HEADER CYTOSOLIC PROTEIN 03-APR-20 6YJK TITLE STRUCTURE OF CYRI-B (FAM49B) FROM RHINCODON TYPUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYRI-B (FAM49B); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHINCODON TYPUS; SOURCE 3 ORGANISM_COMMON: WHALE SHARK; SOURCE 4 ORGANISM_TAXID: 259920; SOURCE 5 GENE: FAM49B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYRI-B, FAM49B, ACTIN ASSEMBLY, RAC BINDING PROTEIN, CELL MOTILITY KEYWDS 2 REGULATOR, CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.KAPLAN REVDAT 3 24-JAN-24 6YJK 1 REMARK REVDAT 2 21-OCT-20 6YJK 1 JRNL REVDAT 1 14-OCT-20 6YJK 0 JRNL AUTH E.KAPLAN,R.STONE,P.J.HUME,N.P.GREENE,V.KORONAKIS JRNL TITL STRUCTURE OF CYRI-B (FAM49B), A KEY REGULATOR OF CELLULAR JRNL TITL 2 ACTIN ASSEMBLY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 1015 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 33021503 JRNL DOI 10.1107/S2059798320010906 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 661 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 60.0000 - 4.0525 1.00 2656 120 0.1858 0.2328 REMARK 3 2 4.0525 - 3.2167 1.00 2503 145 0.2157 0.2761 REMARK 3 3 3.2167 - 2.8101 1.00 2480 136 0.2597 0.3202 REMARK 3 4 2.8101 - 2.5531 1.00 2436 149 0.2892 0.3200 REMARK 3 5 2.5531 - 2.3701 1.00 2471 111 0.3675 0.3685 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.57 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 0 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.6830 14.0076 -26.2348 REMARK 3 T TENSOR REMARK 3 T11: 0.5335 T22: 0.3146 REMARK 3 T33: 0.3755 T12: 0.0133 REMARK 3 T13: 0.0323 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.8994 L22: 3.1476 REMARK 3 L33: 8.4845 L12: 0.1130 REMARK 3 L13: 2.4534 L23: 1.6864 REMARK 3 S TENSOR REMARK 3 S11: -0.1505 S12: -0.4213 S13: 0.2412 REMARK 3 S21: 0.4137 S22: -0.0167 S23: 0.0131 REMARK 3 S31: -0.2328 S32: -0.7818 S33: 0.1400 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 165 THROUGH 324 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3264 4.1536 -20.9671 REMARK 3 T TENSOR REMARK 3 T11: 0.6805 T22: 0.2640 REMARK 3 T33: 0.3596 T12: -0.0250 REMARK 3 T13: 0.0330 T23: -0.0198 REMARK 3 L TENSOR REMARK 3 L11: 3.0076 L22: 2.4712 REMARK 3 L33: 5.7652 L12: -0.2174 REMARK 3 L13: 1.5687 L23: -1.0743 REMARK 3 S TENSOR REMARK 3 S11: -0.0869 S12: 0.0548 S13: -0.0720 REMARK 3 S21: -0.2096 S22: -0.0418 S23: -0.0785 REMARK 3 S31: 0.8966 S32: 0.2236 S33: 0.1149 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 6YJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292106327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-18 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 : DIAMOND REMARK 200 BEAMLINE : I04 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 60.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 1.03000 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 2.8.2 REMARK 200 STARTING MODEL: 6YJJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) GLYCEROL ETHOXYLATE, 0.2 M REMARK 280 AMMONIUM ACETATE AND 0.1 M MES PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 288.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.90500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.90500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.90500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.11500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 VAL A 171 REMARK 465 PRO A 172 REMARK 465 ALA A 173 REMARK 465 GLU A 174 REMARK 465 GLY A 175 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 THR A 9 40.82 -89.34 REMARK 500 SER A 17 -0.41 66.77 REMARK 500 GLN A 27 70.46 51.55 REMARK 500 HIS A 69 77.00 -116.93 REMARK 500 ILE A 168 -72.22 -127.53 REMARK 500 ASN A 212 71.12 -116.21 REMARK 500 PHE A 244 -35.70 -130.96 REMARK 500 SER A 246 -167.25 -120.75 REMARK 500 TYR A 305 -51.13 -120.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YJJ RELATED DB: PDB REMARK 900 SELENOMETHIONINE MODEL DBREF 6YJK A 0 324 PDB 6YJK 6YJK 0 324 SEQRES 1 A 325 SER MET GLY ASN LEU ILE LYS VAL LEU THR ARG ASP ILE SEQRES 2 A 325 ASP HIS ASN ALA SER HIS PHE PHE LEU ASP PHE GLU ASN SEQRES 3 A 325 ALA GLN PRO THR GLU ALA GLU ARG GLU ILE PHE ASN GLN SEQRES 4 A 325 VAL ASN VAL VAL LEU LYS ASP ALA GLU GLY ILE LEU ASN SEQRES 5 A 325 ASP LEU GLN SER TYR ARG GLY ALA GLY HIS GLU ILE ARG SEQRES 6 A 325 GLU ALA ILE GLN HIS PRO ASN ASP GLU ASN LEU GLN GLU SEQRES 7 A 325 LYS ALA TRP SER ALA VAL CYS PRO LEU VAL GLY LYS LEU SEQRES 8 A 325 LYS LYS PHE TYR GLU PHE SER GLN ARG LEU GLU ALA ALA SEQRES 9 A 325 LEU HIS GLY LEU LEU GLY ALA LEU THR SER THR PRO TYR SEQRES 10 A 325 SER PRO THR GLN HIS LEU GLU ARG GLU GLN ALA LEU ALA SEQRES 11 A 325 LYS GLN PHE ALA GLU ILE LEU HIS PHE THR LEU ARG PHE SEQRES 12 A 325 ASP GLU LEU LYS MET THR ASN PRO ALA ILE GLN ASN ASP SEQRES 13 A 325 PHE SER TYR TYR ARG ARG THR LEU SER ARG MET ARG ILE SEQRES 14 A 325 ASN ASN VAL PRO ALA GLU GLY GLU ASN GLU VAL ASN ASN SEQRES 15 A 325 GLU LEU ALA ASN ARG MET SER LEU PHE TYR ALA GLU ALA SEQRES 16 A 325 THR PRO MET LEU LYS THR LEU SER ASP ALA THR THR LYS SEQRES 17 A 325 PHE VAL SER ASP ASN LYS SER LEU PRO ILE GLU ASN THR SEQRES 18 A 325 THR ASP CYS LEU SER THR MET ALA SER VAL CYS ARG VAL SEQRES 19 A 325 MET LEU GLU THR PRO GLU TYR ARG SER ARG PHE ALA SER SEQRES 20 A 325 GLU GLU THR VAL SER PHE CYS LEU ARG VAL MET VAL GLY SEQRES 21 A 325 VAL ILE ILE LEU TYR ASP HIS VAL HIS PRO VAL GLY ALA SEQRES 22 A 325 PHE ALA LYS THR SER LYS ILE ASP MET LYS GLY CYS ILE SEQRES 23 A 325 LYS VAL LEU LYS ASP GLN PRO PRO ASN SER VAL GLU GLY SEQRES 24 A 325 LEU LEU ASN ALA LEU ARG TYR THR THR LYS HIS LEU ASN SEQRES 25 A 325 ASP GLU THR THR SER LYS GLN ILE LYS THR MET LEU GLN FORMUL 2 HOH *8(H2 O) HELIX 1 AA1 MET A 1 THR A 9 1 9 HELIX 2 AA2 ARG A 33 SER A 55 1 23 HELIX 3 AA3 GLY A 60 GLN A 68 1 9 HELIX 4 AA4 GLU A 73 LEU A 111 1 39 HELIX 5 AA5 PRO A 118 ARG A 124 1 7 HELIX 6 AA6 GLN A 126 THR A 148 1 23 HELIX 7 AA7 ALA A 151 ASN A 169 1 19 HELIX 8 AA8 ASN A 181 TYR A 191 1 11 HELIX 9 AA9 PRO A 196 ASP A 211 1 16 HELIX 10 AB1 ILE A 217 GLU A 236 1 20 HELIX 11 AB2 PRO A 238 SER A 242 1 5 HELIX 12 AB3 GLU A 247 VAL A 267 1 21 HELIX 13 AB4 MET A 281 ASP A 290 1 10 HELIX 14 AB5 VAL A 296 TYR A 305 1 10 HELIX 15 AB6 LYS A 317 LEU A 323 1 7 CRYST1 39.810 72.230 107.810 90.00 90.00 90.00 P 21 21 21 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 0.025119 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009276 0.00000