HEADER LIGASE 26-MAY-22 7XWD TITLE APO-ATPRT6 UBR BOX COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PRT6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN GREENING AFTER EXTENDED DARKNESS 1,PROTEIN COMPND 5 PROTEOLYSIS 6,RING-TYPE E3 UBIQUITIN TRANSFERASE PRT6; COMPND 6 EC: 2.3.2.27; COMPND 7 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: PRT6, CER3, GED1, AT5G02310/AT5G02300, T1E22.70/T1E22.60; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRT6, UBR BOX, E3 UBIQUITIN LIGASE, ARABIDOPSIS THALIANA, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.KIM,H.K.SONG REVDAT 3 06-NOV-24 7XWD 1 REMARK REVDAT 2 29-NOV-23 7XWD 1 REMARK REVDAT 1 31-MAY-23 7XWD 0 JRNL AUTH L.KIM,C.C.LIN,T.J.LIN,Y.C.CAO,M.C.CHEN,M.Y.CHOU,W.H.LIN, JRNL AUTH 2 M.KIM,J.L.WU,M.C.SHIH,H.K.SONG,M.C.HO JRNL TITL STRUCTURAL ANALYSES OF PLANT PRT6-UBR BOX FOR JRNL TITL 2 CYS-ARG/N-DEGRON PATHWAY AND INSIGHTS INTO THE PLANT JRNL TITL 3 SUBMERGENCE RESISTANCE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5880 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 589 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 43.5830 - 3.8030 1.00 1392 156 0.1935 0.2580 REMARK 3 2 3.8030 - 3.0188 1.00 1316 146 0.2286 0.2763 REMARK 3 3 3.0188 - 2.6372 1.00 1308 145 0.2753 0.2901 REMARK 3 4 2.6372 - 2.3961 1.00 1275 142 0.2767 0.2767 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.900 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 : 0.011 540 REMARK 3 ANGLE : 1.160 734 REMARK 3 CHIRALITY : 0.059 73 REMARK 3 PLANARITY : 0.008 100 REMARK 3 DIHEDRAL : 4.424 308 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 7XWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300029788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5882 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.396 REMARK 200 RESOLUTION RANGE LOW (A) : 43.583 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 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: 6LHN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 HEPES PH 7.5, 0.1 M NACL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 43.58250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 43.58250 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.17500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.58750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.58250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.76250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.76250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.58250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.58750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 43.58250 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.17500 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 43.58250 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 37.17500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 43.58250 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 55.76250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 18.58750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 43.58250 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 18.58750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 55.76250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 43.58250 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 43.58250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 37.17500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 43.58250 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.76250 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 121 SG REMARK 620 2 CYS A 146 SG 123.2 REMARK 620 3 CYS A 149 SG 107.9 97.9 REMARK 620 4 CYS A 170 SG 100.3 117.8 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 134 SG REMARK 620 2 CYS A 137 SG 115.6 REMARK 620 3 HIS A 155 ND1 122.4 97.9 REMARK 620 4 HIS A 158 ND1 112.6 99.5 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 149 SG REMARK 620 2 CYS A 172 SG 104.9 REMARK 620 3 CYS A 184 SG 113.6 124.0 REMARK 620 4 HIS A 187 ND1 110.0 108.8 94.7 REMARK 620 N 1 2 3 DBREF 7XWD A 119 188 UNP F4KCC2 PRT6_ARATH 119 188 SEQRES 1 A 70 GLY VAL CYS GLY SER VAL TRP GLY GLN ASN ASP ILE ALA SEQRES 2 A 70 TYR ARG CYS ARG THR CYS GLU ASN ASP PRO THR CYS ALA SEQRES 3 A 70 ILE CYS VAL PRO CYS PHE GLN ASN GLY ASP HIS ASN SER SEQRES 4 A 70 HIS ASP TYR SER ILE ILE TYR THR GLY GLY GLY CYS CYS SEQRES 5 A 70 ASP CYS GLY ASP GLU THR ALA TRP LYS PRO ASP GLY PHE SEQRES 6 A 70 CYS SER ASN HIS LYS HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) HELIX 1 AA1 CYS A 146 ASN A 152 1 7 HELIX 2 AA2 LYS A 179 PHE A 183 5 5 HELIX 3 AA3 CYS A 184 LYS A 188 5 5 SHEET 1 AA1 2 VAL A 124 TRP A 125 0 SHEET 2 AA1 2 GLY A 168 CYS A 169 -1 O GLY A 168 N TRP A 125 SHEET 1 AA2 2 ALA A 131 CYS A 134 0 SHEET 2 AA2 2 TYR A 160 ILE A 163 -1 O SER A 161 N ARG A 133 SSBOND 1 CYS A 169 CYS A 169 1555 5555 2.95 LINK SG CYS A 121 ZN ZN A 202 1555 1555 2.18 LINK SG CYS A 134 ZN ZN A 203 1555 1555 2.32 LINK SG CYS A 137 ZN ZN A 203 1555 1555 2.26 LINK SG CYS A 146 ZN ZN A 202 1555 1555 2.28 LINK SG CYS A 149 ZN ZN A 201 1555 1555 2.54 LINK SG CYS A 149 ZN ZN A 202 1555 1555 2.18 LINK ND1 HIS A 155 ZN ZN A 203 1555 1555 2.12 LINK ND1 HIS A 158 ZN ZN A 203 1555 1555 1.96 LINK SG CYS A 170 ZN ZN A 202 1555 1555 2.21 LINK SG CYS A 172 ZN ZN A 201 1555 1555 2.23 LINK SG CYS A 184 ZN ZN A 201 1555 1555 2.33 LINK ND1 HIS A 187 ZN ZN A 201 1555 1555 2.03 CRYST1 87.165 87.165 74.350 90.00 90.00 90.00 I 41 2 2 16 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 0.011472 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013450 0.00000