HEADER GENE REGULATION 11-NOV-20 7KPI TITLE CRYSTAL STRUCTURE OF THE SPOP MATH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECKLE-TYPE POZ PROTEIN; COMPND 3 CHAIN: A; COMPND 4 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: SPOP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, LIGASE, ADAPTOR, PROTEIN, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR E.T.USHER,A.K.BOAL REVDAT 4 18-OCT-23 7KPI 1 REMARK REVDAT 3 21-JUL-21 7KPI 1 JRNL REVDAT 2 05-MAY-21 7KPI 1 JRNL REVDAT 1 28-APR-21 7KPI 0 JRNL AUTH E.T.USHER,N.SABRI,R.ROHAC,A.K.BOAL,T.MITTAG,S.A.SHOWALTER JRNL TITL INTRINSICALLY DISORDERED SUBSTRATES DICTATE SPOP SUBNUCLEAR JRNL TITL 2 LOCALIZATION AND UBIQUITINATION ACTIVITY. JRNL REF J.BIOL.CHEM. V. 296 00693 2021 JRNL REFN ESSN 1083-351X JRNL PMID 33894201 JRNL DOI 10.1016/J.JBC.2021.100693 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 14535 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 730 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 40.7800 - 2.9100 0.99 2847 150 0.1469 0.1926 REMARK 3 2 2.9100 - 2.3100 0.99 2784 145 0.1778 0.1821 REMARK 3 3 2.3100 - 2.0200 0.98 2766 149 0.1553 0.1859 REMARK 3 4 2.0200 - 1.8300 0.98 2734 142 0.1659 0.2049 REMARK 3 5 1.8300 - 1.7000 0.96 2674 144 0.1687 0.2463 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.29 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 1222 REMARK 3 ANGLE : 1.233 1648 REMARK 3 CHIRALITY : 0.079 171 REMARK 3 PLANARITY : 0.008 210 REMARK 3 DIHEDRAL : 10.336 1016 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 7KPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-18 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 : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999995 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 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: 3IVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 23% (W/V) PME REMARK 280 550, 5 MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 31.32100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.62300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 31.32100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.62300 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 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 A 319 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 GLY A 25 REMARK 465 ASP A 166 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 140 O HOH A 201 1.88 REMARK 500 OE1 GLU A 47 O HOH A 202 2.07 REMARK 500 O HOH A 219 O HOH A 336 2.12 REMARK 500 O HOH A 298 O HOH A 303 2.14 REMARK 500 O HOH A 334 O HOH A 344 2.15 REMARK 500 O HOH A 315 O HOH A 346 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 292 O HOH A 335 4546 2.03 REMARK 500 NZ LYS A 95 O HOH A 201 4545 2.04 REMARK 500 O HOH A 237 O HOH A 237 2555 2.09 REMARK 500 O HOH A 202 O HOH A 286 2656 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 95 -143.90 -114.08 REMARK 500 LYS A 95 -145.81 -114.08 REMARK 500 LYS A 135 63.74 -116.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KPI A 28 166 UNP D6RDG8 D6RDG8_HUMAN 28 166 SEQADV 7KPI GLY A 25 UNP D6RDG8 EXPRESSION TAG SEQADV 7KPI PRO A 26 UNP D6RDG8 EXPRESSION TAG SEQADV 7KPI GLY A 27 UNP D6RDG8 EXPRESSION TAG SEQRES 1 A 142 GLY PRO GLY LYS VAL VAL LYS PHE SER TYR MET TRP THR SEQRES 2 A 142 ILE ASN ASN PHE SER PHE CYS ARG GLU GLU MET GLY GLU SEQRES 3 A 142 VAL ILE LYS SER SER THR PHE SER SER GLY ALA ASN ASP SEQRES 4 A 142 LYS LEU LYS TRP CYS LEU ARG VAL ASN PRO LYS GLY LEU SEQRES 5 A 142 ASP GLU GLU SER LYS ASP TYR LEU SER LEU TYR LEU LEU SEQRES 6 A 142 LEU VAL SER CYS PRO LYS SER GLU VAL ARG ALA LYS PHE SEQRES 7 A 142 LYS PHE SER ILE LEU ASN ALA LYS GLY GLU GLU THR LYS SEQRES 8 A 142 ALA MET GLU SER GLN ARG ALA TYR ARG PHE VAL GLN GLY SEQRES 9 A 142 LYS ASP TRP GLY PHE LYS LYS PHE ILE ARG ARG ASP PHE SEQRES 10 A 142 LEU LEU ASP GLU ALA ASN GLY LEU LEU PRO ASP ASP LYS SEQRES 11 A 142 LEU THR LEU PHE CYS GLU VAL SER VAL VAL GLN ASP FORMUL 2 HOH *146(H2 O) HELIX 1 AA1 ASN A 40 CYS A 44 5 5 HELIX 2 AA2 ASP A 77 LYS A 81 5 5 HELIX 3 AA3 ARG A 139 ASP A 144 1 6 HELIX 4 AA4 GLU A 145 GLY A 148 5 4 HELIX 5 AA5 LEU A 150 LYS A 154 5 5 SHEET 1 AA1 4 LYS A 28 VAL A 29 0 SHEET 2 AA1 4 PHE A 57 ALA A 61 -1 O GLY A 60 N VAL A 29 SHEET 3 AA1 4 LEU A 65 ASN A 72 -1 O TRP A 67 N PHE A 57 SHEET 4 AA1 4 ILE A 52 LYS A 53 -1 N ILE A 52 O VAL A 71 SHEET 1 AA2 5 LYS A 28 VAL A 29 0 SHEET 2 AA2 5 PHE A 57 ALA A 61 -1 O GLY A 60 N VAL A 29 SHEET 3 AA2 5 LEU A 65 ASN A 72 -1 O TRP A 67 N PHE A 57 SHEET 4 AA2 5 TYR A 83 SER A 92 -1 O LEU A 89 N CYS A 68 SHEET 5 AA2 5 ASP A 130 ARG A 138 -1 O TRP A 131 N LEU A 88 SHEET 1 AA3 4 LYS A 31 ILE A 38 0 SHEET 2 AA3 4 LEU A 155 GLN A 165 -1 O VAL A 161 N PHE A 32 SHEET 3 AA3 4 VAL A 98 LEU A 107 -1 N LYS A 101 O SER A 162 SHEET 4 AA3 4 GLU A 113 GLU A 118 -1 O MET A 117 N PHE A 104 SHEET 1 AA4 4 LYS A 31 ILE A 38 0 SHEET 2 AA4 4 LEU A 155 GLN A 165 -1 O VAL A 161 N PHE A 32 SHEET 3 AA4 4 VAL A 98 LEU A 107 -1 N LYS A 101 O SER A 162 SHEET 4 AA4 4 TYR A 123 PHE A 125 -1 O PHE A 125 N VAL A 98 CRYST1 62.642 53.246 41.596 90.00 101.39 90.00 C 1 2 1 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 0.015964 0.000000 0.003215 0.00000 SCALE2 0.000000 0.018781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024523 0.00000