HEADER DNA BINDING PROTEIN 14-SEP-18 6MGN TITLE MOUSE ID1 (51-104) - HUMAN HE47 (348-399) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR E2-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 558-609; COMPND 5 SYNONYM: CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 21,BHLHB21, COMPND 6 IMMUNOGLOBULIN ENHANCER-BINDING FACTOR E12/E47,IMMUNOGLOBULIN COMPND 7 TRANSCRIPTION FACTOR 1,KAPPA-E2-BINDING FACTOR,TRANSCRIPTION FACTOR COMPND 8 3,TCF-3,TRANSCRIPTION FACTOR ITF-1; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA-BINDING PROTEIN INHIBITOR ID-1; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 59-104; COMPND 14 SYNONYM: INHIBITOR OF DNA BINDING 1,INHIBITOR OF DIFFERENTIATION 1; COMPND 15 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: TCF3, BHLHB21, E2A, ITF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: ID1, ID, ID-1, IDB1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA-BINDING PROTEIN INHIBITOR ID-1, TRANSCRIPTION FACTOR E2-ALPHA KEYWDS 2 ISOFORM E47 [HOMO SAPIENS], DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BENEZRA,N.P.PAVLETICH,A.-L.GALL,Y.GOLDGUR REVDAT 4 11-OCT-23 6MGN 1 REMARK REVDAT 3 04-DEC-19 6MGN 1 REMARK REVDAT 2 16-OCT-19 6MGN 1 JRNL REVDAT 1 18-SEP-19 6MGN 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 10248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.330 REMARK 3 FREE R VALUE TEST SET COUNT : 1059 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 19.4330 - 3.7928 0.96 1232 138 0.1898 0.2293 REMARK 3 2 3.7928 - 3.0141 0.98 1165 126 0.1746 0.1848 REMARK 3 3 3.0141 - 2.6342 0.98 1132 147 0.1872 0.2110 REMARK 3 4 2.6342 - 2.3938 0.99 1135 141 0.1751 0.2297 REMARK 3 5 2.3938 - 2.2225 0.99 1128 138 0.1694 0.2032 REMARK 3 6 2.2225 - 2.0916 0.99 1142 122 0.1722 0.2107 REMARK 3 7 2.0916 - 1.9870 1.00 1132 130 0.1786 0.2235 REMARK 3 8 1.9870 - 1.9005 0.99 1123 117 0.2326 0.3229 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.860 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 : 0.007 823 REMARK 3 ANGLE : 0.714 1103 REMARK 3 CHIRALITY : 0.048 128 REMARK 3 PLANARITY : 0.004 143 REMARK 3 DIHEDRAL : 11.200 525 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 6MGN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10249 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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) : 0.31700 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: AMORE REMARK 200 STARTING MODEL: 5T9O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM PHOSPHATE (PH 6.0), REMARK 280 0.25 M NACL, 22.5% PEG8000., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 27.48100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.48100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.97000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.48100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.48100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.97000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.48100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.48100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.97000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.48100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.48100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.97000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 A 738 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 753 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 758 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 780 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 259 LIES ON A SPECIAL POSITION. 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 A 739 O HOH A 754 1.81 REMARK 500 O HOH A 749 O HOH B 281 1.89 REMARK 500 O HOH A 727 O HOH B 282 1.95 REMARK 500 O HOH B 206 O HOH B 279 2.08 REMARK 500 O HOH B 245 O HOH B 283 2.09 REMARK 500 OE1 GLN B 99 O HOH B 201 2.11 REMARK 500 O HOH B 228 O HOH B 280 2.11 REMARK 500 O HOH B 261 O HOH B 284 2.15 REMARK 500 O HOH B 208 O HOH B 224 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 703 O HOH B 261 2655 1.85 REMARK 500 O HOH B 272 O HOH B 272 2655 1.99 REMARK 500 O HOH A 741 O HOH A 743 7555 2.00 REMARK 500 O HOH A 742 O HOH B 262 5555 2.14 REMARK 500 O HOH A 708 O HOH A 767 7555 2.18 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 779 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 780 DISTANCE = 6.90 ANGSTROMS DBREF 6MGN A 558 609 UNP P15923 TFE2_HUMAN 558 609 DBREF 6MGN B 59 104 UNP P20067 ID1_MOUSE 59 104 SEQADV 6MGN MET B 58 UNP P20067 INITIATING METHIONINE SEQRES 1 A 52 ARG VAL ARG ASP ILE ASN GLU ALA PHE ARG GLU LEU GLY SEQRES 2 A 52 ARG MET CYS GLN MET HIS LEU LYS SER ASP LYS ALA GLN SEQRES 3 A 52 THR LYS LEU LEU ILE LEU GLN GLN ALA VAL GLN VAL ILE SEQRES 4 A 52 LEU GLY LEU GLU GLN GLN VAL ARG GLU ARG ASN LEU ASN SEQRES 1 B 47 MET LEU TYR ASP MET ASN GLY CYS TYR SER ARG LEU LYS SEQRES 2 B 47 GLU LEU VAL PRO THR LEU PRO GLN ASN ARG LYS VAL SER SEQRES 3 B 47 LYS VAL GLU ILE LEU GLN HIS VAL ILE ASP TYR ILE ARG SEQRES 4 B 47 ASP LEU GLN LEU GLU LEU ASN SER FORMUL 3 HOH *167(H2 O) HELIX 1 AA1 ASP A 561 LYS A 578 1 18 HELIX 2 AA2 THR A 584 ASN A 607 1 24 HELIX 3 AA3 ASP B 61 VAL B 73 1 13 HELIX 4 AA4 SER B 83 ASN B 103 1 21 CRYST1 54.962 54.962 81.940 90.00 90.00 90.00 P 42 21 2 8 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 0.018194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012204 0.00000