HEADER PLANT PROTEIN 07-NOV-18 6IQF TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PROFILIN 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRF3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROFILIN 3; COMPND 5 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: PRF3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACTIN BINDING, REGULATE ACTIN NETWORK, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.QIAO,Y.GAO REVDAT 3 22-NOV-23 6IQF 1 REMARK REVDAT 2 18-DEC-19 6IQF 1 JRNL REVDAT 1 06-NOV-19 6IQF 0 JRNL AUTH Z.QIAO,H.SUN,J.T.Y.NG,Q.MA,S.H.KOH,Y.MU,Y.MIAO,Y.G.GAO JRNL TITL STRUCTURAL AND COMPUTATIONAL EXAMINATION OF JRNL TITL 2 THEARABIDOPSISPROFILIN-POLY-P COMPLEX REVEALS MECHANISTIC JRNL TITL 3 DETAILS IN PROFILIN-REGULATED ACTIN ASSEMBLY. JRNL REF J.BIOL.CHEM. V. 294 18650 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31653702 JRNL DOI 10.1074/JBC.RA119.011307 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 43672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 2079 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 43.4004 - 3.5927 0.99 2807 109 0.1633 0.1740 REMARK 3 2 3.5927 - 2.8518 1.00 2800 148 0.1799 0.2016 REMARK 3 3 2.8518 - 2.4913 1.00 2747 158 0.2015 0.2286 REMARK 3 4 2.4913 - 2.2636 1.00 2780 157 0.1879 0.2361 REMARK 3 5 2.2636 - 2.1013 1.00 2840 122 0.1898 0.1724 REMARK 3 6 2.1013 - 1.9774 1.00 2788 133 0.1920 0.2052 REMARK 3 7 1.9774 - 1.8784 1.00 2796 127 0.1981 0.1859 REMARK 3 8 1.8784 - 1.7966 1.00 2804 118 0.1946 0.2390 REMARK 3 9 1.7966 - 1.7275 1.00 2750 143 0.2165 0.2146 REMARK 3 10 1.7275 - 1.6679 1.00 2808 162 0.2459 0.2373 REMARK 3 11 1.6679 - 1.6157 1.00 2788 152 0.2708 0.2874 REMARK 3 12 1.6157 - 1.5695 1.00 2823 142 0.2911 0.3254 REMARK 3 13 1.5695 - 1.5282 0.98 2714 143 0.3362 0.3275 REMARK 3 14 1.5282 - 1.4909 0.99 2745 139 0.3596 0.3865 REMARK 3 15 1.4909 - 1.4570 0.93 2603 126 0.4271 0.4628 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.000 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 : 0.006 994 REMARK 3 ANGLE : 0.835 1350 REMARK 3 CHIRALITY : 0.079 152 REMARK 3 PLANARITY : 0.006 177 REMARK 3 DIHEDRAL : 3.950 360 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6IQF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.457 REMARK 200 RESOLUTION RANGE LOW (A) : 43.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.260 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3NUL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH 5.0), 1.42M REMARK 280 AMMONIUM SULFATE, EVAPORATION, TEMPERATURE 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 40.49350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.43100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.49350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.43100 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 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 MET A 1 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 GLN A 28 2.72 -66.25 REMARK 500 ILE A 75 -164.42 -122.49 REMARK 500 ALA A 81 -53.78 -145.56 REMARK 500 THR A 97 -169.16 -110.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IQF A 1 131 UNP Q9FE63 PROF5_ARATH 1 131 SEQRES 1 A 131 MET SER TRP GLN THR TYR VAL ASP ASP HIS LEU MET CYS SEQRES 2 A 131 ASP VAL ALA GLY ASN ARG LEU THR ALA ALA ALA ILE LEU SEQRES 3 A 131 GLY GLN ASP GLY SER VAL TRP ALA GLN SER ASN ASN PHE SEQRES 4 A 131 PRO GLN VAL LYS PRO GLU GLU ILE GLN GLY ILE LYS ASP SEQRES 5 A 131 ASP PHE THR THR PRO GLY THR LEU ALA PRO THR GLY LEU SEQRES 6 A 131 PHE LEU GLY GLY ASN LYS TYR MET VAL ILE GLN GLY GLU SEQRES 7 A 131 PRO ASN ALA VAL ILE ARG GLY LYS LYS GLY ALA GLY GLY SEQRES 8 A 131 VAL THR ILE LYS LYS THR THR LEU ALA LEU VAL PHE GLY SEQRES 9 A 131 ILE TYR ASP GLU PRO MET THR PRO GLY GLN CYS ASN MET SEQRES 10 A 131 VAL VAL GLU ASN LEU GLY GLU TYR LEU ILE GLU SER GLY SEQRES 11 A 131 LEU FORMUL 2 HOH *49(H2 O) HELIX 1 AA1 SER A 2 LEU A 11 1 10 HELIX 2 AA2 LYS A 43 THR A 56 1 14 HELIX 3 AA3 THR A 111 SER A 129 1 19 SHEET 1 AA1 7 VAL A 32 GLN A 35 0 SHEET 2 AA1 7 ALA A 22 GLY A 27 -1 N ILE A 25 O ALA A 34 SHEET 3 AA1 7 ALA A 100 TYR A 106 -1 O PHE A 103 N ALA A 24 SHEET 4 AA1 7 GLY A 90 LYS A 96 -1 N LYS A 95 O VAL A 102 SHEET 5 AA1 7 VAL A 82 LYS A 87 -1 N LYS A 87 O GLY A 90 SHEET 6 AA1 7 ASN A 70 GLU A 78 -1 N MET A 73 O LYS A 86 SHEET 7 AA1 7 LEU A 65 LEU A 67 -1 N LEU A 65 O TYR A 72 CISPEP 1 GLU A 108 PRO A 109 0 7.36 CRYST1 80.987 52.862 32.410 90.00 110.38 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 0.012348 0.000000 0.004588 0.00000 SCALE2 0.000000 0.018917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032915 0.00000