HEADER HYDROLASE 20-JUL-09 3ID4 TITLE CRYSTAL STRUCTURE OF RSEP PDZ2 DOMAIN FUSED GKASPV PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF SIGMA E PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ2 DOMAIN, RESIDUES 222-307; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CARBOXY-TERMINALLY FUSED GKASPV PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: RSEP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE, CELL INNER MEMBRANE, CELL MEMBRANE, MEMBRANE, METAL- KEYWDS 2 BINDING, METALLOPROTEASE, PROTEASE, TRANSMEMBRANE, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR X.LI,B.WANG,L.FENG,J.WANG,Y.SHI REVDAT 3 01-NOV-23 3ID4 1 SEQADV REVDAT 2 08-SEP-09 3ID4 1 JRNL REVDAT 1 11-AUG-09 3ID4 0 JRNL AUTH X.LI,B.WANG,L.FENG,H.KANG,Y.QI,J.WANG,Y.SHI JRNL TITL CLEAVAGE OF RSEA BY RSEP REQUIRES A CARBOXYL-TERMINAL JRNL TITL 2 HYDROPHOBIC AMINO ACID FOLLOWING DEGS CLEAVAGE JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14837 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19706448 JRNL DOI 10.1073/PNAS.0903289106 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 21.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 10539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 498 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 21.7680 - 2.5460 0.97 2582 123 0.1880 0.2090 REMARK 3 2 2.5460 - 2.0210 0.98 2643 141 0.1790 0.2190 REMARK 3 3 2.0210 - 1.7660 0.95 2543 128 0.2000 0.2120 REMARK 3 4 1.7660 - 1.6040 0.85 2273 106 0.2340 0.2730 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 : 0.41 REMARK 3 B_SOL : 56.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74300 REMARK 3 B22 (A**2) : 2.74300 REMARK 3 B33 (A**2) : -5.48500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 718 REMARK 3 ANGLE : 0.883 979 REMARK 3 CHIRALITY : 0.056 113 REMARK 3 PLANARITY : 0.004 131 REMARK 3 DIHEDRAL : 15.026 284 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 3.0364 6.5931 8.3741 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.1418 REMARK 3 T33: 0.1673 T12: -0.0107 REMARK 3 T13: 0.0122 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.2288 L22: 0.8241 REMARK 3 L33: 1.3787 L12: -0.5320 REMARK 3 L13: -0.5126 L23: 0.6489 REMARK 3 S TENSOR REMARK 3 S11: 0.1034 S12: -0.0819 S13: 0.0673 REMARK 3 S21: 0.0288 S22: -0.1073 S23: 0.0794 REMARK 3 S31: -0.0814 S32: -0.0548 S33: 0.0093 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 3ID4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96386 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10945 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 33.1000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24600 REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 3ID2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2SO4, 30%(W/V) POLYETHYLENE REMARK 280 GLYCOL 4000, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.79100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.58200 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ID1 RELATED DB: PDB REMARK 900 RSEP PDZ1 DOMAIN REMARK 900 RELATED ID: 3ID2 RELATED DB: PDB REMARK 900 RSEP PDZ2 DOMAIN REMARK 900 RELATED ID: 3ID3 RELATED DB: PDB REMARK 900 RSEP PDZ2 I304A DOMAIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FUSED PEPTIDE OF GLY308 TO VAL313 IS CARBOXT-TERMINUS OF RSEA REMARK 999 BY DEGS CLEAVAGE. THE DEPOSITORS FUSED THIS PEPTIDE TO VERIFY THAT REMARK 999 RSEA V148 CAN BIND TO RSEP PDZ2 DOMAIN. DBREF 3ID4 A 222 307 UNP P0AEH1 RSEP_ECOLI 222 307 SEQADV 3ID4 MET A 221 UNP P0AEH1 EXPRESSION TAG SEQADV 3ID4 GLY A 308 UNP P0AEH1 SEE REMARK 999 SEQADV 3ID4 LYS A 309 UNP P0AEH1 SEE REMARK 999 SEQADV 3ID4 ALA A 310 UNP P0AEH1 SEE REMARK 999 SEQADV 3ID4 SER A 311 UNP P0AEH1 SEE REMARK 999 SEQADV 3ID4 PRO A 312 UNP P0AEH1 SEE REMARK 999 SEQADV 3ID4 VAL A 313 UNP P0AEH1 SEE REMARK 999 SEQRES 1 A 93 MET ILE GLU PRO VAL LEU GLU ASN VAL GLN PRO ASN SER SEQRES 2 A 93 ALA ALA SER LYS ALA GLY LEU GLN ALA GLY ASP ARG ILE SEQRES 3 A 93 VAL LYS VAL ASP GLY GLN PRO LEU THR GLN TRP VAL THR SEQRES 4 A 93 PHE VAL MET LEU VAL ARG ASP ASN PRO GLY LYS SER LEU SEQRES 5 A 93 ALA LEU GLU ILE GLU ARG GLN GLY SER PRO LEU SER LEU SEQRES 6 A 93 THR LEU ILE PRO GLU SER LYS PRO GLY ASN GLY LYS ALA SEQRES 7 A 93 ILE GLY PHE VAL GLY ILE GLU PRO LYS GLY LYS ALA SER SEQRES 8 A 93 PRO VAL FORMUL 2 HOH *70(H2 O) HELIX 1 1 SER A 233 ALA A 238 1 6 HELIX 2 2 GLN A 256 ASP A 266 1 11 SHEET 1 A 2 LEU A 226 VAL A 229 0 SHEET 2 A 2 ILE A 304 PRO A 306 -1 O GLU A 305 N GLU A 227 SHEET 1 B 3 ARG A 245 VAL A 249 0 SHEET 2 B 3 LEU A 272 ARG A 278 -1 O GLU A 275 N VAL A 247 SHEET 3 B 3 SER A 281 LEU A 287 -1 O LEU A 287 N LEU A 272 SHEET 1 C 2 GLU A 290 LYS A 292 0 SHEET 2 C 2 ILE A 299 PHE A 301 -1 O ILE A 299 N LYS A 292 CRYST1 35.094 35.094 62.373 90.00 90.00 120.00 P 31 3 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 0.028495 0.016452 0.000000 0.00000 SCALE2 0.000000 0.032903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016033 0.00000