HEADER STRUCTURAL PROTEIN 16-JAN-23 8I33 TITLE COIL 1A OF LAMIN A (RESIDUE 25-65) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRELAMIN-A/C; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS LAMIN A, COIL 1A, COILED-COIL, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.JEONG,N.C.HA REVDAT 1 24-JAN-24 8I33 0 JRNL AUTH S.JEONG,N.C.HA JRNL TITL COIL 1A OF LAMIN A (RESIDUE 25-65) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 17828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 888 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 33.3100 - 2.9400 0.99 2894 151 0.1998 0.1996 REMARK 3 2 2.9400 - 2.3400 0.98 2886 138 0.1971 0.2350 REMARK 3 3 2.3400 - 2.0400 0.97 2836 170 0.1880 0.2256 REMARK 3 4 2.0400 - 1.8500 0.96 2830 146 0.2003 0.2399 REMARK 3 5 1.8500 - 1.7200 0.95 2796 147 0.2014 0.2757 REMARK 3 6 1.7200 - 1.6200 0.92 2698 136 0.1891 0.2395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.138 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.23 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 : 0.006 1366 REMARK 3 ANGLE : 0.709 1832 REMARK 3 CHIRALITY : 0.046 218 REMARK 3 PLANARITY : 0.008 244 REMARK 3 DIHEDRAL : 3.287 192 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 8I33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-22 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) : 1.0 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 136711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, PEG 6000, SODIUM THIOCYANATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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: 2240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 ACE A 24 REMARK 465 ARG A 25 REMARK 465 NH2 B 66 REMARK 465 NH2 C 66 REMARK 465 ACE D 24 REMARK 465 ARG D 25 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 O HOH B 123 O HOH B 124 1.92 REMARK 500 OH TYR B 45 O HOH B 101 2.09 REMARK 500 O HOH A 115 O HOH A 116 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 111 O HOH D 121 1454 2.04 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8I33 A 25 65 UNP A0A6Q8PFJ0_HUMAN DBREF2 8I33 A A0A6Q8PFJ0 25 65 DBREF1 8I33 B 25 65 UNP A0A6Q8PFJ0_HUMAN DBREF2 8I33 B A0A6Q8PFJ0 25 65 DBREF1 8I33 C 25 65 UNP A0A6Q8PFJ0_HUMAN DBREF2 8I33 C A0A6Q8PFJ0 25 65 DBREF1 8I33 D 25 65 UNP A0A6Q8PFJ0_HUMAN DBREF2 8I33 D A0A6Q8PFJ0 25 65 SEQADV 8I33 ACE A 24 UNP A0A6Q8PFJ ACETYLATION SEQADV 8I33 NH2 A 66 UNP A0A6Q8PFJ AMIDATION SEQADV 8I33 ACE B 24 UNP A0A6Q8PFJ ACETYLATION SEQADV 8I33 NH2 B 66 UNP A0A6Q8PFJ AMIDATION SEQADV 8I33 ACE C 24 UNP A0A6Q8PFJ ACETYLATION SEQADV 8I33 NH2 C 66 UNP A0A6Q8PFJ AMIDATION SEQADV 8I33 ACE D 24 UNP A0A6Q8PFJ ACETYLATION SEQADV 8I33 NH2 D 66 UNP A0A6Q8PFJ AMIDATION SEQRES 1 A 43 ACE ARG ILE THR ARG LEU GLN GLU LYS GLU ASP LEU GLN SEQRES 2 A 43 GLU LEU ASN ASP ARG LEU ALA VAL TYR ILE ASP ARG VAL SEQRES 3 A 43 ARG SER LEU GLU THR GLU ASN ALA GLY LEU ARG LEU ARG SEQRES 4 A 43 ILE THR GLU NH2 SEQRES 1 B 43 ACE ARG ILE THR ARG LEU GLN GLU LYS GLU ASP LEU GLN SEQRES 2 B 43 GLU LEU ASN ASP ARG LEU ALA VAL TYR ILE ASP ARG VAL SEQRES 3 B 43 ARG SER LEU GLU THR GLU ASN ALA GLY LEU ARG LEU ARG SEQRES 4 B 43 ILE THR GLU NH2 SEQRES 1 C 43 ACE ARG ILE THR ARG LEU GLN GLU LYS GLU ASP LEU GLN SEQRES 2 C 43 GLU LEU ASN ASP ARG LEU ALA VAL TYR ILE ASP ARG VAL SEQRES 3 C 43 ARG SER LEU GLU THR GLU ASN ALA GLY LEU ARG LEU ARG SEQRES 4 C 43 ILE THR GLU NH2 SEQRES 1 D 43 ACE ARG ILE THR ARG LEU GLN GLU LYS GLU ASP LEU GLN SEQRES 2 D 43 GLU LEU ASN ASP ARG LEU ALA VAL TYR ILE ASP ARG VAL SEQRES 3 D 43 ARG SER LEU GLU THR GLU ASN ALA GLY LEU ARG LEU ARG SEQRES 4 D 43 ILE THR GLU NH2 HET NH2 A 66 3 HET ACE B 24 3 HET ACE C 24 3 HET NH2 D 66 3 HETNAM NH2 AMINO GROUP HETNAM ACE ACETYL GROUP FORMUL 1 NH2 2(H2 N) FORMUL 2 ACE 2(C2 H4 O) FORMUL 5 HOH *85(H2 O) HELIX 1 AA1 THR A 27 GLU A 65 1 39 HELIX 2 AA2 THR B 27 GLU B 65 1 39 HELIX 3 AA3 THR C 27 GLU C 65 1 39 HELIX 4 AA4 THR D 27 GLU D 65 1 39 LINK C GLU A 65 N NH2 A 66 1555 1555 1.33 LINK C ACE B 24 N ARG B 25 1555 1555 1.33 LINK C ACE C 24 N ARG C 25 1555 1555 1.33 LINK C GLU D 65 N NH2 D 66 1555 1555 1.33 CRYST1 22.933 33.703 49.229 97.28 91.20 94.63 P 1 4 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 0.043605 0.003531 0.001380 0.00000 SCALE2 0.000000 0.029768 0.003868 0.00000 SCALE3 0.000000 0.000000 0.020488 0.00000