HEADER PLANT PROTEIN 08-NOV-18 6IQJ TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PROFILIN 2 COMPLEX WITH TITLE 2 FORMIN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROFILIN-2; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: PRF2; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FORMIN-LIKE PROTEIN 1; COMPND 8 CHAIN: C, D; COMPND 9 FRAGMENT: UNP RESIDUES 524-536; COMPND 10 SYNONYM: ATFORMIN-8; COMPND 11 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: PFN2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 11 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 12 ORGANISM_TAXID: 3702 KEYWDS ACTIN BINDING, REGULATE ACTIN NETWORK, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.QIAO,Y.GAO REVDAT 3 22-NOV-23 6IQJ 1 REMARK REVDAT 2 18-DEC-19 6IQJ 1 JRNL REVDAT 1 06-NOV-19 6IQJ 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.QIAO,Y.GAO REMARK 1 TITL PROFILIN 3 DYNAMICTLY REGULATE FOMRIN BINDING BY ITS N REMARK 1 TITL 2 TERMINAL TAIL REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 18916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 929 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 40.4231 - 3.6755 1.00 2762 157 0.1731 0.2031 REMARK 3 2 3.6755 - 2.9176 0.98 2633 141 0.1673 0.1823 REMARK 3 3 2.9176 - 2.5489 1.00 2645 119 0.1834 0.2489 REMARK 3 4 2.5489 - 2.3159 1.00 2611 141 0.1916 0.2365 REMARK 3 5 2.3159 - 2.1499 0.99 2582 124 0.1851 0.2181 REMARK 3 6 2.1499 - 2.0231 0.97 2502 142 0.2045 0.2189 REMARK 3 7 2.0231 - 1.9218 0.87 2252 105 0.2237 0.3177 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) : 22.150 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 : 0.003 2173 REMARK 3 ANGLE : 0.581 2956 REMARK 3 CHIRALITY : 0.044 315 REMARK 3 PLANARITY : 0.005 393 REMARK 3 DIHEDRAL : 2.855 1285 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 6IQJ 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_1300009724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 40.414 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 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 (%): 38.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS (PH 7.0), 2.0M AMMONIUM REMARK 280 PHOSPHATE DIBASIC, EVAPORATION, TEMPERATURE 291.15K 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 25.76150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.76650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.57800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.76650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.76150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.57800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 ARG C 0 REMARK 465 ARG D -1 REMARK 465 VAL D 0 REMARK 465 LEU D 10 REMARK 465 PRO D 11 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 293 O HOH B 300 1.89 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 VAL B 75 -158.73 -108.76 REMARK 500 ALA B 81 -46.91 -134.87 REMARK 500 VAL A 75 -158.65 -113.97 REMARK 500 ALA A 81 -48.57 -130.62 REMARK 500 PRO C 10 45.00 -78.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 6IQJ B 1 131 UNP Q42418 PROF2_ARATH 1 131 DBREF 6IQJ A 1 131 UNP Q42418 PROF2_ARATH 1 131 DBREF 6IQJ C 0 12 UNP Q9SE97 FH1_ARATH 524 536 DBREF 6IQJ D -1 11 UNP Q9SE97 FH1_ARATH 524 536 SEQRES 1 B 131 MET SER TRP GLN SER TYR VAL ASP ASP HIS LEU MET CYS SEQRES 2 B 131 GLU VAL GLU GLY ASN HIS LEU THR HIS ALA ALA ILE PHE SEQRES 3 B 131 GLY GLN ASP GLY SER VAL TRP ALA GLN SER SER ALA PHE SEQRES 4 B 131 PRO GLN LEU LYS PRO ALA GLU ILE ALA GLY ILE ASN LYS SEQRES 5 B 131 ASP PHE GLU GLU ALA GLY HIS LEU ALA PRO THR GLY LEU SEQRES 6 B 131 PHE LEU GLY GLY GLU LYS TYR MET VAL VAL GLN GLY GLU SEQRES 7 B 131 ALA GLY ALA VAL ILE ARG GLY LYS LYS GLY PRO GLY GLY SEQRES 8 B 131 VAL THR ILE LYS LYS THR THR GLN ALA LEU VAL PHE GLY SEQRES 9 B 131 ILE TYR ASP GLU PRO MET THR GLY GLY GLN CYS ASN LEU SEQRES 10 B 131 VAL VAL GLU ARG LEU GLY ASP TYR LEU ILE GLU SER GLY SEQRES 11 B 131 LEU SEQRES 1 A 131 MET SER TRP GLN SER TYR VAL ASP ASP HIS LEU MET CYS SEQRES 2 A 131 GLU VAL GLU GLY ASN HIS LEU THR HIS ALA ALA ILE PHE SEQRES 3 A 131 GLY GLN ASP GLY SER VAL TRP ALA GLN SER SER ALA PHE SEQRES 4 A 131 PRO GLN LEU LYS PRO ALA GLU ILE ALA GLY ILE ASN LYS SEQRES 5 A 131 ASP PHE GLU GLU ALA GLY HIS LEU ALA PRO THR GLY LEU SEQRES 6 A 131 PHE LEU GLY GLY GLU LYS TYR MET VAL VAL GLN GLY GLU SEQRES 7 A 131 ALA GLY ALA VAL ILE ARG GLY LYS LYS GLY PRO GLY GLY SEQRES 8 A 131 VAL THR ILE LYS LYS THR THR GLN ALA LEU VAL PHE GLY SEQRES 9 A 131 ILE TYR ASP GLU PRO MET THR GLY GLY GLN CYS ASN LEU SEQRES 10 A 131 VAL VAL GLU ARG LEU GLY ASP TYR LEU ILE GLU SER GLY SEQRES 11 A 131 LEU SEQRES 1 C 13 ARG VAL PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU PRO SEQRES 1 D 13 ARG VAL PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU PRO FORMUL 5 HOH *238(H2 O) HELIX 1 AA1 SER B 2 LEU B 11 1 10 HELIX 2 AA2 LYS B 43 GLU B 56 1 14 HELIX 3 AA3 THR B 111 SER B 129 1 19 HELIX 4 AA4 SER A 2 LEU A 11 1 10 HELIX 5 AA5 LYS A 43 GLU A 56 1 14 HELIX 6 AA6 THR A 111 SER A 129 1 19 SHEET 1 AA1 7 VAL B 32 GLN B 35 0 SHEET 2 AA1 7 HIS B 22 GLY B 27 -1 N ILE B 25 O ALA B 34 SHEET 3 AA1 7 ALA B 100 TYR B 106 -1 O PHE B 103 N ALA B 24 SHEET 4 AA1 7 GLY B 90 LYS B 96 -1 N LYS B 95 O VAL B 102 SHEET 5 AA1 7 VAL B 82 LYS B 87 -1 N ILE B 83 O ILE B 94 SHEET 6 AA1 7 GLU B 70 VAL B 74 -1 N MET B 73 O LYS B 86 SHEET 7 AA1 7 LEU B 65 LEU B 67 -1 N LEU B 65 O TYR B 72 SHEET 1 AA2 7 VAL A 32 GLN A 35 0 SHEET 2 AA2 7 HIS A 22 GLY A 27 -1 N ILE A 25 O ALA A 34 SHEET 3 AA2 7 ALA A 100 TYR A 106 -1 O PHE A 103 N ALA A 24 SHEET 4 AA2 7 GLY A 90 LYS A 96 -1 N LYS A 95 O VAL A 102 SHEET 5 AA2 7 VAL A 82 LYS A 87 -1 N ILE A 83 O ILE A 94 SHEET 6 AA2 7 GLU A 70 VAL A 74 -1 N MET A 73 O LYS A 86 SHEET 7 AA2 7 LEU A 65 LEU A 67 -1 N LEU A 65 O TYR A 72 CISPEP 1 GLU B 108 PRO B 109 0 2.53 CISPEP 2 GLU A 108 PRO A 109 0 2.82 CRYST1 51.523 65.156 73.533 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 0.019409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013599 0.00000