HEADER PROTEIN TRANSPORT 03-JUL-25 9PF4 TITLE SACCHAROMYCES CEREVISIAE SRP54 NG DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL RECOGNITION PARTICLE SUBUNIT SRP54; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN HOMOLOG; COMPND 5 EC: 3.6.5.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SRP54, SRH1, YPR088C, P9513.14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SIGNAL RECOGNITION PARTICLE, GTPASE, RNA BINDING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.D.BRUNER REVDAT 1 22-JUL-26 9PF4 0 JRNL AUTH S.D.BRUNER JRNL TITL STRUCTURE OF THE NG DOMAIN OF YEAST SRP54 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21RC1_5156 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1199 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 39.7400 - 5.3000 1.00 1307 146 0.2123 0.2363 REMARK 3 2 5.3000 - 4.2100 1.00 1231 136 0.1692 0.2117 REMARK 3 3 4.2100 - 3.6800 1.00 1212 134 0.1946 0.2444 REMARK 3 4 3.6800 - 3.3400 1.00 1179 131 0.2215 0.2907 REMARK 3 5 3.3400 - 3.1000 1.00 1187 133 0.2421 0.3515 REMARK 3 6 3.1000 - 2.9200 1.00 1183 131 0.2531 0.3656 REMARK 3 7 2.9200 - 2.7700 1.00 1163 129 0.2487 0.3223 REMARK 3 8 2.7700 - 2.6500 1.00 1184 132 0.2501 0.3019 REMARK 3 9 2.6500 - 2.5500 1.00 1144 127 0.2223 0.2834 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) : 0.351 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.98 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 : 0.008 2277 REMARK 3 ANGLE : 0.877 3058 REMARK 3 CHIRALITY : 0.050 358 REMARK 3 PLANARITY : 0.007 391 REMARK 3 DIHEDRAL : 15.201 851 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 9PF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000297444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9202 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11989 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 39.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.130 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69600 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: NULL REMARK 200 REMARK 200 REMARK: PRISMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% V/V TACSIMATE 7.0, 0.1 M HEPES 7.5, REMARK 280 10 % PEG 5000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 30.53200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 79.47700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.53200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 79.47700 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 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 LEU A 62 REMARK 465 SER A 63 REMARK 465 GLU A 64 REMARK 465 ASN A 65 REMARK 465 ARG A 66 REMARK 465 SER A 67 REMARK 465 GLU A 68 REMARK 465 LYS A 69 REMARK 465 SER A 70 REMARK 465 THR A 71 REMARK 465 THR A 72 REMARK 465 ASN A 73 REMARK 465 LEU A 305 REMARK 465 GLU A 306 REMARK 465 HIS A 307 REMARK 465 HIS A 308 REMARK 465 HIS A 309 REMARK 465 HIS A 310 REMARK 465 HIS A 311 REMARK 465 HIS A 312 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 21 34.42 -74.11 REMARK 500 ARG A 107 -6.41 78.25 REMARK 500 LYS A 191 40.89 70.21 REMARK 500 LYS A 221 74.13 39.20 REMARK 500 HIS A 261 158.81 177.66 REMARK 500 HIS A 286 37.20 -147.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 9PF4 A 1 304 UNP P20424 SRP54_YEAST 1 304 SEQADV 9PF4 LEU A 305 UNP P20424 EXPRESSION TAG SEQADV 9PF4 GLU A 306 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 307 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 308 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 309 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 310 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 311 UNP P20424 EXPRESSION TAG SEQADV 9PF4 HIS A 312 UNP P20424 EXPRESSION TAG SEQRES 1 A 312 MET VAL LEU ALA ASP LEU GLY LYS ARG ILE ASN SER ALA SEQRES 2 A 312 VAL ASN ASN ALA ILE SER ASN THR GLN ASP ASP PHE THR SEQRES 3 A 312 THR SER VAL ASP VAL MET LEU LYS GLY ILE VAL THR ALA SEQRES 4 A 312 LEU LEU GLU SER ASP VAL ASN ILE ALA LEU VAL SER LYS SEQRES 5 A 312 LEU ARG ASN ASN ILE ARG SER GLN LEU LEU SER GLU ASN SEQRES 6 A 312 ARG SER GLU LYS SER THR THR ASN ALA GLN THR LYS LYS SEQRES 7 A 312 LEU ILE GLN LYS THR VAL PHE ASP GLU LEU CYS LYS LEU SEQRES 8 A 312 VAL THR CYS GLU GLY SER GLU GLU LYS ALA PHE VAL PRO SEQRES 9 A 312 LYS LYS ARG LYS THR ASN ILE ILE MET PHE VAL GLY LEU SEQRES 10 A 312 GLN GLY SER GLY LYS THR THR SER CYS THR LYS LEU ALA SEQRES 11 A 312 VAL TYR TYR SER LYS ARG GLY PHE LYS VAL GLY LEU VAL SEQRES 12 A 312 CYS ALA ASP THR PHE ARG ALA GLY ALA PHE ASP GLN LEU SEQRES 13 A 312 LYS GLN ASN ALA ILE ARG ALA ARG ILE PRO PHE TYR GLY SEQRES 14 A 312 SER TYR THR GLU THR ASP PRO ALA LYS VAL ALA GLU GLU SEQRES 15 A 312 GLY ILE ASN LYS PHE LYS LYS GLU LYS PHE ASP ILE ILE SEQRES 16 A 312 ILE VAL ASP THR SER GLY ARG HIS HIS GLN GLU GLU GLU SEQRES 17 A 312 LEU PHE GLN GLU MET ILE GLU ILE SER ASN VAL ILE LYS SEQRES 18 A 312 PRO ASN GLN THR ILE MET VAL LEU ASP ALA SER ILE GLY SEQRES 19 A 312 GLN ALA ALA GLU GLN GLN SER LYS ALA PHE LYS GLU SER SEQRES 20 A 312 SER ASP PHE GLY ALA ILE ILE LEU THR LYS MET ASP GLY SEQRES 21 A 312 HIS ALA ARG GLY GLY GLY ALA ILE SER ALA VAL ALA ALA SEQRES 22 A 312 THR ASN THR PRO ILE ILE PHE ILE GLY THR GLY GLU HIS SEQRES 23 A 312 ILE HIS ASP LEU GLU LYS PHE SER PRO LYS SER PHE ILE SEQRES 24 A 312 SER LYS LEU LEU GLY LEU GLU HIS HIS HIS HIS HIS HIS HET ACT A 401 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *29(H2 O) HELIX 1 AA1 VAL A 2 ASN A 16 1 15 HELIX 2 AA2 ASP A 24 SER A 43 1 20 HELIX 3 AA3 ASN A 46 LEU A 61 1 16 HELIX 4 AA4 THR A 76 VAL A 92 1 17 HELIX 5 AA5 GLY A 96 ALA A 101 1 6 HELIX 6 AA6 GLY A 121 LYS A 135 1 15 HELIX 7 AA7 ARG A 149 ALA A 163 1 15 HELIX 8 AA8 ASP A 175 GLU A 190 1 16 HELIX 9 AA9 GLN A 205 LYS A 221 1 17 HELIX 10 AB1 SER A 232 GLN A 235 5 4 HELIX 11 AB2 ALA A 236 SER A 248 1 13 HELIX 12 AB3 ARG A 263 THR A 274 1 12 HELIX 13 AB4 SER A 294 GLY A 304 1 11 SHEET 1 AA1 8 PHE A 167 TYR A 168 0 SHEET 2 AA1 8 VAL A 140 ALA A 145 1 N CYS A 144 O TYR A 168 SHEET 3 AA1 8 ILE A 194 THR A 199 1 O ASP A 198 N VAL A 143 SHEET 4 AA1 8 ASN A 110 GLY A 116 1 N ILE A 112 O VAL A 197 SHEET 5 AA1 8 GLN A 224 ASP A 230 1 O ILE A 226 N MET A 113 SHEET 6 AA1 8 GLY A 251 THR A 256 1 O ALA A 252 N MET A 227 SHEET 7 AA1 8 ILE A 278 GLY A 282 1 O ILE A 279 N ILE A 253 SHEET 8 AA1 8 LEU A 290 LYS A 292 -1 O GLU A 291 N ILE A 281 CRYST1 61.064 158.954 35.811 90.00 90.00 90.00 P 21 21 2 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 0.016376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027924 0.00000 CONECT 2247 2248 2249 2250 CONECT 2248 2247 CONECT 2249 2247 CONECT 2250 2247 MASTER 246 0 1 13 8 0 0 6 2278 1 4 24 END