HEADER SIGNALING PROTEIN 22-APR-23 8J5I TITLE MALT1 DEATH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUCOSA-ASSOCIATED LYMPHOID TISSUE LYMPHOMA TRANSLOCATION COMPND 3 PROTEIN 1; COMPND 4 CHAIN: B; COMPND 5 FRAGMENT: DEATH DOMAIN; COMPND 6 SYNONYM: MALT LYMPHOMA-ASSOCIATED TRANSLOCATION,PARACASPASE; COMPND 7 EC: 3.4.22.-; COMPND 8 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: MALT1, MLT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CARMAS-BCL10-MALT1 COMPLEX, MALT LYMPHOMA, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.LO,B.J.KUO REVDAT 2 23-OCT-24 8J5I 1 REMARK REVDAT 1 24-APR-24 8J5I 0 JRNL AUTH Y.C.LO,B.J.KUO JRNL TITL MALT1 DEATH DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 7594 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 387 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 21.3500 - 3.0300 0.99 2475 130 0.2056 0.2223 REMARK 3 2 3.0300 - 2.4000 0.99 2382 126 0.2477 0.2788 REMARK 3 3 2.4000 - 2.1000 0.99 2350 131 0.2236 0.2742 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.32 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 : 0.005 764 REMARK 3 ANGLE : 0.867 1028 REMARK 3 CHIRALITY : 0.034 121 REMARK 3 PLANARITY : 0.008 133 REMARK 3 DIHEDRAL : 5.012 106 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 71 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4713 33.2924 6.2253 REMARK 3 T TENSOR REMARK 3 T11: 0.3513 T22: 0.2828 REMARK 3 T33: 0.3726 T12: 0.0478 REMARK 3 T13: 0.0366 T23: 0.0902 REMARK 3 L TENSOR REMARK 3 L11: 7.8428 L22: 3.7757 REMARK 3 L33: 6.4152 L12: 1.0221 REMARK 3 L13: -1.1049 L23: -2.0334 REMARK 3 S TENSOR REMARK 3 S11: 0.1859 S12: 0.3786 S13: 0.6895 REMARK 3 S21: -0.1284 S22: 0.2726 S23: 0.2813 REMARK 3 S31: -0.5517 S32: -0.4963 S33: -0.3325 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 103 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8085 17.8097 17.5750 REMARK 3 T TENSOR REMARK 3 T11: 0.3715 T22: 0.4638 REMARK 3 T33: 0.5199 T12: -0.0115 REMARK 3 T13: 0.0259 T23: 0.2617 REMARK 3 L TENSOR REMARK 3 L11: 2.4366 L22: 2.2555 REMARK 3 L33: 2.2118 L12: -1.8482 REMARK 3 L13: 1.8989 L23: -0.6624 REMARK 3 S TENSOR REMARK 3 S11: 0.0125 S12: -0.4828 S13: -0.7165 REMARK 3 S21: -0.1957 S22: 0.1983 S23: 0.5195 REMARK 3 S31: 0.4209 S32: 0.1208 S33: -0.1942 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 28 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1415 32.9493 16.3260 REMARK 3 T TENSOR REMARK 3 T11: 0.4815 T22: 0.2975 REMARK 3 T33: 0.4406 T12: -0.0022 REMARK 3 T13: 0.1092 T23: 0.1141 REMARK 3 L TENSOR REMARK 3 L11: 5.8876 L22: 8.4129 REMARK 3 L33: 9.3491 L12: -0.5284 REMARK 3 L13: 0.6615 L23: 0.9003 REMARK 3 S TENSOR REMARK 3 S11: 0.2487 S12: -0.1553 S13: 0.9863 REMARK 3 S21: 0.4289 S22: -0.0251 S23: 0.5377 REMARK 3 S31: -1.3624 S32: -0.3929 S33: -0.2144 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 48 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2492 24.2576 11.3463 REMARK 3 T TENSOR REMARK 3 T11: 0.4515 T22: 0.5735 REMARK 3 T33: 0.5845 T12: 0.1007 REMARK 3 T13: 0.0223 T23: 0.1451 REMARK 3 L TENSOR REMARK 3 L11: 3.3458 L22: 2.4210 REMARK 3 L33: 9.4271 L12: 2.8418 REMARK 3 L13: 2.0763 L23: 2.0218 REMARK 3 S TENSOR REMARK 3 S11: 0.4524 S12: 0.7725 S13: -0.7754 REMARK 3 S21: 0.7206 S22: -0.2838 S23: -1.0785 REMARK 3 S31: 1.1122 S32: 0.7391 S33: -0.0981 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 65 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8771 19.3133 1.9883 REMARK 3 T TENSOR REMARK 3 T11: 0.7187 T22: 0.7384 REMARK 3 T33: 0.9371 T12: -0.1018 REMARK 3 T13: -0.1004 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 5.4714 L22: 6.1766 REMARK 3 L33: 2.3709 L12: -5.5163 REMARK 3 L13: -0.8617 L23: -0.2191 REMARK 3 S TENSOR REMARK 3 S11: 0.2367 S12: -0.4689 S13: -1.6292 REMARK 3 S21: 0.1675 S22: 0.8331 S23: 2.9064 REMARK 3 S31: 1.4061 S32: 1.0653 S33: -1.0715 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 8J5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MOLECULAR REPLACEMENT REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.980 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 (%): 57.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TACSIMATE PH 6, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z 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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.61600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.61450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.70150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.61600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.61450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.70150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.61600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.61450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.70150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.61600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.61450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.70150 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: 630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 35.23200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 OE1 GLU B 35 NE ARG B 39 2.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 8J5I B 28 124 UNP Q9UDY8 MALT1_HUMAN 28 124 SEQRES 1 B 97 ALA THR LEU ASN ARG LEU ARG GLU PRO LEU LEU ARG ARG SEQRES 2 B 97 LEU SER GLU LEU LEU ASP GLN ALA PRO GLU GLY ARG GLY SEQRES 3 B 97 TRP ARG ARG LEU ALA GLU LEU ALA GLY SER ARG GLY ARG SEQRES 4 B 97 LEU ARG LEU SER CYS LEU ASP LEU GLU GLN CYS SER LEU SEQRES 5 B 97 LYS VAL LEU GLU PRO GLU GLY SER PRO SER LEU CYS LEU SEQRES 6 B 97 LEU LYS LEU MET GLY GLU LYS GLY CYS THR VAL THR GLU SEQRES 7 B 97 LEU SER ASP PHE LEU GLN ALA MET GLU HIS THR GLU VAL SEQRES 8 B 97 LEU GLN LEU LEU SER PRO FORMUL 2 HOH *7(H2 O) HELIX 1 AA1 THR B 29 LEU B 33 5 5 HELIX 2 AA2 ARG B 34 ALA B 48 1 15 HELIX 3 AA3 PRO B 49 ARG B 52 5 4 HELIX 4 AA4 GLY B 53 GLY B 65 1 13 HELIX 5 AA5 SER B 70 LEU B 79 1 10 HELIX 6 AA6 LYS B 80 GLU B 83 5 4 HELIX 7 AA7 SER B 87 LYS B 99 1 13 HELIX 8 AA8 THR B 102 LEU B 122 1 21 SSBOND 1 CYS B 71 CYS B 71 1555 3655 2.04 SSBOND 2 CYS B 77 CYS B 91 1555 1555 2.06 CRYST1 35.232 83.229 85.403 90.00 90.00 90.00 I 2 2 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 0.028383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012015 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011709 0.00000