HEADER DNA BINDING PROTEIN 10-JUN-19 6RY3 TITLE STRUCTURE OF THE WUS HOMEODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN WUSCHEL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATWUS,PLANT GROWTH ACTIVATOR 6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: WUS, PGA6, AT2G17950, T27K22.18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HOMEODOMAIN TRANSCRIPTION FACTOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.SLOAN,K.WILD,I.SINNING REVDAT 3 24-JAN-24 6RY3 1 REMARK REVDAT 2 20-MAY-20 6RY3 1 JRNL REVDAT 1 29-APR-20 6RY3 0 JRNL AUTH J.SLOAN,J.P.HAKENJOS,M.GEBERT,O.ERMAKOVA,A.GUMIERO,G.STIER, JRNL AUTH 2 K.WILD,I.SINNING,J.U.LOHMANN JRNL TITL STRUCTURAL BASIS FOR THE COMPLEX DNA BINDING BEHAVIOR OF THE JRNL TITL 2 PLANT STEM CELL REGULATOR WUSCHEL. JRNL REF NAT COMMUN V. 11 2223 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32376862 JRNL DOI 10.1038/S41467-020-16024-Y REMARK 2 REMARK 2 RESOLUTION. 1.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 836 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 38.1807 - 2.4958 1.00 2853 138 0.1855 0.2088 REMARK 3 2 2.4958 - 1.9810 1.00 2670 148 0.1580 0.1915 REMARK 3 3 1.9810 - 1.7306 1.00 2647 133 0.1691 0.2035 REMARK 3 4 1.7306 - 1.5723 1.00 2630 125 0.2023 0.2087 REMARK 3 5 1.5723 - 1.4596 1.00 2598 147 0.2140 0.2494 REMARK 3 6 1.4596 - 1.3736 0.99 2573 145 0.2532 0.3122 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.52 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 : 0.010 602 REMARK 3 ANGLE : 1.047 804 REMARK 3 CHIRALITY : 0.080 79 REMARK 3 PLANARITY : 0.006 102 REMARK 3 DIHEDRAL : 16.095 376 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 6RY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292102809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-16 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 : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.374 REMARK 200 RESOLUTION RANGE LOW (A) : 38.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 24.50 REMARK 200 R MERGE (I) : 0.03774 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 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: PHASER REMARK 200 STARTING MODEL: 3HDD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE 0.05 M MES (PH REMARK 280 6.0) 0.01 M MAGNESIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 41.00500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.56000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.50250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.56000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.50750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.56000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.50250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.56000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.50750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.00500 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: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 GLY A 30 REMARK 465 ALA A 31 REMARK 465 MET A 32 REMARK 465 GLY A 33 REMARK 465 GLN A 34 REMARK 465 THR A 35 REMARK 465 SER A 36 REMARK 465 THR A 37 REMARK 465 ARG A 38 REMARK 465 GLY A 104 REMARK 465 SER A 105 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 SER A 60 75.53 -151.88 REMARK 500 ILE A 79 146.99 -173.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 204 DBREF 6RY3 A 34 103 UNP Q9SB92 WUS_ARATH 34 103 SEQADV 6RY3 GLY A 30 UNP Q9SB92 EXPRESSION TAG SEQADV 6RY3 ALA A 31 UNP Q9SB92 EXPRESSION TAG SEQADV 6RY3 MET A 32 UNP Q9SB92 EXPRESSION TAG SEQADV 6RY3 GLY A 33 UNP Q9SB92 EXPRESSION TAG SEQADV 6RY3 GLY A 104 UNP Q9SB92 EXPRESSION TAG SEQADV 6RY3 SER A 105 UNP Q9SB92 EXPRESSION TAG SEQRES 1 A 76 GLY ALA MET GLY GLN THR SER THR ARG TRP THR PRO THR SEQRES 2 A 76 THR GLU GLN ILE LYS ILE LEU LYS GLU LEU TYR TYR ASN SEQRES 3 A 76 ASN ALA ILE ARG SER PRO THR ALA ASP GLN ILE GLN LYS SEQRES 4 A 76 ILE THR ALA ARG LEU ARG GLN PHE GLY LYS ILE GLU GLY SEQRES 5 A 76 LYS ASN VAL PHE TYR TRP PHE GLN ASN HIS LYS ALA ARG SEQRES 6 A 76 GLU ARG GLN LYS LYS ARG PHE ASN GLY GLY SER HET SO4 A 201 5 HET ACE A 202 3 HET ACE A 203 3 HET ACE A 204 3 HETNAM SO4 SULFATE ION HETNAM ACE ACETYL GROUP FORMUL 2 SO4 O4 S 2- FORMUL 3 ACE 3(C2 H4 O) FORMUL 6 HOH *50(H2 O) HELIX 1 AA1 THR A 42 ASN A 56 1 15 HELIX 2 AA2 THR A 62 ARG A 74 1 13 HELIX 3 AA3 GLN A 75 GLY A 77 5 3 HELIX 4 AA4 GLU A 80 LYS A 99 1 20 SITE 1 AC1 4 LYS A 82 ARG A 96 ARG A 100 HOH A 303 SITE 1 AC2 3 SER A 60 ARG A 94 LYS A 98 SITE 1 AC3 3 LYS A 78 ARG A 100 HOH A 310 SITE 1 AC4 1 LYS A 68 CRYST1 43.120 43.120 82.010 90.00 90.00 90.00 P 41 21 2 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 0.023191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012194 0.00000