HEADER RNA BINDING PROTEIN 21-JUN-16 5GI0 TITLE CRYSTAL STRUCTURE OF RNA EDITING FACTOR MORF9/RIP9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIPLE ORGANELLAR RNA EDITING FACTOR 9, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA EDITING-INTERACTING PROTEIN 9; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: MORF9, RIP9, AT1G11430, T23J18.10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RNA EDITING FACTOR, MORF9, RIP9, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.YAN,Q.ZHANG,Z.GUAN,T.ZOU,P.YIN REVDAT 2 16-OCT-24 5GI0 1 REMARK REVDAT 1 10-MAY-17 5GI0 0 JRNL AUTH J.YAN,Q.ZHANG,Z.GUAN,Q.WANG,L.LI,F.RUAN,R.LIN,T.ZOU,P.YIN JRNL TITL MORF9 INCREASES THE RNA-BINDING ACTIVITY OF PLS-TYPE JRNL TITL 2 PENTATRICOPEPTIDE REPEAT PROTEIN IN PLASTID RNA EDITING JRNL REF NAT PLANTS V. 3 17037 2017 JRNL REFN ESSN 2055-0278 JRNL PMID 28394309 JRNL DOI 10.1038/NPLANTS.2017.37 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 9116 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 450 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 29.8730 - 2.9479 0.99 2906 148 0.1905 0.2101 REMARK 3 2 2.9479 - 2.3401 1.00 2901 153 0.2272 0.2694 REMARK 3 3 2.3401 - 2.0444 1.00 2859 149 0.2090 0.2867 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1003 REMARK 3 ANGLE : 0.940 1365 REMARK 3 CHIRALITY : 0.054 145 REMARK 3 PLANARITY : 0.006 175 REMARK 3 DIHEDRAL : 13.710 594 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): 10.8742 35.2392 12.4412 REMARK 3 T TENSOR REMARK 3 T11: 0.2217 T22: 0.2173 REMARK 3 T33: 0.2366 T12: 0.0145 REMARK 3 T13: 0.0235 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 0.2657 L22: 0.4238 REMARK 3 L33: 0.4681 L12: -0.2868 REMARK 3 L13: 0.2315 L23: -0.0862 REMARK 3 S TENSOR REMARK 3 S11: 0.0250 S12: 0.0866 S13: 0.0679 REMARK 3 S21: -0.0479 S22: -0.1324 S23: -0.0349 REMARK 3 S31: -0.0085 S32: 0.0372 S33: -0.0000 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 5GI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000802. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979305 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9121 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM BROMIDE,SODIUM THIOCYANATE, PEG REMARK 280 3350, MES, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.40600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.34500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.40600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.34500 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: 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: 7570 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 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 MSE A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 GLU A 6 REMARK 465 THR A 7 REMARK 465 ILE A 8 REMARK 465 MSE A 9 REMARK 465 LEU A 10 REMARK 465 HIS A 133 REMARK 465 HIS A 134 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 HIS A 130 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 131 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 132 CG ND1 CD2 CE1 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 O HOH A 226 O HOH A 232 1.90 REMARK 500 O HOH A 242 O HOH A 246 1.95 REMARK 500 O HOH A 212 O HOH A 247 1.99 REMARK 500 O TYR A 102 O HOH A 201 2.10 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 ASP A 27 -98.30 -7.22 REMARK 500 THR A 63 -76.33 -128.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 5GI0 A 3 124 UNP Q9LPZ1 MORF9_ARATH 75 196 SEQADV 5GI0 MSE A 2 UNP Q9LPZ1 INITIATING METHIONINE SEQADV 5GI0 SER A 13 UNP Q9LPZ1 CYS 85 ENGINEERED MUTATION SEQADV 5GI0 SER A 115 UNP Q9LPZ1 CYS 187 ENGINEERED MUTATION SEQADV 5GI0 LEU A 125 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 GLU A 126 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 127 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 128 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 129 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 130 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 131 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 132 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 133 UNP Q9LPZ1 EXPRESSION TAG SEQADV 5GI0 HIS A 134 UNP Q9LPZ1 EXPRESSION TAG SEQRES 1 A 133 MSE GLU GLN ARG GLU THR ILE MSE LEU PRO GLY SER ASP SEQRES 2 A 133 TYR ASN HIS TRP LEU ILE VAL MSE GLU PHE PRO LYS ASP SEQRES 3 A 133 PRO ALA PRO SER ARG ASP GLN MSE ILE ASP THR TYR LEU SEQRES 4 A 133 ASN THR LEU ALA THR VAL LEU GLY SER MSE GLU GLU ALA SEQRES 5 A 133 LYS LYS ASN MSE TYR ALA PHE SER THR THR THR TYR THR SEQRES 6 A 133 GLY PHE GLN CYS THR ILE ASP GLU GLU THR SER GLU LYS SEQRES 7 A 133 PHE LYS GLY LEU PRO GLY VAL LEU TRP VAL LEU PRO ASP SEQRES 8 A 133 SER TYR ILE ASP VAL LYS ASN LYS ASP TYR GLY GLY ASP SEQRES 9 A 133 LYS TYR ILE ASN GLY GLU ILE ILE PRO SER THR TYR PRO SEQRES 10 A 133 THR TYR GLN PRO LYS GLN LEU GLU HIS HIS HIS HIS HIS SEQRES 11 A 133 HIS HIS HIS MODRES 5GI0 MSE A 22 MET MODIFIED RESIDUE MODRES 5GI0 MSE A 35 MET MODIFIED RESIDUE MODRES 5GI0 MSE A 50 MET MODIFIED RESIDUE MODRES 5GI0 MSE A 57 MET MODIFIED RESIDUE HET MSE A 22 8 HET MSE A 35 8 HET MSE A 50 8 HET MSE A 57 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 SER A 31 GLY A 48 1 18 HELIX 2 AA2 SER A 49 ASN A 56 1 8 HELIX 3 AA3 ASP A 73 LYS A 79 1 7 HELIX 4 AA4 PRO A 122 GLU A 126 5 5 SHEET 1 AA1 6 VAL A 86 PRO A 91 0 SHEET 2 AA1 6 TRP A 18 MSE A 22 -1 N LEU A 19 O LEU A 90 SHEET 3 AA1 6 THR A 66 CYS A 70 -1 O PHE A 68 N ILE A 20 SHEET 4 AA1 6 MSE A 57 THR A 62 -1 N ALA A 59 O GLN A 69 SHEET 5 AA1 6 ASP A 105 ILE A 108 -1 O ASP A 105 N PHE A 60 SHEET 6 AA1 6 GLU A 111 ILE A 113 -1 O GLU A 111 N ILE A 108 LINK C VAL A 21 N MSE A 22 1555 1555 1.32 LINK C MSE A 22 N GLU A 23 1555 1555 1.32 LINK C GLN A 34 N MSE A 35 1555 1555 1.33 LINK C MSE A 35 N ILE A 36 1555 1555 1.34 LINK C SER A 49 N MSE A 50 1555 1555 1.33 LINK C MSE A 50 N GLU A 51 1555 1555 1.34 LINK C ASN A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N TYR A 58 1555 1555 1.34 CRYST1 76.812 50.690 38.318 90.00 103.53 90.00 C 1 2 1 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 0.013019 0.000000 0.003133 0.00000 SCALE2 0.000000 0.019728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026842 0.00000