HEADER DNA BINDING PROTEIN INHIBITOR 09-SEP-16 6U2U TITLE HELIX-LOOP-HELIX MOTIF OF MOUSE DNA-BINDING PROTEIN INHIBITOR ID-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN INHIBITOR ID-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 59-104; COMPND 5 SYNONYM: INHIBITOR OF DNA BINDING 1,INHIBITOR OF DIFFERENTIATION 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ID1, ID, ID-1, IDB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELIX-LOOP-HELIX, DNA-BINDING PROTEIN INHIBITOR, DNA BINDING PROTEIN, KEYWDS 2 DNA BINDING PROTEIN INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR R.BENEZRA,N.P.PAVLETICH,Y.GOLDGUR,A.-L.GALL REVDAT 3 11-OCT-23 6U2U 1 REMARK REVDAT 2 04-DEC-19 6U2U 1 REMARK REVDAT 1 16-OCT-19 6U2U 0 JRNL AUTH P.M.WOJNAROWICZ,R.LIMA E SILVA,M.OHNAKA,S.B.LEE,Y.CHIN, JRNL AUTH 2 A.KULUKIAN,S.H.CHANG,B.DESAI,M.GARCIA ESCOLANO,R.SHAH, JRNL AUTH 3 M.GARCIA-CAO,S.XU,R.KADAM,Y.GOLDGUR,M.A.MILLER,O.OUERFELLI, JRNL AUTH 4 G.YANG,T.ARAKAWA,S.K.ALBANESE,W.A.GARLAND,G.STOLLER, JRNL AUTH 5 J.CHAUDHARY,L.NORTON,R.K.SONI,J.PHILIP,R.C.HENDRICKSON, JRNL AUTH 6 A.IAVARONE,A.J.DANNENBERG,J.D.CHODERA,N.PAVLETICH, JRNL AUTH 7 A.LASORELLA,P.A.CAMPOCHIARO,R.BENEZRA JRNL TITL A SMALL-MOLECULE PAN-ID ANTAGONIST INHIBITS PATHOLOGIC JRNL TITL 2 OCULAR NEOVASCULARIZATION. JRNL REF CELL REP V. 29 62 2019 JRNL REFN ESSN 2211-1247 JRNL PMID 31577956 JRNL DOI 10.1016/J.CELREP.2019.08.073 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 13599 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1362 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 29.2560 - 3.2251 0.90 1141 127 0.1836 0.2175 REMARK 3 2 3.2251 - 2.5603 0.99 1258 142 0.1969 0.2270 REMARK 3 3 2.5603 - 2.2368 1.00 1256 139 0.2004 0.2374 REMARK 3 4 2.2368 - 2.0324 0.99 1233 136 0.1978 0.2443 REMARK 3 5 2.0324 - 1.8867 1.00 1233 141 0.2213 0.2516 REMARK 3 6 1.8867 - 1.7755 0.99 1247 137 0.2318 0.2678 REMARK 3 7 1.7755 - 1.6866 0.99 1221 137 0.2326 0.2520 REMARK 3 8 1.6866 - 1.6132 0.99 1222 135 0.2468 0.3200 REMARK 3 9 1.6132 - 1.5511 0.98 1244 141 0.2514 0.3236 REMARK 3 10 1.5511 - 1.5000 0.95 1182 127 0.2704 0.3193 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.006 758 REMARK 3 ANGLE : 0.803 1023 REMARK 3 CHIRALITY : 0.056 120 REMARK 3 PLANARITY : 0.005 129 REMARK 3 DIHEDRAL : 18.222 301 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -1.9999 -0.3300 1.3341 REMARK 3 T TENSOR REMARK 3 T11: 0.1495 T22: 0.1387 REMARK 3 T33: 0.1258 T12: 0.0135 REMARK 3 T13: 0.0011 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 2.6860 L22: 2.5548 REMARK 3 L33: 1.9824 L12: 0.4125 REMARK 3 L13: -0.3666 L23: -0.5461 REMARK 3 S TENSOR REMARK 3 S11: -0.1371 S12: -0.0636 S13: -0.0073 REMARK 3 S21: 0.1528 S22: 0.0249 S23: 0.0152 REMARK 3 S31: 0.1432 S32: 0.0286 S33: -0.0001 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 6U2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13599 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 35.9000 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25300 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: PHENIX REMARK 200 STARTING MODEL: 6MGM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES (PH 6.5), 0.2 M SODIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 299K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.85600 REMARK 290 SMTRY3 2 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: 2120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 ASN B 103 REMARK 465 SER B 104 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 O HOH B 219 O HOH B 229 1.86 REMARK 500 OE1 GLU B 86 O HOH B 201 1.91 REMARK 500 O HOH B 208 O HOH B 225 1.92 REMARK 500 O HOH B 219 O HOH B 228 1.96 REMARK 500 O HOH A 223 O HOH A 252 1.99 REMARK 500 O HOH A 204 O HOH A 209 2.04 REMARK 500 OE1 GLN B 89 O HOH B 202 2.07 REMARK 500 O HOH A 210 O HOH A 214 2.12 REMARK 500 O HOH A 226 O HOH A 230 2.15 REMARK 500 N LEU B 59 O HOH B 203 2.17 REMARK 500 O HOH A 248 O HOH A 250 2.18 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 254 O HOH B 221 1655 2.16 REMARK 500 OE1 GLU B 71 NH1 ARG B 96 1455 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T9O RELATED DB: PDB DBREF 6U2U A 59 104 UNP P20067 ID1_MOUSE 59 104 DBREF 6U2U B 59 104 UNP P20067 ID1_MOUSE 59 104 SEQRES 1 A 46 LEU TYR ASP MET ASN GLY CYS TYR SER ARG LEU LYS GLU SEQRES 2 A 46 LEU VAL PRO THR LEU PRO GLN ASN ARG LYS VAL SER LYS SEQRES 3 A 46 VAL GLU ILE LEU GLN HIS VAL ILE ASP TYR ILE ARG ASP SEQRES 4 A 46 LEU GLN LEU GLU LEU ASN SER SEQRES 1 B 46 LEU TYR ASP MET ASN GLY CYS TYR SER ARG LEU LYS GLU SEQRES 2 B 46 LEU VAL PRO THR LEU PRO GLN ASN ARG LYS VAL SER LYS SEQRES 3 B 46 VAL GLU ILE LEU GLN HIS VAL ILE ASP TYR ILE ARG ASP SEQRES 4 B 46 LEU GLN LEU GLU LEU ASN SER FORMUL 3 HOH *87(H2 O) HELIX 1 AA1 ASP A 61 VAL A 73 1 13 HELIX 2 AA2 SER A 83 ASN A 103 1 21 HELIX 3 AA3 ASP B 61 VAL B 73 1 13 HELIX 4 AA4 SER B 83 LEU B 102 1 20 CRYST1 25.893 57.712 32.097 90.00 114.29 90.00 P 1 21 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 0.038620 0.000000 0.017430 0.00000 SCALE2 0.000000 0.017327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034181 0.00000