HEADER SPLICING 16-DEC-20 7BB3 TITLE STRUCTURE OF S. POMBE YG-BOX OLIGOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURVIVAL MOTOR NEURON-LIKE PROTEIN 1,SURVIVAL MOTOR NEURON- COMPND 3 LIKE PROTEIN 1; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC SOURCE 3 24843); SOURCE 4 ORGANISM_COMMON: FISSION YEAST; SOURCE 5 ORGANISM_TAXID: 284812; SOURCE 6 STRAIN: 972 / ATCC 24843; SOURCE 7 GENE: SMN1, YAB8, SPAC2G11.08C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS USNRNP, BIOGENESIS, SMN, OLIGOMERIZATION, SPLICING EXPDTA X-RAY DIFFRACTION AUTHOR J.VEEPASCHIT,C.GRIMM,U.FISCHER REVDAT 5 31-JAN-24 7BB3 1 REMARK REVDAT 4 28-JUL-21 7BB3 1 JRNL REVDAT 3 31-MAR-21 7BB3 1 JRNL REVDAT 2 03-FEB-21 7BB3 1 REMARK REVDAT 1 20-JAN-21 7BB3 0 JRNL AUTH J.VEEPASCHIT,A.VISWANATHAN,R.BORDONNE,C.GRIMM,U.FISCHER JRNL TITL IDENTIFICATION AND STRUCTURAL ANALYSIS OF THE JRNL TITL 2 SCHIZOSACCHAROMYCES POMBE SMN COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 49 7207 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33754639 JRNL DOI 10.1093/NAR/GKAB158 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.1_3469 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10263 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 531 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 40.4930 - 3.4253 0.99 2518 147 0.2336 0.2702 REMARK 3 2 3.4253 - 2.7190 1.00 2432 121 0.2722 0.3383 REMARK 3 3 2.7190 - 2.3753 0.99 2407 140 0.2877 0.3010 REMARK 3 4 2.3753 - 2.1582 1.00 2375 123 0.3410 0.3507 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.47 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7BB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292113026. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.8-7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.158 REMARK 200 RESOLUTION RANGE LOW (A) : 40.493 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10460 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 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: 4RG5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65 % 2-METHYLPENTANEDIOL, 80 MM KCL, REMARK 280 40 MM HEPES, PH 6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 80.03000 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 80.03000 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 13.59500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.85500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 13.59500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.85500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 80.03000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 13.59500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.85500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 80.03000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 13.59500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.85500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC 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 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -13.59500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 41.85500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 MET A 0 REMARK 465 GLY A 1 REMARK 465 ASP A 2 REMARK 465 GLN A 3 REMARK 465 SER A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 7 REMARK 465 VAL A 8 REMARK 465 TRP A 9 REMARK 465 GLU A 148 REMARK 465 GLN A 149 REMARK 465 ARG A 150 REMARK 465 LYS A 151 REMARK 465 ASP A 152 REMARK 465 MET B 0 REMARK 465 GLY B 1 REMARK 465 ASP B 2 REMARK 465 GLN B 3 REMARK 465 SER B 4 REMARK 465 GLN B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 7 REMARK 465 VAL B 8 REMARK 465 TRP B 9 REMARK 465 GLU B 148 REMARK 465 GLN B 149 REMARK 465 ARG B 150 REMARK 465 LYS B 151 REMARK 465 ASP B 152 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 203 DBREF 7BB3 A 2 35 UNP Q09808 SMN1_SCHPO 2 35 DBREF 7BB3 A 120 152 UNP Q09808 SMN1_SCHPO 120 152 DBREF 7BB3 B 2 35 UNP Q09808 SMN1_SCHPO 2 35 DBREF 7BB3 B 120 152 UNP Q09808 SMN1_SCHPO 120 152 SEQADV 7BB3 MET A 0 UNP Q09808 INITIATING METHIONINE SEQADV 7BB3 GLY A 1 UNP Q09808 EXPRESSION TAG SEQADV 7BB3 MET B 0 UNP Q09808 INITIATING METHIONINE SEQADV 7BB3 GLY B 1 UNP Q09808 EXPRESSION TAG SEQRES 1 A 69 MET GLY ASP GLN SER GLN LYS GLU VAL TRP ASP ASP SER SEQRES 2 A 69 GLU LEU ARG ASN ALA PHE GLU THR ALA LEU HIS GLU PHE SEQRES 3 A 69 LYS LYS TYR HIS SER ILE GLU ALA LYS GLY TYR ASP GLU SEQRES 4 A 69 THR TYR LYS LYS LEU ILE MET SER TRP TYR TYR ALA GLY SEQRES 5 A 69 TYR TYR THR GLY LEU ALA GLU GLY LEU ALA LYS SER GLU SEQRES 6 A 69 GLN ARG LYS ASP SEQRES 1 B 69 MET GLY ASP GLN SER GLN LYS GLU VAL TRP ASP ASP SER SEQRES 2 B 69 GLU LEU ARG ASN ALA PHE GLU THR ALA LEU HIS GLU PHE SEQRES 3 B 69 LYS LYS TYR HIS SER ILE GLU ALA LYS GLY TYR ASP GLU SEQRES 4 B 69 THR TYR LYS LYS LEU ILE MET SER TRP TYR TYR ALA GLY SEQRES 5 B 69 TYR TYR THR GLY LEU ALA GLU GLY LEU ALA LYS SER GLU SEQRES 6 B 69 GLN ARG LYS ASP HET MPD A 201 22 HET MPD B 201 22 HET MPD B 202 22 HET MPD B 203 22 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 MPD 4(C6 H14 O2) FORMUL 7 HOH *3(H2 O) HELIX 1 AA1 ASP A 10 LYS A 146 1 53 HELIX 2 AA2 ASP B 11 SER B 30 1 20 HELIX 3 AA3 SER B 30 LYS B 146 1 33 SITE 1 AC1 3 TYR A 132 TYR A 133 TYR A 136 SITE 1 AC2 1 MET A 129 SITE 1 AC3 4 TYR A 133 TYR A 137 MET B 129 SER B 130 SITE 1 AC4 1 TYR B 132 CRYST1 27.190 83.710 160.060 90.00 90.00 90.00 C 2 2 21 16 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 0.036778 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006248 0.00000