HEADER PROTEIN-BINDING PROTEIN 26-FEB-14 4CRH TITLE CRYSTAL STRUCTURE OF THE BTB-T1 DOMAIN OF HUMAN SHKBP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3KBP1-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BTB-T1, RESIDUES 18-120; COMPND 5 SYNONYM: SHKBP1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PROTEIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.M.PINKAS,N.SOLCAN,T.KROJER,S.GOUBIN,E.P.WILLIAMS,F.VON DELFT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,A.BULLOCK REVDAT 4 20-DEC-23 4CRH 1 REMARK REVDAT 3 06-DEC-17 4CRH 1 JRNL REVDAT 2 26-MAR-14 4CRH 1 ATOM REVDAT 1 12-MAR-14 4CRH 0 JRNL AUTH D.M.PINKAS,C.E.SANVITALE,J.C.BUFTON,F.J.SORRELL,N.SOLCAN, JRNL AUTH 2 R.CHALK,J.DOUTCH,A.N.BULLOCK JRNL TITL STRUCTURAL COMPLEXITY IN THE KCTD FAMILY OF JRNL TITL 2 CULLIN3-DEPENDENT E3 UBIQUITIN LIGASES. JRNL REF BIOCHEM. J. V. 474 3747 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28963344 JRNL DOI 10.1042/BCJ20170527 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 35.6526 - 2.7304 1.00 2893 155 0.1493 0.1677 REMARK 3 2 2.7304 - 2.1673 1.00 2834 149 0.1722 0.2267 REMARK 3 3 2.1673 - 1.8934 1.00 2837 138 0.1835 0.2080 REMARK 3 4 1.8934 - 1.7203 1.00 2815 130 0.2068 0.2482 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.60 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 : 0.008 787 REMARK 3 ANGLE : 1.211 1065 REMARK 3 CHIRALITY : 0.045 124 REMARK 3 PLANARITY : 0.007 135 REMARK 3 DIHEDRAL : 13.719 295 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 4CRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1290059851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11971 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 38.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: PDB ENTRY 3DRX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 2000, MME 0.1M TRIS PH 8.4, REMARK 280 0.15M TMAO REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.60667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.80333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.20500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 6.40167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.00833 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 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 -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 VAL A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 GLY A 8 REMARK 465 THR A 9 REMARK 465 GLU A 10 REMARK 465 ASN A 11 REMARK 465 LEU A 12 REMARK 465 TYR A 13 REMARK 465 PHE A 14 REMARK 465 GLN A 15 REMARK 465 SER A 16 REMARK 465 GLY A 51 REMARK 465 ARG A 52 REMARK 465 ILE A 53 REMARK 465 SER A 54 REMARK 465 PRO A 86 REMARK 465 ARG A 87 REMARK 465 GLY A 88 REMARK 465 VAL A 89 REMARK 465 HIS A 90 REMARK 465 GLY A 91 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2030 DISTANCE = 6.24 ANGSTROMS DBREF 4CRH A 18 120 UNP Q8TBC3 SHKB1_HUMAN 18 120 SEQADV 4CRH MET A -5 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A -4 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A -3 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A -2 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A -1 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A 0 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH HIS A 1 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH SER A 2 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH SER A 3 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH GLY A 4 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH VAL A 5 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH ASP A 6 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH LEU A 7 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH GLY A 8 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH THR A 9 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH GLU A 10 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH ASN A 11 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH LEU A 12 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH TYR A 13 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH PHE A 14 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH GLN A 15 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH SER A 16 UNP Q8TBC3 EXPRESSION TAG SEQADV 4CRH MET A 17 UNP Q8TBC3 EXPRESSION TAG SEQRES 1 A 126 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 126 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLY GLU VAL SEQRES 3 A 126 ILE HIS LEU ASN VAL GLY GLY LYS ARG PHE SER THR SER SEQRES 4 A 126 ARG GLN THR LEU THR TRP ILE PRO ASP SER PHE PHE SER SEQRES 5 A 126 SER LEU LEU SER GLY ARG ILE SER THR LEU LYS ASP GLU SEQRES 6 A 126 THR GLY ALA ILE PHE ILE ASP ARG ASP PRO THR VAL PHE SEQRES 7 A 126 ALA PRO ILE LEU ASN PHE LEU ARG THR LYS GLU LEU ASP SEQRES 8 A 126 PRO ARG GLY VAL HIS GLY SER SER LEU LEU HIS GLU ALA SEQRES 9 A 126 GLN PHE TYR GLY LEU THR PRO LEU VAL ARG ARG LEU GLN SEQRES 10 A 126 LEU ARG GLU GLU LEU ASP ARG SER SER FORMUL 2 HOH *98(H2 O) HELIX 1 1 ARG A 34 TRP A 39 1 6 HELIX 2 2 SER A 43 LEU A 49 1 7 HELIX 3 3 VAL A 71 LYS A 82 1 12 HELIX 4 4 SER A 92 GLY A 102 1 11 HELIX 5 5 LEU A 103 ARG A 118 1 16 SHEET 1 AA 3 LYS A 28 SER A 33 0 SHEET 2 AA 3 VAL A 20 VAL A 25 -1 O ILE A 21 N THR A 32 SHEET 3 AA 3 ILE A 63 ILE A 65 1 O ILE A 63 N ASN A 24 CRYST1 71.290 71.290 38.410 90.00 90.00 120.00 P 65 6 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 0.014027 0.008099 0.000000 0.00000 SCALE2 0.000000 0.016197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026035 0.00000