PDB Short entry for 4NJ8 HEADER STRUCTURAL PROTEIN 08-NOV-13 4NJ8 TITLE CRYSTAL STRUCTURE OF THE HUMAN ANKS3 SAM DOMAIN L52A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANKYRIN REPEAT AND SAM DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SAM DOMAIN, UNP RESIDUES 421- 490; 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: ANKS3, KIAA1977; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIS-SUMO KEYWDS SAM DOMAIN, PROTEIN-PROTEIN INTERACTION DOMAIN, POLYMERIZATION KEYWDS 2 DOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.N.LEETTOLA,D.CASCIO,J.U.BOWIE REVDAT 3 28-FEB-24 4NJ8 1 SEQADV REVDAT 2 17-JUL-19 4NJ8 1 REMARK REVDAT 1 16-JUL-14 4NJ8 0 JRNL AUTH C.N.LEETTOLA,M.J.KNIGHT,D.CASCIO,S.HOFFMAN,J.U.BOWIE JRNL TITL CHARACTERIZATION OF THE SAM DOMAIN OF THE PKD-RELATED JRNL TITL 2 PROTEIN ANKS6 AND ITS INTERACTION WITH ANKS3. JRNL REF BMC STRUCT.BIOL. V. 14 17 2014 JRNL REFN ESSN 1472-6807 JRNL PMID 24998259 JRNL DOI 10.1186/1472-6807-14-17 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 22797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2280 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 1.6340 - 1.6000 0.99 0 138 0.2582 0.2570 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.48 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 NULL REMARK 3 ANGLE : 0.920 NULL REMARK 3 CHIRALITY : 0.035 NULL REMARK 3 PLANARITY : 0.004 NULL REMARK 3 DIHEDRAL : 11.932 NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -11.4956 29.1551 -1.3195 REMARK 3 T TENSOR REMARK 3 T11: 0.1561 T22: 0.1923 REMARK 3 T33: 0.1876 T12: -0.0152 REMARK 3 T13: 0.0169 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 1.9306 L22: 3.2477 REMARK 3 L33: 4.0038 L12: 1.7164 REMARK 3 L13: 1.8834 L23: 2.2088 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: -0.0134 S13: -0.1105 REMARK 3 S21: -0.0375 S22: 0.0330 S23: 0.0462 REMARK 3 S31: 0.1630 S32: -0.2247 S33: -0.0197 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 4NJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL 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 : 22798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 15.15 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG-8000, 100MM SODIUM/POTASSIUM REMARK 280 PHOSPHATE, 0.3M SODIUM CHLORIDE, PH 6.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 16.77000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.38500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.15500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 1 REMARK 465 SER A 69 REMARK 465 ALA A 70 REMARK 465 ARG A 71 REMARK 465 SER B 1 REMARK 465 ARG B 2 REMARK 465 ALA B 3 REMARK 465 PRO B 4 REMARK 465 TYR B 5 REMARK 465 SER B 6 REMARK 465 GLY B 7 REMARK 465 ARG B 71 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 2 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NL9 RELATED DB: PDB DBREF 4NJ8 A 2 71 UNP Q6ZW76 ANKS3_HUMAN 421 490 DBREF 4NJ8 B 2 71 UNP Q6ZW76 ANKS3_HUMAN 421 490 SEQADV 4NJ8 SER A 1 UNP Q6ZW76 EXPRESSION TAG SEQADV 4NJ8 ALA A 52 UNP Q6ZW76 LEU 471 ENGINEERED MUTATION SEQADV 4NJ8 SER B 1 UNP Q6ZW76 EXPRESSION TAG SEQADV 4NJ8 ALA B 52 UNP Q6ZW76 LEU 471 ENGINEERED MUTATION SEQRES 1 A 71 SER ARG ALA PRO TYR SER GLY PRO GLN ASP LEU ALA ALA SEQRES 2 A 71 LEU LEU GLU GLN ILE GLY CYS LEU LYS TYR LEU GLN VAL SEQRES 3 A 71 PHE GLU GLU GLN ASP VAL ASP LEU ARG ILE PHE LEU THR SEQRES 4 A 71 LEU THR GLU SER ASP LEU LYS GLU ILE GLY ILE THR ALA SEQRES 5 A 71 PHE GLY PRO LYS ARG LYS MET THR SER ALA ILE ALA ARG SEQRES 6 A 71 TRP HIS SER SER ALA ARG SEQRES 1 B 71 SER ARG ALA PRO TYR SER GLY PRO GLN ASP LEU ALA ALA SEQRES 2 B 71 LEU LEU GLU GLN ILE GLY CYS LEU LYS TYR LEU GLN VAL SEQRES 3 B 71 PHE GLU GLU GLN ASP VAL ASP LEU ARG ILE PHE LEU THR SEQRES 4 B 71 LEU THR GLU SER ASP LEU LYS GLU ILE GLY ILE THR ALA SEQRES 5 B 71 PHE GLY PRO LYS ARG LYS MET THR SER ALA ILE ALA ARG SEQRES 6 B 71 TRP HIS SER SER ALA ARG FORMUL 3 HOH *50(H2 O) HELIX 1 1 ASP A 10 ILE A 18 1 9 HELIX 2 2 CYS A 20 LYS A 22 5 3 HELIX 3 3 TYR A 23 GLN A 30 1 8 HELIX 4 4 ASP A 33 LEU A 38 1 6 HELIX 5 5 THR A 41 GLY A 49 1 9 HELIX 6 6 ALA A 52 HIS A 67 1 16 HELIX 7 7 ASP B 10 GLY B 19 1 10 HELIX 8 8 CYS B 20 LYS B 22 5 3 HELIX 9 9 TYR B 23 GLN B 30 1 8 HELIX 10 10 ASP B 33 LEU B 38 1 6 HELIX 11 11 THR B 41 GLY B 49 1 9 HELIX 12 12 ALA B 52 SER B 69 1 18 CRYST1 71.890 71.890 33.540 90.00 90.00 90.00 P 41 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 0.013910 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029815 0.00000