PDB Short entry for 1QB2 HEADER SIGNALING PROTEIN 29-APR-99 1QB2 TITLE CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN PROTEIN SRP54M TITLE 2 AT 2.1A RESOLUTION: EVIDENCE FOR THE MECHANISM OF SIGNAL PEPTIDE TITLE 3 BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN SIGNAL RECOGNITION PARTICLE 54 KD PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SRP54; COMPND 5 SYNONYM: SRP54; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLACENTA; SOURCE 6 TISSUE: PLACENTA; SOURCE 7 CELLULAR_LOCATION: CYTOPLASM; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PET19; SOURCE 13 OTHER_DETAILS: T7 BASED EXPRESSION SYSTEM KEYWDS ALPHA-HELIX, HELIX-TURN-HELIX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.M.CLEMONS JR.,K.GOWDA,S.D.BLACK,C.ZWIEB,V.RAMAKRISHNAN REVDAT 5 14-FEB-24 1QB2 1 REMARK REVDAT 4 04-OCT-17 1QB2 1 REMARK REVDAT 3 24-FEB-09 1QB2 1 VERSN REVDAT 2 01-APR-03 1QB2 1 JRNL REVDAT 1 20-OCT-99 1QB2 0 JRNL AUTH W.M.CLEMONS JR.,K.GOWDA,S.D.BLACK,C.ZWIEB,V.RAMAKRISHNAN JRNL TITL CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN JRNL TITL 2 PROTEIN SRP54M AT 2.1 A RESOLUTION: EVIDENCE FOR THE JRNL TITL 3 MECHANISM OF SIGNAL PEPTIDE BINDING. JRNL REF J.MOL.BIOL. V. 292 697 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10497032 JRNL DOI 10.1006/JMBI.1999.3090 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 25396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : ~10% OF REFLECTIONS RANDOMLY REMARK 3 PICKED REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2609 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 : 1706 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.065 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 1QB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000009058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-98; NULL; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL; NULL; NULL REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS; NSLS; NSLS REMARK 200 BEAMLINE : X12C; X25; X25; X25 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93; 0.93; 0.9796; 0.9793 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : BRANDEIS; NULL; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25000 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 2K, PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 14.45500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.61000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.61000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.45500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.67000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 LYS A 433 REMARK 465 MET A 434 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 LYS A 432 CA C O CB CG CD CE REMARK 470 LYS A 432 NZ 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 ASP A 358 41.44 -106.33 REMARK 500 VAL A 431 -94.66 -95.25 REMARK 500 MET B 360 66.95 65.36 REMARK 500 LYS B 362 -104.09 47.03 REMARK 500 ASN B 364 55.47 -110.95 REMARK 500 PRO B 400 -7.98 -56.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QB2 A 326 434 UNP P61011 SRP54_HUMAN 326 434 DBREF 1QB2 B 326 434 UNP P61011 SRP54_HUMAN 326 434 SEQRES 1 A 109 GLN PHE THR LEU ARG ASP MET TYR GLU GLN PHE GLN ASN SEQRES 2 A 109 ILE MET LYS MET GLY PRO PHE SER GLN ILE LEU GLY MET SEQRES 3 A 109 ILE PRO GLY PHE GLY THR ASP PHE MET SER LYS GLY ASN SEQRES 4 A 109 GLU GLN GLU SER MET ALA ARG LEU LYS LYS LEU MET THR SEQRES 5 A 109 ILE MET ASP SER MET ASN ASP GLN GLU LEU ASP SER THR SEQRES 6 A 109 ASP GLY ALA LYS VAL PHE SER LYS GLN PRO GLY ARG ILE SEQRES 7 A 109 GLN ARG VAL ALA ARG GLY SER GLY VAL SER THR ARG ASP SEQRES 8 A 109 VAL GLN GLU LEU LEU THR GLN TYR THR LYS PHE ALA GLN SEQRES 9 A 109 MET VAL LYS LYS MET SEQRES 1 B 109 GLN PHE THR LEU ARG ASP MET TYR GLU GLN PHE GLN ASN SEQRES 2 B 109 ILE MET LYS MET GLY PRO PHE SER GLN ILE LEU GLY MET SEQRES 3 B 109 ILE PRO GLY PHE GLY THR ASP PHE MET SER LYS GLY ASN SEQRES 4 B 109 GLU GLN GLU SER MET ALA ARG LEU LYS LYS LEU MET THR SEQRES 5 B 109 ILE MET ASP SER MET ASN ASP GLN GLU LEU ASP SER THR SEQRES 6 B 109 ASP GLY ALA LYS VAL PHE SER LYS GLN PRO GLY ARG ILE SEQRES 7 B 109 GLN ARG VAL ALA ARG GLY SER GLY VAL SER THR ARG ASP SEQRES 8 B 109 VAL GLN GLU LEU LEU THR GLN TYR THR LYS PHE ALA GLN SEQRES 9 B 109 MET VAL LYS LYS MET FORMUL 3 HOH *84(H2 O) HELIX 1 1 THR A 328 MET A 342 1 15 HELIX 2 2 MET A 342 ILE A 352 1 11 HELIX 3 3 ASN A 364 ASP A 380 1 17 HELIX 4 4 ASN A 383 SER A 389 1 7 HELIX 5 5 GLY A 392 GLN A 399 1 8 HELIX 6 6 PRO A 400 SER A 410 1 11 HELIX 7 7 SER A 413 VAL A 431 1 19 HELIX 8 8 THR B 328 GLY B 350 1 23 HELIX 9 9 GLU B 365 ASP B 380 1 16 HELIX 10 10 ASN B 383 SER B 389 1 7 HELIX 11 11 ASP B 391 GLN B 399 1 9 HELIX 12 12 PRO B 400 SER B 410 1 11 HELIX 13 13 SER B 413 LYS B 433 1 21 CRYST1 28.910 61.340 129.220 90.00 90.00 90.00 P 21 21 21 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 0.034590 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007739 0.00000