PDB Short entry for 1OW1 HEADER TRANSCRIPTION 28-MAR-03 1OW1 TITLE CRYSTAL STRUCTURE OF THE SPOC DOMAIN OF THE HUMAN TRANSCRIPTIONAL TITLE 2 COREPRESSOR, SHARP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMART/HDAC1 ASSOCIATED REPRESSOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPOC DOMAIN; COMPND 5 SYNONYM: MSX2 INTERACTING NUCLEAR TARGET (MINT) HOMOLOG; 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: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSSETTA BL21(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS BETA-ALPHA-BARREL, SPOC DOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.W.SCHWABE,M.ARIYOSHI REVDAT 3 14-FEB-24 1OW1 1 REMARK REVDAT 2 24-FEB-09 1OW1 1 VERSN REVDAT 1 19-AUG-03 1OW1 0 JRNL AUTH J.W.SCHWABE,M.ARIYOSHI JRNL TITL A CONSERVED STRUCTURAL MOTIF REVEALS THE ESSENTIAL JRNL TITL 2 TRANSCRIPTIONAL REPRESSION FUNCTION OF SPEN PROTEINS AND JRNL TITL 3 THEIR ROLE IN DEVELOPMENTAL SIGNALING JRNL REF GENES DEV. V. 17 1909 2003 JRNL REFN ISSN 0890-9369 JRNL PMID 12897056 JRNL DOI 10.1101/GAD.266203 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 16731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1674 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2430 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 261 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1286 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.55000 REMARK 3 B22 (A**2) : 4.21000 REMARK 3 B33 (A**2) : -1.67000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.880 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.270 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 44.98 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_REP.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.2 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16853 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, GLYCEROL, TRIS-HCL, NACL, PH REMARK 280 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 20.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.99000 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 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 3470 REMARK 465 LEU A 3471 REMARK 465 VAL A 3472 REMARK 465 LEU A 3473 REMARK 465 PRO A 3474 REMARK 465 HIS A 3475 REMARK 465 THR A 3476 REMARK 465 GLU A 3477 REMARK 465 PHE A 3478 REMARK 465 GLN A 3479 REMARK 465 PRO A 3480 REMARK 465 ALA A 3481 REMARK 465 PRO A 3482 REMARK 465 LYS A 3483 REMARK 465 GLN A 3484 REMARK 465 ASP A 3485 REMARK 465 SER A 3486 REMARK 465 SER A 3487 REMARK 465 PRO A 3488 REMARK 465 HIS A 3489 REMARK 465 LEU A 3490 REMARK 465 THR A 3491 REMARK 465 SER A 3492 REMARK 465 GLN A 3493 REMARK 465 ARG A 3494 REMARK 465 GLU A 3542 REMARK 465 GLY A 3543 REMARK 465 GLY A 3544 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 A3516 -126.30 58.37 REMARK 500 ALA A3557 -71.56 -37.97 REMARK 500 PHE A3599 -62.12 -107.84 REMARK 500 ALA A3623 -76.32 -108.18 REMARK 500 ALA A3643 64.76 -153.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 1OW1 A 3470 3664 UNP Q96T58 MINT_HUMAN 3470 3664 SEQRES 1 A 195 GLY LEU VAL LEU PRO HIS THR GLU PHE GLN PRO ALA PRO SEQRES 2 A 195 LYS GLN ASP SER SER PRO HIS LEU THR SER GLN ARG PRO SEQRES 3 A 195 VAL ASP MET VAL GLN LEU LEU LYS LYS TYR PRO ILE VAL SEQRES 4 A 195 TRP GLN GLY LEU LEU ALA LEU LYS ASN ASP THR ALA ALA SEQRES 5 A 195 VAL GLN LEU HIS PHE VAL SER GLY ASN ASN VAL LEU ALA SEQRES 6 A 195 HIS ARG SER LEU PRO LEU SER GLU GLY GLY PRO PRO LEU SEQRES 7 A 195 ARG ILE ALA GLN ARG MET ARG LEU GLU ALA THR GLN LEU SEQRES 8 A 195 GLU GLY VAL ALA ARG ARG MET THR VAL GLU THR ASP TYR SEQRES 9 A 195 CYS LEU LEU LEU ALA LEU PRO CYS GLY ARG ASP GLN GLU SEQRES 10 A 195 ASP VAL VAL SER GLN THR GLU SER LEU LYS ALA ALA PHE SEQRES 11 A 195 ILE THR TYR LEU GLN ALA LYS GLN ALA ALA GLY ILE ILE SEQRES 12 A 195 ASN VAL PRO ASN PRO GLY SER ASN GLN PRO ALA TYR VAL SEQRES 13 A 195 LEU GLN ILE PHE PRO PRO CYS GLU PHE SER GLU SER HIS SEQRES 14 A 195 LEU SER ARG LEU ALA PRO ASP LEU LEU ALA SER ILE SER SEQRES 15 A 195 ASN ILE SER PRO HIS LEU MET ILE VAL ILE ALA SER VAL FORMUL 2 HOH *82(H2 O) HELIX 1 1 GLN A 3500 TYR A 3505 1 6 HELIX 2 2 ASN A 3530 LEU A 3538 1 9 HELIX 3 3 GLU A 3556 MET A 3567 1 12 HELIX 4 4 ASP A 3584 PHE A 3599 1 16 HELIX 5 5 PHE A 3599 GLN A 3607 1 9 HELIX 6 6 CYS A 3632 ALA A 3643 1 12 HELIX 7 7 ALA A 3643 SER A 3651 1 9 SHEET 1 A 8 LEU A3547 ILE A3549 0 SHEET 2 A 8 ILE A3507 LEU A3515 1 N ALA A3514 O ILE A3549 SHEET 3 A 8 ASP A3518 GLY A3529 -1 O LEU A3524 N TRP A3509 SHEET 4 A 8 TYR A3573 PRO A3580 -1 O LEU A3575 N SER A3528 SHEET 5 A 8 LEU A3657 SER A3663 -1 O ILE A3659 N LEU A3576 SHEET 6 A 8 TYR A3624 PHE A3629 -1 N PHE A3629 O MET A3658 SHEET 7 A 8 ALA A3608 VAL A3614 -1 N ILE A3612 O LEU A3626 SHEET 8 A 8 GLN A3551 ARG A3554 -1 N MET A3553 O ALA A3609 CRYST1 41.300 61.980 68.400 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 0.024213 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016134 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014620 0.00000