HEADER SIGNALING PROTEIN 02-AUG-01 1JPJ TITLE GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL RECOGNITION PARTICLE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NG DOMAIN; COMPND 5 SYNONYM: FIFTY-FOUR HOMOLOG; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3 KEYWDS FFH, SRP, GMPPNP, SIGNAL RECOGNITION PARTICLE, SRP54, NG DOMAIN, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.PADMANABHAN,D.M.FREYMANN REVDAT 3 16-AUG-23 1JPJ 1 REMARK REVDAT 2 24-FEB-09 1JPJ 1 VERSN REVDAT 1 02-FEB-02 1JPJ 0 JRNL AUTH S.PADMANABHAN,D.M.FREYMANN JRNL TITL THE CONFORMATION OF BOUND GMPPNP SUGGESTS A MECHANISM FOR JRNL TITL 2 GATING THE ACTIVE SITE OF THE SRP GTPASE. JRNL REF STRUCTURE V. 9 859 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11566135 JRNL DOI 10.1016/S0969-2126(01)00641-4 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.3 REMARK 3 NUMBER OF REFLECTIONS : 10233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 830 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2266 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.943 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.57 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10955 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : 0.17100 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: AMORE REMARK 200 STARTING MODEL: 1FFH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 1000, 10% PEG 6000, PH 8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 26.34500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.03000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.03000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.20500 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 GLY A 295 REMARK 465 ASP A 296 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 ARG A 21 137.42 65.52 REMARK 500 GLU A 66 51.90 -104.06 REMARK 500 THR A 69 88.11 -153.45 REMARK 500 LYS A 96 -151.60 -115.45 REMARK 500 VAL A 237 -42.49 -130.50 REMARK 500 ARG A 252 -72.63 -91.08 REMARK 500 SER A 273 163.53 177.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 967 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JPN RELATED DB: PDB REMARK 900 1JPN CONTAINS THE SAME PROTEIN WITH DIFFERENT HET GROUPS DBREF 1JPJ A 1 296 UNP O07347 SRP54_THEAQ 1 296 SEQRES 1 A 296 MET PHE GLN GLN LEU SER ALA ARG LEU GLN GLU ALA ILE SEQRES 2 A 296 GLY ARG LEU ARG GLY ARG GLY ARG ILE THR GLU GLU ASP SEQRES 3 A 296 LEU LYS ALA THR LEU ARG GLU ILE ARG ARG ALA LEU MET SEQRES 4 A 296 ASP ALA ASP VAL ASN LEU GLU VAL ALA ARG ASP PHE VAL SEQRES 5 A 296 GLU ARG VAL ARG GLU GLU ALA LEU GLY LYS GLN VAL LEU SEQRES 6 A 296 GLU SER LEU THR PRO ALA GLU VAL ILE LEU ALA THR VAL SEQRES 7 A 296 TYR GLU ALA LEU LYS GLU ALA LEU GLY GLY GLU ALA ARG SEQRES 8 A 296 LEU PRO VAL LEU LYS ASP ARG ASN LEU TRP PHE LEU VAL SEQRES 9 A 296 GLY LEU GLN GLY SER GLY LYS THR THR THR ALA ALA LYS SEQRES 10 A 296 LEU ALA LEU TYR TYR LYS GLY LYS GLY ARG ARG PRO LEU SEQRES 11 A 296 LEU VAL ALA ALA ASP THR GLN ARG PRO ALA ALA ARG GLU SEQRES 12 A 296 GLN LEU ARG LEU LEU GLY GLU LYS VAL GLY VAL PRO VAL SEQRES 13 A 296 LEU GLU VAL MET ASP GLY GLU SER PRO GLU SER ILE ARG SEQRES 14 A 296 ARG ARG VAL GLU GLU LYS ALA ARG LEU GLU ALA ARG ASP SEQRES 15 A 296 LEU ILE LEU VAL ASP THR ALA GLY ARG LEU GLN ILE ASP SEQRES 16 A 296 GLU PRO LEU MET GLY GLU LEU ALA ARG LEU LYS GLU VAL SEQRES 17 A 296 LEU GLY PRO ASP GLU VAL LEU LEU VAL LEU ASP ALA MET SEQRES 18 A 296 THR GLY GLN GLU ALA LEU SER VAL ALA ARG ALA PHE ASP SEQRES 19 A 296 GLU LYS VAL GLY VAL THR GLY LEU VAL LEU THR LYS LEU SEQRES 20 A 296 ASP GLY ASP ALA ARG GLY GLY ALA ALA LEU SER ALA ARG SEQRES 21 A 296 HIS VAL THR GLY LYS PRO ILE TYR PHE ALA GLY VAL SER SEQRES 22 A 296 GLU LYS PRO GLU GLY LEU GLU PRO PHE TYR PRO GLU ARG SEQRES 23 A 296 LEU ALA GLY ARG ILE LEU GLY MET GLY ASP HET GNP A 967 32 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 2 GNP C10 H17 N6 O13 P3 FORMUL 3 HOH *59(H2 O) HELIX 1 1 PHE A 2 ARG A 15 1 14 HELIX 2 2 LEU A 16 GLY A 20 5 5 HELIX 3 3 THR A 23 ALA A 41 1 19 HELIX 4 4 ASN A 44 LYS A 62 1 19 HELIX 5 5 GLN A 63 SER A 67 5 5 HELIX 6 6 THR A 69 GLY A 87 1 19 HELIX 7 7 GLY A 110 GLY A 124 1 15 HELIX 8 8 ARG A 138 GLY A 153 1 16 HELIX 9 9 SER A 164 ALA A 180 1 17 HELIX 10 10 ASP A 195 GLY A 210 1 16 HELIX 11 11 MET A 221 GLY A 223 5 3 HELIX 12 12 GLN A 224 VAL A 237 1 14 HELIX 13 13 GLY A 253 GLY A 264 1 12 HELIX 14 14 TYR A 283 GLY A 293 1 11 SHEET 1 A 8 VAL A 156 GLU A 158 0 SHEET 2 A 8 PRO A 129 ALA A 133 1 N LEU A 131 O LEU A 157 SHEET 3 A 8 LEU A 183 ASP A 187 1 O LEU A 185 N LEU A 130 SHEET 4 A 8 ASN A 99 VAL A 104 1 N TRP A 101 O VAL A 186 SHEET 5 A 8 GLU A 213 ASP A 219 1 O VAL A 217 N VAL A 104 SHEET 6 A 8 GLY A 241 THR A 245 1 O GLY A 241 N LEU A 216 SHEET 7 A 8 ILE A 267 GLY A 271 1 O GLY A 271 N LEU A 244 SHEET 8 A 8 LEU A 279 PRO A 281 -1 O GLU A 280 N ALA A 270 SITE 1 AC1 20 ARG A 91 LEU A 106 GLN A 107 GLY A 108 SITE 2 AC1 20 SER A 109 GLY A 110 LYS A 111 THR A 112 SITE 3 AC1 20 THR A 113 LYS A 117 GLN A 144 GLY A 190 SITE 4 AC1 20 LYS A 246 ASP A 248 GLY A 271 VAL A 272 SITE 5 AC1 20 SER A 273 GLU A 274 HOH A1012 HOH A1055 CRYST1 52.690 60.410 86.060 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 0.018979 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011620 0.00000