HEADER RNA BINDING PROTEIN 21-MAY-20 7C6B TITLE CRYSTAL STRUCTURE OF AGO2 MID DOMAIN IN COMPLEX WITH 6-(3-(2- TITLE 2 CARBOXYETHYL)PHENYL)PURINE RIBOSIDE MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ARGONAUTE-2; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: HAGO2,ARGONAUTE RISC CATALYTIC COMPONENT 2,EUKARYOTIC COMPND 5 TRANSLATION INITIATION FACTOR 2C 2,EIF2C 2,PAZ PIWI DOMAIN PROTEIN, COMPND 6 PPD,PROTEIN SLICER; COMPND 7 EC: 3.1.26.-; COMPND 8 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: AGO2, EIF2C2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARGONAUTE, MID DOMAIN, RIBONUCLEOPROTEIN, RNA-BINDING, RNA-MEDIATED KEYWDS 2 GENE SILENCING, TRANSLATION REGULATION, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SUZUKI,Y.TAKAHASHI,J.SAITO,H.MIYAGI,F.SHINOHARA REVDAT 3 29-NOV-23 7C6B 1 REMARK REVDAT 2 03-FEB-21 7C6B 1 JRNL REVDAT 1 25-NOV-20 7C6B 0 JRNL AUTH F.SHINOHARA,T.OASHI,T.HARUMOTO,T.NISHIKAWA,Y.TAKAYAMA, JRNL AUTH 2 H.MIYAGI,Y.TAKAHASHI,T.NAKAJIMA,T.SAWADA,Y.KODA,A.MAKINO, JRNL AUTH 3 A.SATO,K.HAMAGUCHI,M.SUZUKI,J.YAMAMOTO,Y.TOMARI,J.I.SAITO JRNL TITL SIRNA POTENCY ENHANCEMENT VIA CHEMICAL MODIFICATIONS OF JRNL TITL 2 NUCLEOTIDE BASES AT THE 5'-END OF THE SIRNA GUIDE STRAND. JRNL REF RNA V. 27 163 2021 JRNL REFN ESSN 1469-9001 JRNL PMID 33177188 JRNL DOI 10.1261/RNA.073783.119 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 48783 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2589 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3583 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 205 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : -0.57000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : 0.14000 REMARK 3 B13 (A**2) : -0.49000 REMARK 3 B23 (A**2) : 0.57000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.614 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3304 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3131 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4485 ; 1.717 ; 1.696 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7282 ; 1.377 ; 1.596 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 404 ; 6.716 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;34.788 ;22.329 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 584 ;15.173 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.285 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 437 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3575 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 644 ; 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): 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 : 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 : A 441 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4337 -10.7326 -23.8075 REMARK 3 T TENSOR REMARK 3 T11: 0.1514 T22: 0.0109 REMARK 3 T33: 0.0758 T12: -0.0101 REMARK 3 T13: -0.0864 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 1.8147 L22: 3.5402 REMARK 3 L33: 3.7279 L12: -0.2573 REMARK 3 L13: 0.7953 L23: 0.1293 REMARK 3 S TENSOR REMARK 3 S11: -0.0709 S12: -0.0488 S13: -0.0272 REMARK 3 S21: -0.0135 S22: 0.0860 S23: 0.1568 REMARK 3 S31: -0.0315 S32: 0.0587 S33: -0.0150 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 : B 441 B 601 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8425 1.0475 -2.7079 REMARK 3 T TENSOR REMARK 3 T11: 0.2589 T22: 0.0372 REMARK 3 T33: 0.1728 T12: 0.0485 REMARK 3 T13: -0.1549 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 4.5892 L22: 2.8693 REMARK 3 L33: 1.6291 L12: 1.3667 REMARK 3 L13: 0.6444 L23: 0.3489 REMARK 3 S TENSOR REMARK 3 S11: 0.2503 S12: -0.1219 S13: 0.1069 REMARK 3 S21: 0.2069 S22: -0.0730 S23: -0.0220 REMARK 3 S31: 0.0341 S32: -0.1775 S33: -0.1773 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 : C 441 C 601 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0860 22.3642 -10.1524 REMARK 3 T TENSOR REMARK 3 T11: 0.4392 T22: 0.0801 REMARK 3 T33: 0.2746 T12: 0.0220 REMARK 3 T13: -0.0540 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 1.7634 L22: 3.5554 REMARK 3 L33: 3.7431 L12: -0.1389 REMARK 3 L13: -0.6274 L23: 1.5221 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: 0.2230 S13: -0.0639 REMARK 3 S21: -0.7154 S22: 0.0562 S23: -0.2679 REMARK 3 S31: -0.2522 S32: 0.2501 S33: -0.0838 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7C6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300017095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51572 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 38.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.429 REMARK 200 R MERGE (I) : 0.19100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.35 REMARK 200 R MERGE FOR SHELL (I) : 1.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 6L45 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE PH8.0, 0.2M NACL, 0.46M REMARK 280 NAH2PO4, 1.84M K2HPO4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 LYS A 440 REMARK 465 ASN A 575 REMARK 465 ASN A 576 REMARK 465 ILE A 577 REMARK 465 LEU A 578 REMARK 465 LYS B 440 REMARK 465 GLY B 573 REMARK 465 VAL B 574 REMARK 465 ASN B 575 REMARK 465 ASN B 576 REMARK 465 ILE B 577 REMARK 465 LEU B 578 REMARK 465 LYS C 440 REMARK 465 ASN C 575 REMARK 465 ASN C 576 REMARK 465 ILE C 577 REMARK 465 LEU C 578 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 792 O HOH A 797 1.95 REMARK 500 O HOH C 768 O HOH C 770 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 ALA C 513 -82.99 -36.71 REMARK 500 VAL C 539 -60.70 -108.95 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 B 791 DISTANCE = 5.89 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K2R A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K2R B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K2R C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6L45 RELATED DB: PDB REMARK 900 PDB ENTRY FOR THE SAME CITATION DBREF 7C6B A 440 578 UNP Q9UKV8 AGO2_HUMAN 440 578 DBREF 7C6B B 440 578 UNP Q9UKV8 AGO2_HUMAN 440 578 DBREF 7C6B C 440 578 UNP Q9UKV8 AGO2_HUMAN 440 578 SEQRES 1 A 139 LYS GLN PHE HIS THR GLY ILE GLU ILE LYS VAL TRP ALA SEQRES 2 A 139 ILE ALA CYS PHE ALA PRO GLN ARG GLN CYS THR GLU VAL SEQRES 3 A 139 HIS LEU LYS SER PHE THR GLU GLN LEU ARG LYS ILE SER SEQRES 4 A 139 ARG ASP ALA GLY MET PRO ILE GLN GLY GLN PRO CYS PHE SEQRES 5 A 139 CYS LYS TYR ALA GLN GLY ALA ASP SER VAL GLU PRO MET SEQRES 6 A 139 PHE ARG HIS LEU LYS ASN THR TYR ALA GLY LEU GLN LEU SEQRES 7 A 139 VAL VAL VAL ILE LEU PRO GLY LYS THR PRO VAL TYR ALA SEQRES 8 A 139 GLU VAL LYS ARG VAL GLY ASP THR VAL LEU GLY MET ALA SEQRES 9 A 139 THR GLN CYS VAL GLN MET LYS ASN VAL GLN ARG THR THR SEQRES 10 A 139 PRO GLN THR LEU SER ASN LEU CYS LEU LYS ILE ASN VAL SEQRES 11 A 139 LYS LEU GLY GLY VAL ASN ASN ILE LEU SEQRES 1 B 139 LYS GLN PHE HIS THR GLY ILE GLU ILE LYS VAL TRP ALA SEQRES 2 B 139 ILE ALA CYS PHE ALA PRO GLN ARG GLN CYS THR GLU VAL SEQRES 3 B 139 HIS LEU LYS SER PHE THR GLU GLN LEU ARG LYS ILE SER SEQRES 4 B 139 ARG ASP ALA GLY MET PRO ILE GLN GLY GLN PRO CYS PHE SEQRES 5 B 139 CYS LYS TYR ALA GLN GLY ALA ASP SER VAL GLU PRO MET SEQRES 6 B 139 PHE ARG HIS LEU LYS ASN THR TYR ALA GLY LEU GLN LEU SEQRES 7 B 139 VAL VAL VAL ILE LEU PRO GLY LYS THR PRO VAL TYR ALA SEQRES 8 B 139 GLU VAL LYS ARG VAL GLY ASP THR VAL LEU GLY MET ALA SEQRES 9 B 139 THR GLN CYS VAL GLN MET LYS ASN VAL GLN ARG THR THR SEQRES 10 B 139 PRO GLN THR LEU SER ASN LEU CYS LEU LYS ILE ASN VAL SEQRES 11 B 139 LYS LEU GLY GLY VAL ASN ASN ILE LEU SEQRES 1 C 139 LYS GLN PHE HIS THR GLY ILE GLU ILE LYS VAL TRP ALA SEQRES 2 C 139 ILE ALA CYS PHE ALA PRO GLN ARG GLN CYS THR GLU VAL SEQRES 3 C 139 HIS LEU LYS SER PHE THR GLU GLN LEU ARG LYS ILE SER SEQRES 4 C 139 ARG ASP ALA GLY MET PRO ILE GLN GLY GLN PRO CYS PHE SEQRES 5 C 139 CYS LYS TYR ALA GLN GLY ALA ASP SER VAL GLU PRO MET SEQRES 6 C 139 PHE ARG HIS LEU LYS ASN THR TYR ALA GLY LEU GLN LEU SEQRES 7 C 139 VAL VAL VAL ILE LEU PRO GLY LYS THR PRO VAL TYR ALA SEQRES 8 C 139 GLU VAL LYS ARG VAL GLY ASP THR VAL LEU GLY MET ALA SEQRES 9 C 139 THR GLN CYS VAL GLN MET LYS ASN VAL GLN ARG THR THR SEQRES 10 C 139 PRO GLN THR LEU SER ASN LEU CYS LEU LYS ILE ASN VAL SEQRES 11 C 139 LYS LEU GLY GLY VAL ASN ASN ILE LEU HET K2R A 601 33 HET K2R B 601 33 HET K2R C 601 33 HET PO4 C 602 5 HET PO4 C 603 5 HETNAM K2R 3-[3-[9-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5- HETNAM 2 K2R (PHOSPHONOOXYMETHYL)OXOLAN-2-YL]PURIN-6- HETNAM 3 K2R YL]PHENYL]PROPANOIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 4 K2R 3(C19 H21 N4 O9 P) FORMUL 7 PO4 2(O4 P 3-) FORMUL 9 HOH *283(H2 O) HELIX 1 AA1 THR A 463 ALA A 481 1 19 HELIX 2 AA2 GLY A 497 ASP A 499 5 3 HELIX 3 AA3 SER A 500 TYR A 512 1 13 HELIX 4 AA4 PRO A 527 THR A 538 1 12 HELIX 5 AA5 MET A 549 ARG A 554 1 6 HELIX 6 AA6 THR A 556 GLY A 572 1 17 HELIX 7 AA7 THR B 463 ALA B 481 1 19 HELIX 8 AA8 GLY B 497 ASP B 499 5 3 HELIX 9 AA9 SER B 500 TYR B 512 1 13 HELIX 10 AB1 PRO B 527 THR B 538 1 12 HELIX 11 AB2 MET B 549 ARG B 554 1 6 HELIX 12 AB3 THR B 556 GLY B 572 1 17 HELIX 13 AB4 THR C 463 ALA C 481 1 19 HELIX 14 AB5 GLY C 497 ASP C 499 5 3 HELIX 15 AB6 SER C 500 TYR C 512 1 13 HELIX 16 AB7 PRO C 527 VAL C 539 1 13 HELIX 17 AB8 MET C 549 ARG C 554 1 6 HELIX 18 AB9 THR C 556 GLY C 572 1 17 SHEET 1 AA1 4 PHE A 491 TYR A 494 0 SHEET 2 AA1 4 TRP A 451 CYS A 455 1 N ILE A 453 O PHE A 491 SHEET 3 AA1 4 LEU A 517 LEU A 522 1 O VAL A 519 N ALA A 452 SHEET 4 AA1 4 THR A 544 GLN A 548 1 O VAL A 547 N LEU A 522 SHEET 1 AA2 4 PHE B 491 TYR B 494 0 SHEET 2 AA2 4 TRP B 451 CYS B 455 1 N CYS B 455 O LYS B 493 SHEET 3 AA2 4 LEU B 517 LEU B 522 1 O VAL B 519 N ALA B 452 SHEET 4 AA2 4 THR B 544 GLN B 548 1 O VAL B 547 N LEU B 522 SHEET 1 AA3 4 PHE C 491 TYR C 494 0 SHEET 2 AA3 4 TRP C 451 CYS C 455 1 N CYS C 455 O LYS C 493 SHEET 3 AA3 4 LEU C 517 LEU C 522 1 O VAL C 519 N ALA C 452 SHEET 4 AA3 4 THR C 544 GLN C 548 1 O GLN C 545 N VAL C 518 SITE 1 AC1 20 LEU A 522 GLY A 524 LYS A 525 THR A 526 SITE 2 AC1 20 PRO A 527 TYR A 529 LYS A 533 THR A 544 SITE 3 AC1 20 GLN A 545 CYS A 546 GLN A 548 LYS A 570 SITE 4 AC1 20 HOH A 716 HOH A 735 HOH A 740 HOH A 749 SITE 5 AC1 20 HOH A 753 HOH A 787 HOH A 788 HOH A 792 SITE 1 AC2 17 HOH A 722 LEU B 522 GLY B 524 LYS B 525 SITE 2 AC2 17 THR B 526 PRO B 527 TYR B 529 LYS B 533 SITE 3 AC2 17 THR B 544 GLN B 545 CYS B 546 GLN B 548 SITE 4 AC2 17 LYS B 570 HOH B 703 HOH B 710 HOH B 711 SITE 5 AC2 17 HOH B 756 SITE 1 AC3 14 VAL B 569 LYS B 570 LEU C 522 GLY C 524 SITE 2 AC3 14 LYS C 525 THR C 526 TYR C 529 LYS C 533 SITE 3 AC3 14 GLN C 545 CYS C 546 GLN C 548 LYS C 570 SITE 4 AC3 14 HOH C 716 HOH C 747 SITE 1 AC4 3 ARG C 475 LYS C 476 ARG C 479 SITE 1 AC5 7 ARG B 475 ARG B 479 LYS C 493 HIS C 507 SITE 2 AC5 7 TYR C 512 HOH C 708 HOH C 724 CRYST1 47.280 66.460 40.420 107.06 95.63 86.40 P 1 3 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 0.021151 -0.001329 0.001775 0.00000 SCALE2 0.000000 0.015076 0.004555 0.00000 SCALE3 0.000000 0.000000 0.025970 0.00000