HEADER RNA BINDING PROTEIN 26-MAR-16 5IZW TITLE CRYSTAL STRUCTURE OF RNA EDITING SPECIFIC FACTOR OF DESIGNER PLS-TYPE TITLE 2 PPR-9R PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLS9-PPR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PENTATRICOPEPTIDE REPEAT, COMPLEX, MORF, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.YAN,Q.ZHANG,Z.GUAN,T.ZOU,P.YIN REVDAT 4 20-MAR-24 5IZW 1 REMARK REVDAT 3 15-NOV-17 5IZW 1 JRNL REVDAT 2 27-SEP-17 5IZW 1 REMARK REVDAT 1 29-MAR-17 5IZW 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. 1.74 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26272 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 1257 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 36.5086 - 3.6148 1.00 2875 115 0.1568 0.1998 REMARK 3 2 3.6148 - 2.8695 1.00 2782 154 0.1726 0.1862 REMARK 3 3 2.8695 - 2.5069 1.00 2775 128 0.1814 0.2029 REMARK 3 4 2.5069 - 2.2777 1.00 2765 158 0.1793 0.2061 REMARK 3 5 2.2777 - 2.1145 1.00 2774 149 0.1651 0.1937 REMARK 3 6 2.1145 - 1.9898 1.00 2761 142 0.1885 0.2229 REMARK 3 7 1.9898 - 1.8902 1.00 2766 142 0.2114 0.2463 REMARK 3 8 1.8902 - 1.8079 1.00 2756 128 0.2212 0.3205 REMARK 3 9 1.8079 - 1.7383 0.99 2761 141 0.2576 0.3155 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750 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 : 0.011 1596 REMARK 3 ANGLE : 1.106 2140 REMARK 3 CHIRALITY : 0.338 244 REMARK 3 PLANARITY : 0.005 270 REMARK 3 DIHEDRAL : 19.179 602 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): 15.6247 116.7232 7.9213 REMARK 3 T TENSOR REMARK 3 T11: 0.1822 T22: 0.1821 REMARK 3 T33: 0.2085 T12: -0.0077 REMARK 3 T13: -0.0194 T23: 0.0208 REMARK 3 L TENSOR REMARK 3 L11: 0.4592 L22: 0.4755 REMARK 3 L33: 0.5989 L12: -0.2399 REMARK 3 L13: -0.1889 L23: 0.2760 REMARK 3 S TENSOR REMARK 3 S11: -0.0045 S12: -0.0092 S13: 0.0042 REMARK 3 S21: 0.0031 S22: -0.0042 S23: 0.0030 REMARK 3 S31: -0.0163 S32: -0.0051 S33: -0.0089 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 5IZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.738 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 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 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 (%): 57.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM SULFATE HEPTAHYDRATE, 1,3 REMARK 280 -BIS[TRIS(HYDROXYMETHYL)METHYLAMINO]PROPANE, PEG 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 28.37600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.18800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.56400 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 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 B 356 O HOH B 388 2.19 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 N VAL B 110 C ASP B 210 4474 1.36 REMARK 500 N VAL A 9 C ASP A 109 3775 1.37 REMARK 500 O HOH A 239 O HOH B 313 4375 2.17 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 43 -168.65 -114.15 REMARK 500 SER A 77 -5.48 179.23 REMARK 500 LEU A 94 71.98 -101.27 REMARK 500 ASP B 144 -168.86 -116.72 REMARK 500 LEU B 195 73.05 -101.95 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 A 294 DISTANCE = 6.25 ANGSTROMS DBREF 5IZW A 9 109 PDB 5IZW 5IZW 9 109 DBREF 5IZW B 110 210 PDB 5IZW 5IZW 110 210 SEQRES 1 A 101 VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU CYS LYS SEQRES 2 A 101 ALA GLY LYS LEU ASP GLU ALA LEU LYS LEU PHE GLU GLU SEQRES 3 A 101 MET VAL GLU LYS GLY ILE LYS PRO ASP GLU PHE THR PHE SEQRES 4 A 101 SER SER VAL LEU LYS ALA CYS ALA ARG LEU GLY ALA LEU SEQRES 5 A 101 GLU LEU GLY LYS GLN ILE HIS GLY TYR VAL ILE LYS SER SEQRES 6 A 101 GLY PHE GLU SER ASN VAL VAL VAL TYR ASN ALA LEU ILE SEQRES 7 A 101 ASP MET TYR SER LYS CYS GLY LEU LEU GLU GLU ALA ARG SEQRES 8 A 101 LYS VAL PHE ASP GLU MET PRO GLU LYS ASP SEQRES 1 B 101 VAL VAL THR TYR ASN THR LEU ILE ASP GLY LEU CYS LYS SEQRES 2 B 101 ALA GLY LYS LEU ASP GLU ALA LEU LYS LEU PHE GLU GLU SEQRES 3 B 101 MET VAL GLU LYS GLY ILE LYS PRO ASP GLU PHE THR PHE SEQRES 4 B 101 SER SER VAL LEU LYS ALA CYS ALA ARG LEU GLY ALA LEU SEQRES 5 B 101 GLU LEU GLY LYS GLN ILE HIS GLY TYR VAL ILE LYS SER SEQRES 6 B 101 GLY PHE GLU SER ASN VAL VAL VAL TYR ASN ALA LEU ILE SEQRES 7 B 101 ASP MET TYR SER LYS CYS GLY LEU LEU GLU GLU ALA ARG SEQRES 8 B 101 LYS VAL PHE ASP GLU MET PRO GLU LYS ASP FORMUL 3 HOH *189(H2 O) HELIX 1 AA1 VAL A 9 ALA A 22 1 14 HELIX 2 AA2 LYS A 24 GLY A 39 1 16 HELIX 3 AA3 ASP A 43 GLY A 58 1 16 HELIX 4 AA4 ALA A 59 SER A 73 1 15 HELIX 5 AA5 ASN A 78 CYS A 92 1 15 HELIX 6 AA6 LEU A 94 MET A 105 1 12 HELIX 7 AA7 VAL B 111 ALA B 123 1 13 HELIX 8 AA8 LYS B 125 GLY B 140 1 16 HELIX 9 AA9 ASP B 144 GLY B 159 1 16 HELIX 10 AB1 ALA B 160 SER B 174 1 15 HELIX 11 AB2 ASN B 179 CYS B 193 1 15 HELIX 12 AB3 LEU B 195 MET B 206 1 12 CRYST1 67.412 67.412 56.752 90.00 90.00 90.00 P 41 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 0.014834 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017621 0.00000