG A 298 ASP A 312 1 15 HELIX 18 AB9 ASP A 318 GLY A 340 1 23 HELIX 19 AC1 ASP A 341 GLU A 345 5 5 HELIX 20 AC2 ASN A 346 PHE A 360 1 15 HELIX 21 AC3 THR A 374 ASP A 387 1 14 HELIX 22 AC4 THR A 414 TYR A 427 1 14 HELIX 23 AC5 SER A 437 GLU A 440 5 4 HELIX 24 AC6 ASN A 459 GLY A 468 1 10 HELIX 25 AC7 SER A 485 MET A 511 1 27 HELIX 26 AC8 PRO A 512 GLN A 543 1 32 HELIX 27 AC9 ASP A 546 ASP A 549 5 4 HELIX 28 AD1 ASN A 581 PHE A 584 5 4 HELIX 29 AD2 SER A 661 GLN A 670 1 10 SHEET 1 AA1 7 VAL A 77 VAL A 80 0 SHEET 2 AA1 7 VAL A 99 THR A 103 1 O ILE A 101 N VAL A 80 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 TRP A 23 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 VAL A 451 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 CYS A 562 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 2 ILE A 567 VAL A 570 0 SHEET 2 AA4 2 HIS A 574 ASN A 577 -1 O VAL A 576 N ARG A 568 SHEET 1 AA5 4 TYR A 586 VAL A 588 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 O3' GTP X 1 P G X 2 1555 1555 1.60 LINK O3' GTP Y 1 P G Y 2 1555 1555 1.62 LINK SG CYS A 554 ZN ZN A 701 1555 1555 2.23 LINK SG CYS A 557 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 610 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 613 ZN ZN A 701 1555 1555 2.36 LINK O3B ADP A 702 MG MG A 704 1555 1555 2.07 LINK MG MG A 704 O HOH A 819 1555 1555 2.18 LINK MG MG A 704 O HOH A 828 1555 1555 2.24 LINK MG MG A 704 O HOH A 934 1555 1555 1.98 LINK O HOH A 812 MG MG X 101 1555 1555 2.18 LINK O1B GTP X 1 MG MG X 101 1555 1555 2.09 LINK O2A GTP X 1 MG MG X 101 1555 1555 2.05 LINK OP2 G X 2 MG MG X 101 1555 1555 1.99 LINK MG MG X 101 O HOH X 215 1555 1555 2.17 LINK MG MG X 101 O HOH X 224 1555 1555 2.24 CISPEP 1 GLN A 361 PRO A 362 0 3.65 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 HOH A 804 SITE 5 AC2 21 HOH A 828 HOH A 869 HOH A 934 HOH A 935 SITE 6 AC2 21 HOH A 999 SITE 1 AC3 14 THR A 26 GLY A 27 LYS A 30 GLU A 132 SITE 2 AC3 14 GLY A 442 ARG A 469 ARG A 471 ADP A 702 SITE 3 AC3 14 MG A 704 HOH A 817 HOH A 819 HOH A 852 SITE 4 AC3 14 HOH A 934 HOH A 988 SITE 1 AC4 5 ADP A 702 ALF A 703 HOH A 819 HOH A 828 SITE 2 AC4 5 HOH A 934 SITE 1 AC5 5 HOH A 812 GTP X 1 G X 2 HOH X 215 SITE 2 AC5 5 HOH X 224 CRYST1 70.140 96.580 122.860 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 0.014257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008139 0.00000