HEADER NUCLEAR PROTEIN 04-MAR-22 7X5D TITLE CRYSTAL STRUCTURE OF THE K316C MUTANT OF HUMAN LAMIN A/C COIL 2 TITLE 2 (RESIDUES 244-340) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LAMIN-A/C; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 70 KDA LAMIN,RENAL CARCINOMA ANTIGEN NY-REN-32; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LMNA, LMN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LAMIN, INTERMEDIATE FILAMENT, NUCLEAR, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.AHN,I.JO,N.-C.HA REVDAT 1 08-MAR-23 7X5D 0 JRNL AUTH J.AHN,I.JO,N.-C.HA JRNL TITL ATOMIC STRUCTURE OF THE ANTIPARALLEL FOUR-HELIX BUNDLE JRNL TITL 2 INTERACTIONS FOR THE FORMATION OF LAMIN FILAMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 13924 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 695 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 20.1000 - 3.1100 0.99 3197 179 0.2333 0.2877 REMARK 3 2 3.1100 - 2.4700 1.00 3076 158 0.2489 0.2594 REMARK 3 3 2.4700 - 2.1600 0.99 3004 155 0.2330 0.2783 REMARK 3 4 2.1600 - 1.9600 0.85 2550 133 0.2385 0.2674 REMARK 3 5 1.9600 - 1.8200 0.47 1402 70 0.2574 0.3302 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) : 31.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.04 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 : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 239 THROUGH 337 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.9700 2.9647 58.0176 REMARK 3 T TENSOR REMARK 3 T11: -0.0630 T22: 0.0315 REMARK 3 T33: 0.0997 T12: 0.0496 REMARK 3 T13: -0.1275 T23: -0.0608 REMARK 3 L TENSOR REMARK 3 L11: 0.6736 L22: 0.6447 REMARK 3 L33: 1.1377 L12: -0.0911 REMARK 3 L13: -0.1373 L23: 0.4330 REMARK 3 S TENSOR REMARK 3 S11: 0.2200 S12: 0.0934 S13: -0.1092 REMARK 3 S21: -0.0622 S22: -0.0675 S23: 0.1131 REMARK 3 S31: 0.0349 S32: -0.1982 S33: -0.0041 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 244 THROUGH 337 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1042 2.9620 14.7034 REMARK 3 T TENSOR REMARK 3 T11: 0.3449 T22: 0.2035 REMARK 3 T33: 0.1102 T12: 0.0702 REMARK 3 T13: -0.0378 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: -0.2067 L22: -0.0171 REMARK 3 L33: 1.4380 L12: -0.0935 REMARK 3 L13: -0.1625 L23: 0.5584 REMARK 3 S TENSOR REMARK 3 S11: -0.0815 S12: 0.1454 S13: -0.0917 REMARK 3 S21: -0.2160 S22: -0.0215 S23: -0.0728 REMARK 3 S31: -0.4127 S32: -0.3888 S33: 0.2065 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 7X5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15449 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TACSIMATE (PH 5.5), PEG 3350, METHYL REMARK 280 MERCURY ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 14.89400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.48300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.89400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.48300 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 29.78800 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 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 B 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 413 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 454 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 GLY A 237 REMARK 465 ALA A 238 REMARK 465 LEU A 338 REMARK 465 ALA A 339 REMARK 465 GLY B 237 REMARK 465 ALA B 238 REMARK 465 MET B 239 REMARK 465 ASP B 240 REMARK 465 PRO B 241 REMARK 465 GLU B 242 REMARK 465 PHE B 243 REMARK 465 LEU B 338 REMARK 465 ALA B 339 DBREF 7X5D A 244 339 UNP P02545 LMNA_HUMAN 244 339 DBREF 7X5D B 244 339 UNP P02545 LMNA_HUMAN 244 339 SEQADV 7X5D GLY A 237 UNP P02545 EXPRESSION TAG SEQADV 7X5D ALA A 238 UNP P02545 EXPRESSION TAG SEQADV 7X5D MET A 239 UNP P02545 EXPRESSION TAG SEQADV 7X5D ASP A 240 UNP P02545 EXPRESSION TAG SEQADV 7X5D PRO A 241 UNP P02545 EXPRESSION TAG SEQADV 7X5D GLU A 242 UNP P02545 EXPRESSION TAG SEQADV 7X5D PHE A 243 UNP P02545 EXPRESSION TAG SEQADV 7X5D CYS A 316 UNP P02545 LYS 316 ENGINEERED MUTATION SEQADV 7X5D GLY B 237 UNP P02545 EXPRESSION TAG SEQADV 7X5D ALA B 238 UNP P02545 EXPRESSION TAG SEQADV 7X5D MET B 239 UNP P02545 EXPRESSION TAG SEQADV 7X5D ASP B 240 UNP P02545 EXPRESSION TAG SEQADV 7X5D PRO B 241 UNP P02545 EXPRESSION TAG SEQADV 7X5D GLU B 242 UNP P02545 EXPRESSION TAG SEQADV 7X5D PHE B 243 UNP P02545 EXPRESSION TAG SEQADV 7X5D CYS B 316 UNP P02545 LYS 316 ENGINEERED MUTATION SEQRES 1 A 103 GLY ALA MET ASP PRO GLU PHE ALA LEU GLN GLU LEU ARG SEQRES 2 A 103 ALA GLN HIS GLU ASP GLN VAL GLU GLN TYR LYS LYS GLU SEQRES 3 A 103 LEU GLU LYS THR TYR SER ALA LYS LEU ASP ASN ALA ARG SEQRES 4 A 103 GLN SER ALA GLU ARG ASN SER ASN LEU VAL GLY ALA ALA SEQRES 5 A 103 HIS GLU GLU LEU GLN GLN SER ARG ILE ARG ILE ASP SER SEQRES 6 A 103 LEU SER ALA GLN LEU SER GLN LEU GLN LYS GLN LEU ALA SEQRES 7 A 103 ALA CYS GLU ALA LYS LEU ARG ASP LEU GLU ASP SER LEU SEQRES 8 A 103 ALA ARG GLU ARG ASP THR SER ARG ARG LEU LEU ALA SEQRES 1 B 103 GLY ALA MET ASP PRO GLU PHE ALA LEU GLN GLU LEU ARG SEQRES 2 B 103 ALA GLN HIS GLU ASP GLN VAL GLU GLN TYR LYS LYS GLU SEQRES 3 B 103 LEU GLU LYS THR TYR SER ALA LYS LEU ASP ASN ALA ARG SEQRES 4 B 103 GLN SER ALA GLU ARG ASN SER ASN LEU VAL GLY ALA ALA SEQRES 5 B 103 HIS GLU GLU LEU GLN GLN SER ARG ILE ARG ILE ASP SER SEQRES 6 B 103 LEU SER ALA GLN LEU SER GLN LEU GLN LYS GLN LEU ALA SEQRES 7 B 103 ALA CYS GLU ALA LYS LEU ARG ASP LEU GLU ASP SER LEU SEQRES 8 B 103 ALA ARG GLU ARG ASP THR SER ARG ARG LEU LEU ALA FORMUL 3 HOH *124(H2 O) HELIX 1 AA1 ASP A 240 ARG A 336 1 97 HELIX 2 AA2 LEU B 245 LEU B 337 1 93 CRYST1 29.788 40.966 140.714 90.00 90.00 90.00 P 21 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 0.033571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007107 0.00000