HEADER HYDROLASE 26-DEC-17 6FDO TITLE RIO2 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE RIO2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RIO KINASE 2; COMPND 5 EC: 2.7.11.1; COMPND 6 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: RIOK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS KINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FRIBOURG REVDAT 5 08-MAY-24 6FDO 1 REMARK REVDAT 4 09-OCT-19 6FDO 1 JRNL REVDAT 3 11-SEP-19 6FDO 1 JRNL REVDAT 2 27-FEB-19 6FDO 1 HEADER KEYWDS REVDAT 1 30-JAN-19 6FDO 0 JRNL AUTH F.MAURICE,N.PEREBASKINE,S.THORE,S.FRIBOURG JRNL TITL IN VITRO DIMERIZATION OF HUMAN RIO2 KINASE. JRNL REF RNA BIOL. V. 16 1633 2019 JRNL REFN ESSN 1555-8584 JRNL PMID 31390939 JRNL DOI 10.1080/15476286.2019.1653679 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24612 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1193 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2985 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2343 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2838 REMARK 3 BIN R VALUE (WORKING SET) : 0.2294 REMARK 3 BIN FREE R VALUE : 0.3326 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.92 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4614 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.17750 REMARK 3 B22 (A**2) : 4.17750 REMARK 3 B33 (A**2) : -8.35490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.350 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.402 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.271 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.449 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.282 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4714 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 6357 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1675 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 798 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4714 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 591 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5297 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.68 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.96 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 70.4745 -8.7822 11.1506 REMARK 3 T TENSOR REMARK 3 T11: -0.4136 T22: -0.2161 REMARK 3 T33: -0.4350 T12: 0.1184 REMARK 3 T13: -0.0710 T23: -0.1043 REMARK 3 L TENSOR REMARK 3 L11: 1.7220 L22: 2.2370 REMARK 3 L33: 2.6583 L12: -0.0562 REMARK 3 L13: 0.5722 L23: 0.2094 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.2451 S13: 0.0168 REMARK 3 S21: 0.1252 S22: -0.0413 S23: -0.2182 REMARK 3 S31: -0.1063 S32: 0.6058 S33: 0.0087 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 47.6100 -19.7951 8.4806 REMARK 3 T TENSOR REMARK 3 T11: -0.4464 T22: -0.3486 REMARK 3 T33: -0.2515 T12: 0.1169 REMARK 3 T13: -0.0169 T23: -0.2238 REMARK 3 L TENSOR REMARK 3 L11: 3.0454 L22: 3.6990 REMARK 3 L33: 1.7514 L12: -0.8402 REMARK 3 L13: 0.1572 L23: 0.3132 REMARK 3 S TENSOR REMARK 3 S11: -0.0913 S12: 0.0837 S13: -0.5547 REMARK 3 S21: 0.1679 S22: -0.1262 S23: 0.6003 REMARK 3 S31: 0.1406 S32: -0.2671 S33: 0.2175 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200008141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 279056 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : NULL 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.490 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS D2, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 208.13000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.06500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 156.09750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.03250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 260.16250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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 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 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 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 MET A 1 REMARK 465 GLY A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 4 REMARK 465 ASN A 5 REMARK 465 VAL A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 8 REMARK 465 LEU A 9 REMARK 465 THR A 67 REMARK 465 LYS A 68 REMARK 465 SER A 131 REMARK 465 PHE A 132 REMARK 465 ARG A 133 REMARK 465 ASN A 134 REMARK 465 LEU A 135 REMARK 465 LYS A 136 REMARK 465 ASN A 137 REMARK 465 LYS A 138 REMARK 465 ARG A 139 REMARK 465 ASP A 140 REMARK 465 TYR A 141 REMARK 465 HIS A 142 REMARK 465 LYS A 143 REMARK 465 HIS A 144 REMARK 465 ARG A 145 REMARK 465 HIS A 146 REMARK 465 GLU A 314 REMARK 465 LEU A 315 REMARK 465 LEU A 316 REMARK 465 HIS A 317 REMARK 465 PRO A 318 REMARK 465 LEU A 319 REMARK 465 GLY A 320 REMARK 465 PRO A 321 REMARK 465 ASP A 322 REMARK 465 ASP A 323 REMARK 465 LYS A 324 REMARK 465 ASN A 325 REMARK 465 ILE A 326 REMARK 465 GLU A 327 REMARK 465 THR A 328 REMARK 465 LYS A 329 REMARK 465 GLU A 330 REMARK 465 GLY A 331 REMARK 465 SER A 332 REMARK 465 GLU A 333 REMARK 465 PHE A 334 REMARK 465 SER A 335 REMARK 465 PHE A 336 REMARK 465 SER A 337 REMARK 465 ASP A 338 REMARK 465 GLY A 339 REMARK 465 GLU A 340 REMARK 465 VAL A 341 REMARK 465 ALA A 342 REMARK 465 GLU A 343 REMARK 465 LYS A 344 REMARK 465 ALA A 345 REMARK 465 GLU A 346 REMARK 465 VAL A 347 REMARK 465 TYR A 348 REMARK 465 GLY A 349 REMARK 465 SER A 350 REMARK 465 GLU A 351 REMARK 465 ASN A 352 REMARK 465 GLU A 353 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 LYS B 3 REMARK 465 VAL B 4 REMARK 465 ASN B 5 REMARK 465 VAL B 6 REMARK 465 ALA B 7 REMARK 465 LYS B 8 REMARK 465 LEU B 9 REMARK 465 LYS B 45 REMARK 465 HIS B 46 REMARK 465 THR B 69 REMARK 465 SER B 131 REMARK 465 PHE B 132 REMARK 465 ARG B 133 REMARK 465 ASN B 134 REMARK 465 LEU B 135 REMARK 465 LYS B 136 REMARK 465 ASN B 137 REMARK 465 LYS B 138 REMARK 465 ARG B 139 REMARK 465 ASP B 140 REMARK 465 TYR B 141 REMARK 465 HIS B 142 REMARK 465 LYS B 143 REMARK 465 HIS B 144 REMARK 465 ARG B 145 REMARK 465 HIS B 146 REMARK 465 ASP B 313 REMARK 465 GLU B 314 REMARK 465 LEU B 315 REMARK 465 LEU B 316 REMARK 465 HIS B 317 REMARK 465 PRO B 318 REMARK 465 LEU B 319 REMARK 465 GLY B 320 REMARK 465 PRO B 321 REMARK 465 ASP B 322 REMARK 465 ASP B 323 REMARK 465 LYS B 324 REMARK 465 ASN B 325 REMARK 465 ILE B 326 REMARK 465 GLU B 327 REMARK 465 THR B 328 REMARK 465 LYS B 329 REMARK 465 GLU B 330 REMARK 465 GLY B 331 REMARK 465 SER B 332 REMARK 465 GLU B 333 REMARK 465 PHE B 334 REMARK 465 SER B 335 REMARK 465 PHE B 336 REMARK 465 SER B 337 REMARK 465 ASP B 338 REMARK 465 GLY B 339 REMARK 465 GLU B 340 REMARK 465 VAL B 341 REMARK 465 ALA B 342 REMARK 465 GLU B 343 REMARK 465 LYS B 344 REMARK 465 ALA B 345 REMARK 465 GLU B 346 REMARK 465 VAL B 347 REMARK 465 TYR B 348 REMARK 465 GLY B 349 REMARK 465 SER B 350 REMARK 465 GLU B 351 REMARK 465 ASN B 352 REMARK 465 GLU B 353 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 THR A 69 OG1 CG2 REMARK 470 ARG B 292 CG CD NE CZ NH1 NH2 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 LEU A 296 N VAL A 298 2.16 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 CZ ARG A 66 OD1 ASP A 294 5665 2.14 REMARK 500 NE ARG A 66 OD1 ASP A 294 5665 2.15 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 GLN A 71 C - N - CA ANGL. DEV. = 16.8 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 MET A 12 -68.71 -96.97 REMARK 500 SER A 13 139.29 83.53 REMARK 500 HIS A 30 131.08 61.88 REMARK 500 SER A 43 167.79 73.24 REMARK 500 LEU A 44 -116.99 -166.41 REMARK 500 LYS A 45 108.49 108.93 REMARK 500 HIS A 46 29.96 -76.97 REMARK 500 GLN A 71 112.16 163.73 REMARK 500 ARG A 183 -111.62 54.51 REMARK 500 ASP A 228 37.08 -141.25 REMARK 500 PHE A 247 62.96 -150.32 REMARK 500 GLU A 293 -81.33 -133.08 REMARK 500 THR A 295 90.22 -17.09 REMARK 500 LEU A 296 -78.11 -92.29 REMARK 500 ASP A 297 -50.79 50.02 REMARK 500 ALA B 42 -75.97 -76.69 REMARK 500 SER B 43 148.01 66.39 REMARK 500 CYS B 49 -111.97 -89.15 REMARK 500 ASN B 50 -28.84 57.96 REMARK 500 LYS B 60 34.67 39.21 REMARK 500 THR B 67 13.97 46.72 REMARK 500 GLN B 71 125.37 51.81 REMARK 500 GLU B 106 45.62 -145.19 REMARK 500 LEU B 127 -84.54 -114.12 REMARK 500 ARG B 183 -117.27 53.12 REMARK 500 ASP B 228 54.83 -149.61 REMARK 500 LEU B 283 63.96 -103.88 REMARK 500 ARG B 291 -103.07 -95.76 REMARK 500 ARG B 292 159.80 138.33 REMARK 500 THR B 295 -140.45 -103.10 REMARK 500 ASP B 297 133.51 82.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 295 LEU A 296 49.53 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 A 429 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 430 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 431 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH A 432 DISTANCE = 11.78 ANGSTROMS REMARK 525 HOH A 433 DISTANCE = 13.39 ANGSTROMS REMARK 525 HOH B 424 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B 425 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH B 426 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH B 427 DISTANCE = 8.49 ANGSTROMS REMARK 525 HOH B 428 DISTANCE = 9.75 ANGSTROMS DBREF 6FDO A 1 353 UNP Q9BVS4 RIOK2_HUMAN 1 353 DBREF 6FDO B 1 353 UNP Q9BVS4 RIOK2_HUMAN 1 353 SEQRES 1 A 353 MET GLY LYS VAL ASN VAL ALA LYS LEU ARG TYR MET SER SEQRES 2 A 353 ARG ASP ASP PHE ARG VAL LEU THR ALA VAL GLU MET GLY SEQRES 3 A 353 MET LYS ASN HIS GLU ILE VAL PRO GLY SER LEU ILE ALA SEQRES 4 A 353 SER ILE ALA SER LEU LYS HIS GLY GLY CYS ASN LYS VAL SEQRES 5 A 353 LEU ARG GLU LEU VAL LYS HIS LYS LEU ILE ALA TRP GLU SEQRES 6 A 353 ARG THR LYS THR VAL GLN GLY TYR ARG LEU THR ASN ALA SEQRES 7 A 353 GLY TYR ASP TYR LEU ALA LEU LYS THR LEU SER SER ARG SEQRES 8 A 353 GLN VAL VAL GLU SER VAL GLY ASN GLN MET GLY VAL GLY SEQRES 9 A 353 LYS GLU SER ASP ILE TYR ILE VAL ALA ASN GLU GLU GLY SEQRES 10 A 353 GLN GLN PHE ALA LEU LYS LEU HIS ARG LEU GLY ARG THR SEQRES 11 A 353 SER PHE ARG ASN LEU LYS ASN LYS ARG ASP TYR HIS LYS SEQRES 12 A 353 HIS ARG HIS ASN VAL SER TRP LEU TYR LEU SER ARG LEU SEQRES 13 A 353 SER ALA MET LYS GLU PHE ALA TYR MET LYS ALA LEU TYR SEQRES 14 A 353 GLU ARG LYS PHE PRO VAL PRO LYS PRO ILE ASP TYR ASN SEQRES 15 A 353 ARG HIS ALA VAL VAL MET GLU LEU ILE ASN GLY TYR PRO SEQRES 16 A 353 LEU CYS GLN ILE HIS HIS VAL GLU ASP PRO ALA SER VAL SEQRES 17 A 353 TYR ASP GLU ALA MET GLU LEU ILE VAL LYS LEU ALA ASN SEQRES 18 A 353 HIS GLY LEU ILE HIS GLY ASP PHE ASN GLU PHE ASN LEU SEQRES 19 A 353 ILE LEU ASP GLU SER ASP HIS ILE THR MET ILE ASP PHE SEQRES 20 A 353 PRO GLN MET VAL SER THR SER HIS PRO ASN ALA GLU TRP SEQRES 21 A 353 TYR PHE ASP ARG ASP VAL LYS CYS ILE LYS ASP PHE PHE SEQRES 22 A 353 MET LYS ARG PHE SER TYR GLU SER GLU LEU PHE PRO THR SEQRES 23 A 353 PHE LYS ASP ILE ARG ARG GLU ASP THR LEU ASP VAL GLU SEQRES 24 A 353 VAL SER ALA SER GLY TYR THR LYS GLU MET GLN ALA ASP SEQRES 25 A 353 ASP GLU LEU LEU HIS PRO LEU GLY PRO ASP ASP LYS ASN SEQRES 26 A 353 ILE GLU THR LYS GLU GLY SER GLU PHE SER PHE SER ASP SEQRES 27 A 353 GLY GLU VAL ALA GLU LYS ALA GLU VAL TYR GLY SER GLU SEQRES 28 A 353 ASN GLU SEQRES 1 B 353 MET GLY LYS VAL ASN VAL ALA LYS LEU ARG TYR MET SER SEQRES 2 B 353 ARG ASP ASP PHE ARG VAL LEU THR ALA VAL GLU MET GLY SEQRES 3 B 353 MET LYS ASN HIS GLU ILE VAL PRO GLY SER LEU ILE ALA SEQRES 4 B 353 SER ILE ALA SER LEU LYS HIS GLY GLY CYS ASN LYS VAL SEQRES 5 B 353 LEU ARG GLU LEU VAL LYS HIS LYS LEU ILE ALA TRP GLU SEQRES 6 B 353 ARG THR LYS THR VAL GLN GLY TYR ARG LEU THR ASN ALA SEQRES 7 B 353 GLY TYR ASP TYR LEU ALA LEU LYS THR LEU SER SER ARG SEQRES 8 B 353 GLN VAL VAL GLU SER VAL GLY ASN GLN MET GLY VAL GLY SEQRES 9 B 353 LYS GLU SER ASP ILE TYR ILE VAL ALA ASN GLU GLU GLY SEQRES 10 B 353 GLN GLN PHE ALA LEU LYS LEU HIS ARG LEU GLY ARG THR SEQRES 11 B 353 SER PHE ARG ASN LEU LYS ASN LYS ARG ASP TYR HIS LYS SEQRES 12 B 353 HIS ARG HIS ASN VAL SER TRP LEU TYR LEU SER ARG LEU SEQRES 13 B 353 SER ALA MET LYS GLU PHE ALA TYR MET LYS ALA LEU TYR SEQRES 14 B 353 GLU ARG LYS PHE PRO VAL PRO LYS PRO ILE ASP TYR ASN SEQRES 15 B 353 ARG HIS ALA VAL VAL MET GLU LEU ILE ASN GLY TYR PRO SEQRES 16 B 353 LEU CYS GLN ILE HIS HIS VAL GLU ASP PRO ALA SER VAL SEQRES 17 B 353 TYR ASP GLU ALA MET GLU LEU ILE VAL LYS LEU ALA ASN SEQRES 18 B 353 HIS GLY LEU ILE HIS GLY ASP PHE ASN GLU PHE ASN LEU SEQRES 19 B 353 ILE LEU ASP GLU SER ASP HIS ILE THR MET ILE ASP PHE SEQRES 20 B 353 PRO GLN MET VAL SER THR SER HIS PRO ASN ALA GLU TRP SEQRES 21 B 353 TYR PHE ASP ARG ASP VAL LYS CYS ILE LYS ASP PHE PHE SEQRES 22 B 353 MET LYS ARG PHE SER TYR GLU SER GLU LEU PHE PRO THR SEQRES 23 B 353 PHE LYS ASP ILE ARG ARG GLU ASP THR LEU ASP VAL GLU SEQRES 24 B 353 VAL SER ALA SER GLY TYR THR LYS GLU MET GLN ALA ASP SEQRES 25 B 353 ASP GLU LEU LEU HIS PRO LEU GLY PRO ASP ASP LYS ASN SEQRES 26 B 353 ILE GLU THR LYS GLU GLY SER GLU PHE SER PHE SER ASP SEQRES 27 B 353 GLY GLU VAL ALA GLU LYS ALA GLU VAL TYR GLY SER GLU SEQRES 28 B 353 ASN GLU FORMUL 3 HOH *61(H2 O) HELIX 1 AA1 SER A 13 MET A 27 1 15 HELIX 2 AA2 PRO A 34 SER A 43 1 10 HELIX 3 AA3 GLY A 48 HIS A 59 1 12 HELIX 4 AA4 THR A 76 ARG A 91 1 16 HELIX 5 AA5 THR A 130 ARG A 171 1 26 HELIX 6 AA6 CYS A 197 ILE A 199 5 3 HELIX 7 AA7 ASP A 204 HIS A 222 1 19 HELIX 8 AA8 ASN A 257 PHE A 277 1 21 HELIX 9 AA9 THR A 286 ILE A 290 5 5 HELIX 10 AB1 ASP A 297 ALA A 311 1 15 HELIX 11 AB2 SER B 13 MET B 27 1 15 HELIX 12 AB3 PRO B 34 SER B 43 1 10 HELIX 13 AB4 ASN B 50 HIS B 59 1 10 HELIX 14 AB5 THR B 76 ARG B 91 1 16 HELIX 15 AB6 THR B 130 GLU B 170 1 25 HELIX 16 AB7 CYS B 197 ILE B 199 5 3 HELIX 17 AB8 ASP B 204 ASN B 221 1 18 HELIX 18 AB9 ASN B 257 SER B 278 1 22 HELIX 19 AC1 ASP B 297 ALA B 311 1 15 SHEET 1 AA1 2 ILE A 62 GLU A 65 0 SHEET 2 AA1 2 GLY A 72 LEU A 75 -1 O GLY A 72 N GLU A 65 SHEET 1 AA2 5 SER A 96 GLY A 104 0 SHEET 2 AA2 5 SER A 107 ALA A 113 -1 O SER A 107 N GLY A 104 SHEET 3 AA2 5 GLN A 119 HIS A 125 -1 O PHE A 120 N VAL A 112 SHEET 4 AA2 5 ALA A 185 GLU A 189 -1 O VAL A 186 N LYS A 123 SHEET 5 AA2 5 PRO A 178 ASN A 182 -1 N ASN A 182 O ALA A 185 SHEET 1 AA3 3 TYR A 194 PRO A 195 0 SHEET 2 AA3 3 LEU A 234 LEU A 236 -1 O LEU A 236 N TYR A 194 SHEET 3 AA3 3 ILE A 242 MET A 244 -1 O THR A 243 N ILE A 235 SHEET 1 AA4 2 LEU A 224 ILE A 225 0 SHEET 2 AA4 2 VAL A 251 SER A 252 -1 O VAL A 251 N ILE A 225 SHEET 1 AA5 2 ILE B 62 GLU B 65 0 SHEET 2 AA5 2 GLY B 72 LEU B 75 -1 O ARG B 74 N ALA B 63 SHEET 1 AA6 5 SER B 96 VAL B 103 0 SHEET 2 AA6 5 SER B 107 ALA B 113 -1 O ILE B 111 N GLY B 98 SHEET 3 AA6 5 GLN B 119 HIS B 125 -1 O LEU B 122 N TYR B 110 SHEET 4 AA6 5 ALA B 185 GLU B 189 -1 O VAL B 186 N LYS B 123 SHEET 5 AA6 5 PRO B 178 ASN B 182 -1 N ASN B 182 O ALA B 185 SHEET 1 AA7 3 TYR B 194 PRO B 195 0 SHEET 2 AA7 3 LEU B 234 LEU B 236 -1 O LEU B 236 N TYR B 194 SHEET 3 AA7 3 ILE B 242 MET B 244 -1 O THR B 243 N ILE B 235 SHEET 1 AA8 2 LEU B 224 ILE B 225 0 SHEET 2 AA8 2 VAL B 251 SER B 252 -1 O VAL B 251 N ILE B 225 CISPEP 1 LYS A 45 HIS A 46 0 7.39 CISPEP 2 VAL A 70 GLN A 71 0 -0.96 CRYST1 67.555 67.555 312.195 90.00 90.00 120.00 P 65 12 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 0.014803 0.008546 0.000000 0.00000 SCALE2 0.000000 0.017093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003203 0.00000