HEADER LIGASE 09-AUG-22 7YRB TITLE UBR BOX OF HUMAN UBR6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: F-BOX PROTEIN 11, ISOFORM CRA_F; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E3 UBIQUITIN LIGASE UBR6,HIGHLY SIMILAR TO F-BOX ONLY COMPND 5 PROTEIN 11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FBXO11, HCG_1987171; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 UBIQUITIN-PROTEIN LIGASE, UBR-BOX DOMAIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR B.KIM,H.K.SONG REVDAT 1 15-NOV-23 7YRB 0 JRNL AUTH B.KIM,B.H.KIM,H.K.SONG JRNL TITL CRYSTAL STRUCTURE OF UBR BOX FROM HUMAN UBR6 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 11370 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1146 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 29.4700 - 3.0100 0.99 1362 155 0.1604 0.1954 REMARK 3 2 3.0100 - 2.3900 1.00 1300 146 0.1764 0.2040 REMARK 3 3 2.3900 - 2.0900 1.00 1295 147 0.1552 0.2012 REMARK 3 4 2.0900 - 1.9000 1.00 1267 144 0.1644 0.1920 REMARK 3 5 1.9000 - 1.7600 1.00 1270 140 0.1587 0.1760 REMARK 3 6 1.7600 - 1.6600 1.00 1263 140 0.1704 0.1837 REMARK 3 7 1.6600 - 1.5700 0.99 1254 135 0.1838 0.2207 REMARK 3 8 1.5700 - 1.5100 0.96 1213 139 0.2109 0.2727 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.081 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.64 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 : 0.009 664 REMARK 3 ANGLE : 1.061 895 REMARK 3 CHIRALITY : 0.050 94 REMARK 3 PLANARITY : 0.012 117 REMARK 3 DIHEDRAL : 6.483 91 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 7YRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 55.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.83400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 0.1M HEPES REMARK 280 SODIUM PH 7.5, 1% PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K 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 19.42400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.62400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.67950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.62400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.42400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.67950 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 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 841 -156.01 51.55 REMARK 500 ARG A 861 72.55 -100.99 REMARK 500 ILE A 881 -65.51 -101.98 REMARK 500 REMARK 500 REMARK: NULL 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 A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 835 SG REMARK 620 2 CYS A 865 SG 117.1 REMARK 620 3 CYS A 868 SG 103.0 101.1 REMARK 620 4 CYS A 888 SG 110.1 112.5 112.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 853 SG REMARK 620 2 CYS A 856 SG 118.0 REMARK 620 3 HIS A 873 ND1 113.4 103.9 REMARK 620 4 HIS A 876 ND1 112.4 102.7 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 868 SG REMARK 620 2 CYS A 872 SG 107.6 REMARK 620 3 CYS A 890 SG 109.6 106.7 REMARK 620 4 CYS A 899 SG 107.8 108.0 116.8 REMARK 620 N 1 2 3 DBREF 7YRB A 824 904 UNP B3KUR1 B3KUR1_HUMAN 248 328 SEQADV 7YRB GLY A 822 UNP B3KUR1 EXPRESSION TAG SEQADV 7YRB SER A 823 UNP B3KUR1 EXPRESSION TAG SEQRES 1 A 83 GLY SER ASP ALA ILE GLU LYS ALA VAL SER ARG GLY GLN SEQRES 2 A 83 CYS LEU TYR LYS ILE SER SER TYR THR SER TYR PRO MET SEQRES 3 A 83 HIS ASP PHE TYR ARG CYS HIS THR CYS ASN THR THR ASP SEQRES 4 A 83 ARG ASN ALA ILE CYS VAL ASN CYS ILE LYS LYS CYS HIS SEQRES 5 A 83 GLN GLY HIS ASP VAL GLU PHE ILE ARG HIS ASP ARG PHE SEQRES 6 A 83 PHE CYS ASP CYS GLY ALA GLY THR LEU SER ASN PRO CYS SEQRES 7 A 83 THR LEU ALA GLY GLU HET ZN A1001 1 HET ZN A1002 1 HET ZN A1003 1 HET SO4 A1004 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *35(H2 O) HELIX 1 AA1 ASP A 824 ARG A 832 1 9 HELIX 2 AA2 LEU A 836 SER A 841 1 6 HELIX 3 AA3 CYS A 865 CYS A 872 1 8 SHEET 1 AA1 2 MET A 847 CYS A 853 0 SHEET 2 AA1 2 VAL A 878 ARG A 885 -1 O GLU A 879 N ARG A 852 LINK SG CYS A 835 ZN ZN A1002 1555 1555 2.31 LINK SG CYS A 853 ZN ZN A1003 1555 1555 2.29 LINK SG CYS A 856 ZN ZN A1003 1555 1555 2.29 LINK SG CYS A 865 ZN ZN A1002 1555 1555 2.35 LINK SG CYS A 868 ZN ZN A1001 1555 1555 2.36 LINK SG CYS A 868 ZN ZN A1002 1555 1555 2.37 LINK SG CYS A 872 ZN ZN A1001 1555 1555 2.42 LINK ND1 HIS A 873 ZN ZN A1003 1555 1555 2.13 LINK ND1 HIS A 876 ZN ZN A1003 1555 1555 2.04 LINK SG CYS A 888 ZN ZN A1002 1555 1555 2.33 LINK SG CYS A 890 ZN ZN A1001 1555 1555 2.35 LINK SG CYS A 899 ZN ZN A1001 1555 1555 2.29 CRYST1 38.848 39.359 45.248 90.00 90.00 90.00 P 21 21 21 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 0.025741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022100 0.00000