HEADER HYDROLASE 20-JUL-09 3ID1 TITLE CRYSTAL STRUCTURE OF RSEP PDZ1 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF SIGMA E PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ1 DOMAIN, RESIDUES 127-220; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES 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 20-MAR-24 3ID1 1 SEQADV REVDAT 2 08-SEP-09 3ID1 1 JRNL REVDAT 1 11-AUG-09 3ID1 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. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 13868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 694 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 29.8748 - 2.8555 1.00 3005 141 0.1758 0.2062 REMARK 3 2 2.8555 - 2.2668 0.99 2856 143 0.1990 0.2634 REMARK 3 3 2.2668 - 1.9803 0.96 2750 146 0.1827 0.2325 REMARK 3 4 1.9803 - 1.7993 0.88 2490 141 0.2176 0.2511 REMARK 3 5 1.7993 - 1.6703 0.74 2073 123 0.2725 0.2985 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 : 0.33 REMARK 3 B_SOL : 62.53 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.90900 REMARK 3 B22 (A**2) : 2.90900 REMARK 3 B33 (A**2) : -5.81800 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 : 0.004 743 REMARK 3 ANGLE : 0.847 1015 REMARK 3 CHIRALITY : 0.051 117 REMARK 3 PLANARITY : 0.003 136 REMARK 3 DIHEDRAL : 12.902 283 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): 24.2485 -12.6654 1.6656 REMARK 3 T TENSOR REMARK 3 T11: 0.1180 T22: 0.0903 REMARK 3 T33: 0.1080 T12: -0.0665 REMARK 3 T13: -0.0055 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.4983 L22: 2.5258 REMARK 3 L33: 3.2741 L12: -0.2435 REMARK 3 L13: -0.9385 L23: -1.1559 REMARK 3 S TENSOR REMARK 3 S11: -0.0214 S12: 0.1203 S13: 0.0837 REMARK 3 S21: -0.1103 S22: 0.0554 S23: 0.1993 REMARK 3 S31: -0.0651 S32: -0.1583 S33: -0.0924 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 3ID1 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_1000054258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR-H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 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 (%) : 93.1 REMARK 200 DATA REDUNDANCY : 5.910 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.75 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PROPANE, PH7.0, 2.5M REMARK 280 (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 20.56433 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 41.12867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.12867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.56433 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 53 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 85 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 123 LIES ON A SPECIAL POSITION. 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 PRO A 220 REMARK 900 REMARK 900 RELATED ENTRIES 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 900 RELATED ID: 3ID4 RELATED DB: PDB REMARK 900 RSEP PDZ2 FUSED GKASPV PEPTIDE DOMAIN DBREF 3ID1 A 127 220 UNP P0AEH1 RSEP_ECOLI 127 220 SEQADV 3ID1 MET A 126 UNP P0AEH1 EXPRESSION TAG SEQRES 1 A 95 MET VAL ARG PRO VAL VAL GLY GLU ILE ALA ALA ASN SER SEQRES 2 A 95 ILE ALA ALA GLU ALA GLN ILE ALA PRO GLY THR GLU LEU SEQRES 3 A 95 LYS ALA VAL ASP GLY ILE GLU THR PRO ASP TRP ASP ALA SEQRES 4 A 95 VAL ARG LEU GLN LEU VAL ASP LYS ILE GLY ASP GLU SER SEQRES 5 A 95 THR THR ILE THR VAL ALA PRO PHE GLY SER ASP GLN ARG SEQRES 6 A 95 ARG ASP VAL LYS LEU ASP LEU ARG HIS TRP ALA PHE GLU SEQRES 7 A 95 PRO ASP LYS GLU ASP PRO VAL SER SER LEU GLY ILE ARG SEQRES 8 A 95 PRO ARG GLY PRO FORMUL 2 HOH *131(H2 O) HELIX 1 1 SER A 138 ALA A 143 1 6 HELIX 2 2 ASP A 161 LYS A 172 1 12 HELIX 3 3 ASP A 208 LEU A 213 1 6 SHEET 1 A 2 VAL A 131 ILE A 134 0 SHEET 2 A 2 ILE A 215 PRO A 217 -1 O ARG A 216 N GLY A 132 SHEET 1 B 4 ILE A 157 GLU A 158 0 SHEET 2 B 4 GLU A 150 VAL A 154 -1 N VAL A 154 O ILE A 157 SHEET 3 B 4 SER A 177 ALA A 183 -1 O THR A 181 N LYS A 152 SHEET 4 B 4 ARG A 191 ASP A 196 -1 O LEU A 195 N THR A 178 CISPEP 1 ARG A 218 GLY A 219 0 -0.46 CRYST1 59.740 59.740 61.693 90.00 90.00 120.00 P 31 2 1 6 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 0.016739 0.009664 0.000000 0.00000 SCALE2 0.000000 0.019329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016209 0.00000