HEADER NUCLEAR PROTEIN 30-NOV-17 5YWZ TITLE AID-SUN TANDEM OF SUN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUN DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN UNC-84 HOMOLOG A,SAD1/UNC-84 PROTEIN-LIKE 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SUN1, UNC84A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LINC COMPLEX; SUN PROTEINS; SUN1; AUTOINHIBITION, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,W.LI,W.FENG REVDAT 3 22-NOV-23 5YWZ 1 REMARK REVDAT 2 28-FEB-18 5YWZ 1 JRNL REVDAT 1 21-FEB-18 5YWZ 0 JRNL AUTH Y.XU,W.LI,H.KE,W.FENG JRNL TITL STRUCTURAL CONSERVATION OF THE AUTOINHIBITORY DOMAIN IN SUN JRNL TITL 2 PROTEINS JRNL REF BIOCHEM. BIOPHYS. RES. V. 496 1337 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29408528 JRNL DOI 10.1016/J.BBRC.2018.02.015 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 15636 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 773 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 34.4463 - 3.9966 1.00 2677 115 0.1656 0.2131 REMARK 3 2 3.9966 - 3.1730 1.00 2552 136 0.1653 0.1952 REMARK 3 3 3.1730 - 2.7721 1.00 2479 145 0.1782 0.1985 REMARK 3 4 2.7721 - 2.5187 1.00 2530 131 0.1980 0.2357 REMARK 3 5 2.5187 - 2.3382 1.00 2476 128 0.2135 0.3111 REMARK 3 6 2.3382 - 2.2004 0.87 2149 118 0.2356 0.2708 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 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 : 0.010 1955 REMARK 3 ANGLE : 1.105 2660 REMARK 3 CHIRALITY : 0.041 298 REMARK 3 PLANARITY : 0.005 343 REMARK 3 DIHEDRAL : 14.444 710 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 5YWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006047. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-16 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18348 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 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) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : 0.70700 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: PHASER REMARK 200 STARTING MODEL: 5ED8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 6.3, 0.6M MGSO4, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 32.48533 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 64.97067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.97067 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 32.48533 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 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 A 1154 O HOH A 1175 2.01 REMARK 500 O HOH A 1148 O HOH A 1156 2.05 REMARK 500 OH TYR A 851 O HOH A 1001 2.14 REMARK 500 O HOH A 1114 O HOH A 1153 2.18 REMARK 500 O HOH A 1004 O HOH A 1167 2.19 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 A 1152 O HOH A 1161 3454 1.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 735 50.66 -106.29 REMARK 500 GLN A 782 -157.59 -126.13 REMARK 500 ASP A 791 -162.45 54.45 REMARK 500 LYS A 840 -92.70 -117.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YWZ A 672 913 UNP Q9D666 SUN1_MOUSE 672 913 SEQRES 1 A 242 SER LYS ASP GLU LEU GLN VAL LEU LEU HIS ASP LEU GLU SEQRES 2 A 242 LEU LYS LEU LEU GLN ASN ILE THR HIS HIS ILE THR VAL SEQRES 3 A 242 THR GLY GLN ALA PRO THR SER GLU ALA ILE VAL SER ALA SEQRES 4 A 242 VAL ASN GLN ALA GLY ILE SER GLY ILE THR GLU ALA GLN SEQRES 5 A 242 ALA HIS ILE ILE VAL ASN ASN ALA LEU LYS LEU TYR SER SEQRES 6 A 242 GLN ASP LYS THR GLY MET VAL ASP PHE ALA LEU GLU SER SEQRES 7 A 242 GLY GLY GLY SER ILE LEU SER THR ARG CYS SER GLU THR SEQRES 8 A 242 TYR GLU THR LYS THR ALA LEU LEU SER LEU PHE GLY VAL SEQRES 9 A 242 PRO LEU TRP TYR PHE SER GLN SER PRO ARG VAL VAL ILE SEQRES 10 A 242 GLN PRO ASP ILE TYR PRO GLY ASN CYS TRP ALA PHE LYS SEQRES 11 A 242 GLY SER GLN GLY TYR LEU VAL VAL ARG LEU SER MET LYS SEQRES 12 A 242 ILE TYR PRO THR THR PHE THR MET GLU HIS ILE PRO LYS SEQRES 13 A 242 THR LEU SER PRO THR GLY ASN ILE SER SER ALA PRO LYS SEQRES 14 A 242 ASP PHE ALA VAL TYR GLY LEU GLU THR GLU TYR GLN GLU SEQRES 15 A 242 GLU GLY GLN PRO LEU GLY ARG PHE THR TYR ASP GLN GLU SEQRES 16 A 242 GLY ASP SER LEU GLN MET PHE HIS THR LEU GLU ARG PRO SEQRES 17 A 242 ASP GLN ALA PHE GLN ILE VAL GLU LEU ARG VAL LEU SER SEQRES 18 A 242 ASN TRP GLY HIS PRO GLU TYR THR CYS LEU TYR ARG PHE SEQRES 19 A 242 ARG VAL HIS GLY GLU PRO ILE GLN FORMUL 2 HOH *182(H2 O) HELIX 1 AA1 SER A 672 GLY A 699 1 28 HELIX 2 AA2 THR A 703 ALA A 714 1 12 HELIX 3 AA3 THR A 720 TYR A 735 1 16 HELIX 4 AA4 LEU A 747 GLY A 751 5 5 HELIX 5 AA5 SER A 756 CYS A 759 5 4 HELIX 6 AA6 SER A 783 GLN A 789 5 7 HELIX 7 AA7 PRO A 826 SER A 830 5 5 SHEET 1 AA1 3 SER A 753 ILE A 754 0 SHEET 2 AA1 3 GLY A 805 GLU A 823 -1 O ARG A 810 N SER A 753 SHEET 3 AA1 3 LEU A 870 HIS A 874 -1 O GLN A 871 N MET A 822 SHEET 1 AA2 5 GLN A 856 THR A 862 0 SHEET 2 AA2 5 ASP A 841 LEU A 847 -1 N VAL A 844 O LEU A 858 SHEET 3 AA2 5 PHE A 883 VAL A 890 -1 O ARG A 889 N ALA A 843 SHEET 4 AA2 5 GLY A 805 GLU A 823 -1 N ILE A 815 O PHE A 883 SHEET 5 AA2 5 ARG A 904 PRO A 911 -1 O ARG A 906 N THR A 821 SHEET 1 AA3 2 LYS A 766 LEU A 770 0 SHEET 2 AA3 2 PRO A 776 PHE A 780 -1 O TYR A 779 N THR A 767 SHEET 1 AA4 2 TRP A 798 LYS A 801 0 SHEET 2 AA4 2 TYR A 899 LEU A 902 -1 O LEU A 902 N TRP A 798 CRYST1 73.636 73.636 97.456 90.00 90.00 120.00 P 31 2 1 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 0.013580 0.007841 0.000000 0.00000 SCALE2 0.000000 0.015681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010261 0.00000