HEADER PROTEIN BINDING 11-DEC-21 7T58 TITLE CRYSTAL STRUCTURE OF MIZ1 BTB DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 17; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PROTEIN-PROTEIN INTERACTION DOMAIN (UNP RESIDUES 1-115); COMPND 5 SYNONYM: MYC-INTERACTING ZINC FINGER PROTEIN 1,MIZ-1,ZINC FINGER COMPND 6 PROTEIN 151,ZINC FINGER PROTEIN 60; COMPND 7 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: ZBTB17, MIZ1, ZNF151, ZNF60; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-PROTEIN INTERACTION DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.M.LINHARES,T.CIERPICKI REVDAT 2 25-OCT-23 7T58 1 REMARK REVDAT 1 14-DEC-22 7T58 0 JRNL AUTH B.M.LINHARES,V.KHARCHENKO,T.CIERPICKI,L.JAREMKO JRNL TITL PREDICTION OF BTB DOMAIN LIGANDABILITY GUIDED BY PROTEIN JRNL TITL 2 DYNAMICS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.378 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 13322 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) : 0.182 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.556 REMARK 3 FREE R VALUE TEST SET COUNT : 607 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 41.3040 - 3.2591 0.97 3500 169 0.1598 0.1938 REMARK 3 2 3.2591 - 2.5869 0.96 3326 149 0.1898 0.2563 REMARK 3 3 2.5869 - 2.2600 0.95 3243 169 0.2126 0.2658 REMARK 3 4 2.2600 - 2.0534 0.77 2646 120 0.2333 0.3219 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.62 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 : 0.002 1771 REMARK 3 ANGLE : 0.425 2396 REMARK 3 CHIRALITY : 0.038 284 REMARK 3 PLANARITY : 0.003 306 REMARK 3 DIHEDRAL : 10.689 1056 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 7T58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-17 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 : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 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 : 13322 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.053 REMARK 200 RESOLUTION RANGE LOW (A) : 41.305 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43810 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Q81 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% W/V PEG1500, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.12600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.12600 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.45950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.94900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.45950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.94900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.12600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.45950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.94900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.12600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.45950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.94900 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 379 LIES ON A SPECIAL POSITION. 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 LYS A 57 REMARK 465 ASP A 58 REMARK 465 VAL A 59 REMARK 465 VAL A 60 REMARK 465 HIS A 61 REMARK 465 ALA B 115 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 GLN A 56 CG CD OE1 NE2 REMARK 470 LEU A 62 CG CD1 CD2 REMARK 470 ASP A 63 CG OD1 OD2 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 ASP A 55 -128.85 -90.85 REMARK 500 REMARK 500 REMARK: NULL 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 A 390 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 424 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B 425 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH B 426 DISTANCE = 6.97 ANGSTROMS DBREF 7T58 A 1 115 UNP Q13105 ZBT17_HUMAN 1 115 DBREF 7T58 B 1 115 UNP Q13105 ZBT17_HUMAN 1 115 SEQRES 1 A 115 MET ASP PHE PRO GLN HIS SER GLN HIS VAL LEU GLU GLN SEQRES 2 A 115 LEU ASN GLN GLN ARG GLN LEU GLY LEU LEU CYS ASP CYS SEQRES 3 A 115 THR PHE VAL VAL ASP GLY VAL HIS PHE LYS ALA HIS LYS SEQRES 4 A 115 ALA VAL LEU ALA ALA CYS SER GLU TYR PHE LYS MET LEU SEQRES 5 A 115 PHE VAL ASP GLN LYS ASP VAL VAL HIS LEU ASP ILE SER SEQRES 6 A 115 ASN ALA ALA GLY LEU GLY GLN VAL LEU GLU PHE MET TYR SEQRES 7 A 115 THR ALA LYS LEU SER LEU SER PRO GLU ASN VAL ASP ASP SEQRES 8 A 115 VAL LEU ALA VAL ALA THR PHE LEU GLN MET GLN ASP ILE SEQRES 9 A 115 ILE THR ALA CYS HIS ALA LEU LYS SER LEU ALA SEQRES 1 B 115 MET ASP PHE PRO GLN HIS SER GLN HIS VAL LEU GLU GLN SEQRES 2 B 115 LEU ASN GLN GLN ARG GLN LEU GLY LEU LEU CYS ASP CYS SEQRES 3 B 115 THR PHE VAL VAL ASP GLY VAL HIS PHE LYS ALA HIS LYS SEQRES 4 B 115 ALA VAL LEU ALA ALA CYS SER GLU TYR PHE LYS MET LEU SEQRES 5 B 115 PHE VAL ASP GLN LYS ASP VAL VAL HIS LEU ASP ILE SER SEQRES 6 B 115 ASN ALA ALA GLY LEU GLY GLN VAL LEU GLU PHE MET TYR SEQRES 7 B 115 THR ALA LYS LEU SER LEU SER PRO GLU ASN VAL ASP ASP SEQRES 8 B 115 VAL LEU ALA VAL ALA THR PHE LEU GLN MET GLN ASP ILE SEQRES 9 B 115 ILE THR ALA CYS HIS ALA LEU LYS SER LEU ALA HET DMS A 201 4 HET DMS B 201 4 HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 DMS 2(C2 H6 O S) FORMUL 5 HOH *216(H2 O) HELIX 1 AA1 GLN A 5 LEU A 20 1 16 HELIX 2 AA2 HIS A 38 SER A 46 1 9 HELIX 3 AA3 SER A 46 ASP A 55 1 10 HELIX 4 AA4 ASN A 66 ALA A 80 1 15 HELIX 5 AA5 ASN A 88 LEU A 99 1 12 HELIX 6 AA6 MET A 101 ALA A 115 1 15 HELIX 7 AA7 GLN B 5 LEU B 20 1 16 HELIX 8 AA8 HIS B 38 SER B 46 1 9 HELIX 9 AA9 SER B 46 VAL B 54 1 9 HELIX 10 AB1 ASN B 66 ALA B 80 1 15 HELIX 11 AB2 ASN B 88 GLN B 100 1 13 HELIX 12 AB3 MET B 101 LEU B 114 1 14 SHEET 1 AA1 2 CYS A 26 VAL A 30 0 SHEET 2 AA1 2 VAL A 33 ALA A 37 -1 O PHE A 35 N PHE A 28 SHEET 1 AA2 2 CYS B 26 VAL B 30 0 SHEET 2 AA2 2 VAL B 33 ALA B 37 -1 O PHE B 35 N PHE B 28 CRYST1 60.919 115.898 64.252 90.00 90.00 90.00 C 2 2 21 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 0.016415 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015564 0.00000