HEADER RNA BINDING PROTEIN 13-SEP-17 5YDG TITLE CRYSTAL STRUCTURE OF THE ARABIDOPSIS THALIANA CHLOROPLAST RNA EDITING TITLE 2 FACTORS 2(MORF2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIPLE ORGANELLAR RNA EDITING FACTOR 2, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 79-194; COMPND 5 SYNONYM: PROTEIN DIFFERENTIATION AND GREENING-LIKE 1,PROTEIN DAG-LIKE COMPND 6 1,RNA EDITING-INTERACTING PROTEIN 2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: MORF2, DAL1, RIP2, AT2G33430; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA EDITING, MORFS, ARABIDOPSIS THALIANA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,J.Y.YANG,Y.L.WANG,Y.S.GAO REVDAT 4 27-MAR-24 5YDG 1 REMARK REVDAT 3 17-JAN-18 5YDG 1 JRNL REVDAT 2 27-DEC-17 5YDG 1 JRNL REVDAT 1 20-DEC-17 5YDG 0 JRNL AUTH J.YANG,M.ZHANG,X.WANG JRNL TITL CRYSTAL STRUCTURE OF THE CHLOROPLAST RNA EDITING FACTOR JRNL TITL 2 MORF2 JRNL REF BIOCHEM. BIOPHYS. RES. V. 495 2038 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29229384 JRNL DOI 10.1016/J.BBRC.2017.12.044 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 9973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.6456 - 3.4679 0.87 3326 166 0.1849 0.2337 REMARK 3 2 3.4679 - 2.7533 0.96 3500 186 0.2271 0.2470 REMARK 3 3 2.7533 - 2.4054 0.74 2675 120 0.2295 0.3063 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1875 REMARK 3 ANGLE : 0.903 2535 REMARK 3 CHIRALITY : 0.058 266 REMARK 3 PLANARITY : 0.005 339 REMARK 3 DIHEDRAL : 11.875 721 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -10.5512 -1.7505 -14.8697 REMARK 3 T TENSOR REMARK 3 T11: 0.3675 T22: 0.3648 REMARK 3 T33: 0.3456 T12: -0.0012 REMARK 3 T13: -0.0045 T23: 0.0313 REMARK 3 L TENSOR REMARK 3 L11: 1.1431 L22: 0.9342 REMARK 3 L33: 0.8022 L12: -0.2678 REMARK 3 L13: -0.1352 L23: 0.6767 REMARK 3 S TENSOR REMARK 3 S11: -0.0344 S12: 0.0970 S13: 0.0340 REMARK 3 S21: -0.0307 S22: 0.0288 S23: 0.0406 REMARK 3 S31: -0.0365 S32: 0.0096 S33: -0.0158 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 25% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 19.10450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.27950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.27950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.10450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.94000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLU A 193 REMARK 465 PRO A 194 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 GLU A 167 CG CD OE1 OE2 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 211 O HOH A 214 2.18 REMARK 500 OD2 ASP A 83 O HOH A 201 2.18 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 LYS A 93 73.48 49.41 REMARK 500 ARG A 133 -58.62 65.39 REMARK 500 ALA A 173 -153.07 54.25 REMARK 500 ASP B 92 -76.22 -80.82 REMARK 500 ARG B 133 -59.18 65.53 REMARK 500 ALA B 173 -152.22 53.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YDG A 79 194 UNP O22793 MORF2_ARATH 79 194 DBREF 5YDG B 79 194 UNP O22793 MORF2_ARATH 79 194 SEQRES 1 A 116 PHE PRO GLY CYS ASP TYR GLU HIS TRP LEU ILE VAL MET SEQRES 2 A 116 ASP LYS PRO GLY GLY GLU GLY ALA THR LYS GLN GLN MET SEQRES 3 A 116 ILE ASP CYS TYR ILE GLN THR LEU ALA LYS VAL VAL GLY SEQRES 4 A 116 SER GLU GLU GLU ALA LYS LYS ARG ILE TYR ASN VAL SER SEQRES 5 A 116 CYS GLU ARG TYR LEU GLY PHE GLY CYS GLU ILE ASP GLU SEQRES 6 A 116 GLU THR SER THR LYS LEU GLU GLY LEU PRO GLY VAL LEU SEQRES 7 A 116 PHE VAL LEU PRO ASP SER TYR VAL ASP PRO GLU ASN LYS SEQRES 8 A 116 ASP TYR GLY ALA GLU LEU PHE VAL ASN GLY GLU ILE VAL SEQRES 9 A 116 GLN ARG SER PRO GLU ARG GLN ARG ARG VAL GLU PRO SEQRES 1 B 116 PHE PRO GLY CYS ASP TYR GLU HIS TRP LEU ILE VAL MET SEQRES 2 B 116 ASP LYS PRO GLY GLY GLU GLY ALA THR LYS GLN GLN MET SEQRES 3 B 116 ILE ASP CYS TYR ILE GLN THR LEU ALA LYS VAL VAL GLY SEQRES 4 B 116 SER GLU GLU GLU ALA LYS LYS ARG ILE TYR ASN VAL SER SEQRES 5 B 116 CYS GLU ARG TYR LEU GLY PHE GLY CYS GLU ILE ASP GLU SEQRES 6 B 116 GLU THR SER THR LYS LEU GLU GLY LEU PRO GLY VAL LEU SEQRES 7 B 116 PHE VAL LEU PRO ASP SER TYR VAL ASP PRO GLU ASN LYS SEQRES 8 B 116 ASP TYR GLY ALA GLU LEU PHE VAL ASN GLY GLU ILE VAL SEQRES 9 B 116 GLN ARG SER PRO GLU ARG GLN ARG ARG VAL GLU PRO FORMUL 3 HOH *43(H2 O) HELIX 1 AA1 THR A 100 GLY A 117 1 18 HELIX 2 AA2 SER A 118 ARG A 125 1 8 HELIX 3 AA3 ASP A 142 LEU A 152 1 11 HELIX 4 AA4 ASP A 165 LYS A 169 5 5 HELIX 5 AA5 SER A 185 VAL A 192 1 8 HELIX 6 AA6 THR B 100 GLY B 117 1 18 HELIX 7 AA7 SER B 118 ARG B 125 1 8 HELIX 8 AA8 ASP B 142 GLY B 151 1 10 HELIX 9 AA9 ASP B 165 LYS B 169 5 5 HELIX 10 AB1 SER B 185 GLU B 193 1 9 SHEET 1 AA1 6 VAL A 155 PRO A 160 0 SHEET 2 AA1 6 HIS A 86 MET A 91 -1 N LEU A 88 O LEU A 159 SHEET 3 AA1 6 LEU A 135 GLU A 140 -1 O LEU A 135 N MET A 91 SHEET 4 AA1 6 ILE A 126 CYS A 131 -1 N SER A 130 O GLY A 136 SHEET 5 AA1 6 GLU A 174 VAL A 177 -1 O GLU A 174 N VAL A 129 SHEET 6 AA1 6 GLU A 180 VAL A 182 -1 O GLU A 180 N VAL A 177 SHEET 1 AA2 6 VAL B 155 PRO B 160 0 SHEET 2 AA2 6 HIS B 86 MET B 91 -1 N LEU B 88 O LEU B 159 SHEET 3 AA2 6 LEU B 135 GLU B 140 -1 O PHE B 137 N ILE B 89 SHEET 4 AA2 6 ILE B 126 CYS B 131 -1 N SER B 130 O GLY B 136 SHEET 5 AA2 6 GLU B 174 VAL B 177 -1 O PHE B 176 N TYR B 127 SHEET 6 AA2 6 GLU B 180 ILE B 181 -1 O GLU B 180 N VAL B 177 CISPEP 1 PRO B 94 GLY B 95 0 -21.07 CRYST1 38.209 85.880 86.559 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011644 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011553 0.00000