HEADER PROTEIN BINDING 10-JUL-14 4QUC TITLE CRYSTAL STRUCTURE OF CHROMODOMAIN OF RHINO COMPND MOL_ID: 1; COMPND 2 MOLECULE: RE36324P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHROMODOMAIN; COMPND 5 SYNONYM: RHINO; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG10683, DMEL_CG10683, RHI, RHINO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETSUMO KEYWDS HISTONE BINDING, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.LI,D.J.PATEL REVDAT 2 20-SEP-23 4QUC 1 SEQADV REVDAT 1 20-AUG-14 4QUC 0 JRNL AUTH A.LE THOMAS,E.STUWE,S.LI,J.DU,G.MARINOV,N.ROZHKOV,Y.C.CHEN, JRNL AUTH 2 Y.LUO,R.SACHIDANANDAM,K.F.TOTH,D.PATEL,A.A.ARAVIN JRNL TITL TRANSGENERATIONALLY INHERITED PIRNAS TRIGGER PIRNA JRNL TITL 2 BIOGENESIS BY CHANGING THE CHROMATIN OF PIRNA CLUSTERS AND JRNL TITL 3 INDUCING PRECURSOR PROCESSING. JRNL REF GENES DEV. V. 28 1667 2014 JRNL REFN ISSN 0890-9369 JRNL PMID 25085419 JRNL DOI 10.1101/GAD.245514.114 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 9265 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 441 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 14.5902 - 2.1651 0.95 3076 146 0.1996 0.2387 REMARK 3 2 2.1651 - 1.7194 0.97 2979 157 0.2496 0.2773 REMARK 3 3 1.7194 - 1.5023 0.91 2769 138 0.2439 0.3313 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.920 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 : 0.010 472 REMARK 3 ANGLE : 1.252 638 REMARK 3 CHIRALITY : 0.080 67 REMARK 3 PLANARITY : 0.005 83 REMARK 3 DIHEDRAL : 13.451 176 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4000 76.3656 12.5135 REMARK 3 T TENSOR REMARK 3 T11: 0.4039 T22: 0.3222 REMARK 3 T33: 0.2260 T12: 0.0945 REMARK 3 T13: -0.0368 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.9308 L22: 7.9193 REMARK 3 L33: 2.9887 L12: -2.6685 REMARK 3 L13: 1.5600 L23: 2.0398 REMARK 3 S TENSOR REMARK 3 S11: 0.2253 S12: 0.5688 S13: -0.0844 REMARK 3 S21: -0.1837 S22: -0.1838 S23: 0.2365 REMARK 3 S31: -0.5466 S32: -0.4659 S33: 0.0014 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1500 73.5393 17.7890 REMARK 3 T TENSOR REMARK 3 T11: 0.2561 T22: 0.2792 REMARK 3 T33: 0.2320 T12: 0.0152 REMARK 3 T13: 0.0003 T23: -0.0652 REMARK 3 L TENSOR REMARK 3 L11: 6.9603 L22: 4.1988 REMARK 3 L33: 5.5917 L12: -2.2121 REMARK 3 L13: 3.7175 L23: -2.8372 REMARK 3 S TENSOR REMARK 3 S11: -0.1568 S12: -0.3094 S13: 0.2682 REMARK 3 S21: 0.2310 S22: 0.1242 S23: -0.2735 REMARK 3 S31: -0.0496 S32: -0.4944 S33: 0.0722 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8874 67.9653 5.8660 REMARK 3 T TENSOR REMARK 3 T11: 0.4070 T22: 0.3320 REMARK 3 T33: 0.3384 T12: 0.0048 REMARK 3 T13: 0.0474 T23: -0.1150 REMARK 3 L TENSOR REMARK 3 L11: 2.1529 L22: 6.5172 REMARK 3 L33: 6.8017 L12: -1.7594 REMARK 3 L13: -0.8231 L23: 1.6032 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.4273 S13: -0.1821 REMARK 3 S21: -0.4869 S22: 0.2266 S23: -0.6430 REMARK 3 S31: -0.3622 S32: 0.3781 S33: -0.1372 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 4QUC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.029 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9293 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 61.9000 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 (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : 0.65300 REMARK 200 FOR SHELL : 3.100 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: PDB ENTRY 1KNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM NITRATE AND 20%(W/V) REMARK 280 PEG3350, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.74333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.37167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.37167 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.74333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 125 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 126 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 129 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 SER A 18 REMARK 465 ASP A 19 REMARK 465 HIS A 20 REMARK 465 VAL A 21 REMARK 465 GLU A 22 REMARK 465 HIS A 79 REMARK 465 ARG A 80 REMARK 465 LYS A 81 REMARK 465 ALA A 82 REMARK 465 ALA A 83 REMARK 465 ALA A 84 REMARK 465 LYS A 85 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QUF RELATED DB: PDB DBREF 4QUC A 19 85 UNP Q7JXA8 Q7JXA8_DROME 19 85 SEQADV 4QUC SER A 18 UNP Q7JXA8 EXPRESSION TAG SEQRES 1 A 68 SER ASP HIS VAL GLU GLU TYR VAL VAL GLU LYS ILE LEU SEQRES 2 A 68 GLY LYS ARG PHE VAL ASN GLY ARG PRO GLN VAL LEU VAL SEQRES 3 A 68 LYS TRP SER GLY PHE PRO ASN GLU ASN ASN THR TRP GLU SEQRES 4 A 68 PRO LEU GLU ASN VAL GLY ASN CYS MET LYS LEU VAL SER SEQRES 5 A 68 ASP PHE GLU SER GLU VAL PHE ARG LEU HIS ARG LYS ALA SEQRES 6 A 68 ALA ALA LYS FORMUL 2 HOH *45(H2 O) HELIX 1 1 PRO A 49 ASN A 53 5 5 HELIX 2 2 GLU A 59 VAL A 61 5 3 HELIX 3 3 CYS A 64 LEU A 78 1 15 SHEET 1 A 3 VAL A 26 VAL A 35 0 SHEET 2 A 3 ARG A 38 TRP A 45 -1 O LEU A 42 N LEU A 30 SHEET 3 A 3 THR A 54 PRO A 57 -1 O THR A 54 N VAL A 43 CRYST1 36.480 36.480 76.115 90.00 90.00 120.00 P 32 2 1 6 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 0.027412 0.015826 0.000000 0.00000 SCALE2 0.000000 0.031653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013138 0.00000