HEADER GENE REGULATION 04-FEB-24 8Y76 TITLE CRYSTAL STRUCTURE OF THE SAM DOMAIN OF L3MBTL3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: H-L(3)MBT-LIKE PROTEIN 3,L(3)MBT-LIKE PROTEIN 3,L3MBT-LIKE COMPND 5 3,MBT-1; 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 GENE: L3MBTL3, KIAA1798, MBT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EPIGENETIC, CHROMATIN-BINDING, POLYMER, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.CAO,Z.WANG REVDAT 2 03-SEP-25 8Y76 1 JRNL REVDAT 1 12-FEB-25 8Y76 0 JRNL AUTH M.GELLER,Y.CAO,C.SIMON,B.STIELOW,J.XU,P.WEI,A.NIST,I.ROHNER, JRNL AUTH 2 L.M.JEUDE,T.HUBER,T.STIEWE,Z.WANG,R.LIEFKE JRNL TITL COOPERATION OF A POLYMERIZING SAM DOMAIN AND AN JRNL TITL 2 INTRINSICALLY DISORDERED REGION ENABLES FULL SAMD1 FUNCTION JRNL TITL 3 ON CHROMATIN. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40183636 JRNL DOI 10.1093/NAR/GKAF259 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5284 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.730 REMARK 3 FREE R VALUE TEST SET COUNT : 303 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 25.9100 - 2.5100 1.00 2500 161 0.1730 0.2218 REMARK 3 2 2.5100 - 1.9900 1.00 2481 142 0.1579 0.2408 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) : 0.121 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.85 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 : 0.009 557 REMARK 3 ANGLE : 0.780 748 REMARK 3 CHIRALITY : 0.054 86 REMARK 3 PLANARITY : 0.004 94 REMARK 3 DIHEDRAL : 2.439 340 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 8Y76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300045127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.71900 REMARK 200 R SYM FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M SODIUM MALONATE PH 6.0, 0.1 M REMARK 280 MES MONOHYDRATE PH 6.0 AND 0.5%(W/V) POLYETHYLENE GLYCOL 10000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 33.22267 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 16.61133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.91700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.30567 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 41.52833 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 DBREF 8Y76 A 459 527 UNP Q96JM7 LMBL3_HUMAN 705 773 SEQADV 8Y76 SER A 458 UNP Q96JM7 EXPRESSION TAG SEQRES 1 A 70 SER VAL SER LYS TRP SER THR ASP GLU VAL SER GLU PHE SEQRES 2 A 70 ILE GLN SER LEU PRO GLY CYS GLU GLU HIS GLY LYS VAL SEQRES 3 A 70 PHE LYS ASP GLU GLN ILE ASP GLY GLU ALA PHE LEU LEU SEQRES 4 A 70 MET THR GLN THR ASP ILE VAL LYS ILE MET SER ILE LYS SEQRES 5 A 70 LEU GLY PRO ALA LEU LYS ILE PHE ASN SER ILE LEU MET SEQRES 6 A 70 PHE LYS ALA ALA GLU FORMUL 2 HOH *55(H2 O) HELIX 1 AA1 SER A 458 TRP A 462 5 5 HELIX 2 AA2 SER A 463 SER A 473 1 11 HELIX 3 AA3 CYS A 477 GLU A 479 5 3 HELIX 4 AA4 HIS A 480 GLU A 487 1 8 HELIX 5 AA5 ASP A 490 LEU A 495 1 6 HELIX 6 AA6 THR A 498 LYS A 504 1 7 HELIX 7 AA7 LYS A 509 ALA A 526 1 18 CRYST1 51.820 51.820 49.834 90.00 90.00 120.00 P 65 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 0.019298 0.011141 0.000000 0.00000 SCALE2 0.000000 0.022283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020067 0.00000 TER 549 GLU A 527 HETATM 550 O HOH A 601 -33.813 5.204 0.174 1.00 31.61 O HETATM 551 O HOH A 602 -21.622 22.611 4.953 1.00 27.27 O HETATM 552 O HOH A 603 -25.693 4.459 -8.065 1.00 25.41 O HETATM 553 O HOH A 604 -11.551 -1.733 2.468 1.00 22.86 O HETATM 554 O HOH A 605 -26.010 -0.179 12.155 1.00 26.07 O HETATM 555 O HOH A 606 -18.669 9.721 -9.211 1.00 31.24 O HETATM 556 O HOH A 607 -22.745 -0.213 20.897 1.00 29.32 O HETATM 557 O HOH A 608 -33.945 2.440 4.444 1.00 33.13 O HETATM 558 O HOH A 609 -12.586 9.458 14.319 1.00 29.64 O HETATM 559 O HOH A 610 -15.084 15.823 -5.247 1.00 21.14 O HETATM 560 O HOH A 611 -31.193 4.988 -7.755 1.00 33.13 O HETATM 561 O HOH A 612 -8.440 0.814 0.501 1.00 29.62 O HETATM 562 O HOH A 613 -8.459 -0.166 3.042 1.00 35.26 O HETATM 563 O HOH A 614 -22.931 -3.135 -9.002 1.00 23.72 O HETATM 564 O HOH A 615 -18.057 13.010 11.654 1.00 29.90 O HETATM 565 O HOH A 616 -15.915 2.029 15.766 1.00 28.63 O HETATM 566 O HOH A 617 -14.829 21.759 -2.798 1.00 24.55 O HETATM 567 O HOH A 618 -21.678 5.402 18.812 1.00 27.32 O HETATM 568 O HOH A 619 -5.987 7.079 4.433 1.00 32.52 O HETATM 569 O HOH A 620 -29.746 0.925 -1.542 1.00 23.81 O HETATM 570 O HOH A 621 -12.838 15.026 -3.971 1.00 25.27 O HETATM 571 O HOH A 622 -20.741 -3.239 11.039 1.00 38.99 O HETATM 572 O HOH A 623 -23.739 19.954 4.739 1.00 29.63 O HETATM 573 O HOH A 624 -19.047 13.330 -5.750 1.00 23.21 O HETATM 574 O HOH A 625 -24.559 6.330 -1.518 1.00 23.44 O HETATM 575 O HOH A 626 -22.803 -3.992 10.851 1.00 32.86 O HETATM 576 O HOH A 627 -7.368 2.598 5.897 1.00 28.15 O HETATM 577 O HOH A 628 -13.661 19.424 5.518 1.00 25.87 O HETATM 578 O HOH A 629 -25.736 18.777 -2.074 1.00 35.93 O HETATM 579 O HOH A 630 -14.691 19.899 3.199 1.00 28.00 O HETATM 580 O HOH A 631 -21.482 -3.875 7.155 1.00 25.51 O HETATM 581 O HOH A 632 -13.246 -3.353 4.537 1.00 30.24 O HETATM 582 O HOH A 633 -14.459 12.079 -5.739 1.00 26.37 O HETATM 583 O HOH A 634 -26.250 15.059 9.885 1.00 34.53 O HETATM 584 O HOH A 635 -27.703 -1.268 3.539 1.00 25.79 O HETATM 585 O HOH A 636 -28.775 15.874 2.965 1.00 39.37 O HETATM 586 O HOH A 637 -24.896 2.666 -10.094 1.00 24.25 O HETATM 587 O HOH A 638 -29.954 9.387 5.771 1.00 25.17 O HETATM 588 O HOH A 639 -18.181 19.664 -0.509 1.00 25.00 O HETATM 589 O HOH A 640 -15.095 -0.129 8.748 1.00 30.87 O HETATM 590 O HOH A 641 -7.588 12.113 -1.949 1.00 33.01 O HETATM 591 O HOH A 642 -27.576 -4.019 2.310 1.00 35.81 O HETATM 592 O HOH A 643 -23.190 15.326 -4.689 1.00 34.96 O HETATM 593 O HOH A 644 -16.543 13.485 -4.692 1.00 23.12 O HETATM 594 O HOH A 645 -9.135 3.131 8.277 1.00 22.45 O HETATM 595 O HOH A 646 -19.825 -2.413 19.101 1.00 39.20 O HETATM 596 O HOH A 647 -25.148 1.685 21.519 1.00 30.20 O HETATM 597 O HOH A 648 -31.547 4.125 -2.815 1.00 27.44 O HETATM 598 O HOH A 649 -12.539 16.403 -1.657 1.00 25.12 O HETATM 599 O HOH A 650 -16.611 15.205 14.737 1.00 33.71 O HETATM 600 O HOH A 651 -26.269 6.617 -9.823 1.00 32.38 O HETATM 601 O HOH A 652 -35.301 2.724 2.345 1.00 37.33 O HETATM 602 O HOH A 653 -18.688 12.822 -8.524 1.00 27.43 O HETATM 603 O HOH A 654 -32.725 8.035 8.137 1.00 31.41 O HETATM 604 O HOH A 655 -10.519 1.098 9.375 1.00 34.69 O MASTER 197 0 0 7 0 0 0 6 603 1 0 6 END