HEADER HYDROLASE 31-JAN-07 2OQ5 TITLE CRYSTAL STRUCTURE OF DESC1, A NEW MEMBER OF THE TYPE II TRANSMEMBRANE TITLE 2 SERINE PROTEINASES FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEASE, SERINE 11E; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SERINE PROTEASE DESC1, TRANSMEMBRANE PROTEASE, SERINE 11E COMPND 5 CATALYTIC CHAIN; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TMPRSS11E, DESC1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SMD 1168; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS TYPE II TRANS-MEMBRANE SERINE PROTEINASES, TRYPSIN-LIKE SERINE KEYWDS 2 PROTEASE, TUMOR MARKER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR O.J.P.KYRIELEIS,R.HUBER,E.L.MADISON,U.JACOB REVDAT 6 03-APR-24 2OQ5 1 REMARK REVDAT 5 27-DEC-23 2OQ5 1 REMARK REVDAT 4 24-JAN-18 2OQ5 1 AUTHOR REVDAT 3 18-OCT-17 2OQ5 1 REMARK REVDAT 2 24-FEB-09 2OQ5 1 VERSN REVDAT 1 10-APR-07 2OQ5 0 JRNL AUTH O.J.P.KYRIELEIS,R.HUBER,E.ONG,R.OEHLER,M.HUNTER,E.L.MADISON, JRNL AUTH 2 U.JACOB JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DESC1, A NEW JRNL TITL 2 MEMBER OF THE TYPE II TRANSMEMBRANE SERINE PROTEINASE JRNL TITL 3 FAMILY. JRNL REF FEBS J. V. 274 2148 2007 JRNL REFN ISSN 1742-464X JRNL PMID 17388811 JRNL DOI 10.1111/J.1742-4658.2007.05756.X REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1104423.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 31409 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) : 0.210 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1556 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3407 REMARK 3 BIN R VALUE (WORKING SET) : 0.5030 REMARK 3 BIN FREE R VALUE : 0.4720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 185 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1795 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : 0.79000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.760 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.130 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 50.34 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : BEN.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : BEN.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 8.5 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.79000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: ENTEROPEPTIDASE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS , 8 % (M/W) PEG 8000 , PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.10000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.10000 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 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 LYS A 76 -90.86 -57.31 REMARK 500 ALA A 171 -115.58 -95.13 REMARK 500 ASN A 173 66.70 39.31 REMARK 500 LYS A 187 -56.73 51.74 REMARK 500 GLU A 218 -138.09 59.42 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 BEN A 245 DBREF 2OQ5 A 16 244 UNP Q9UL52 TM11E_HUMAN 192 423 SEQRES 1 A 232 ILE VAL GLY GLY THR GLU VAL GLU GLU GLY GLU TRP PRO SEQRES 2 A 232 TRP GLN ALA SER LEU GLN TRP ASP GLY SER HIS ARG CYS SEQRES 3 A 232 GLY ALA THR LEU ILE ASN ALA THR TRP LEU VAL SER ALA SEQRES 4 A 232 ALA HIS CYS PHE THR THR TYR LYS ASN PRO ALA ARG TRP SEQRES 5 A 232 THR ALA SER PHE GLY VAL THR ILE LYS PRO SER LYS MET SEQRES 6 A 232 LYS ARG GLY LEU ARG ARG ILE ILE VAL HIS GLU LYS TYR SEQRES 7 A 232 LYS HIS PRO SER HIS ASP TYR ASP ILE SER LEU ALA GLU SEQRES 8 A 232 LEU SER SER PRO VAL PRO TYR THR ASN ALA VAL HIS ARG SEQRES 9 A 232 VAL CYS LEU PRO ASP ALA SER TYR GLU PHE GLN PRO GLY SEQRES 10 A 232 ASP VAL MET PHE VAL THR GLY PHE GLY ALA LEU LYS ASN SEQRES 11 A 232 ASP GLY TYR SER GLN ASN HIS LEU ARG GLN ALA GLN VAL SEQRES 12 A 232 THR LEU ILE ASP ALA THR THR CYS ASN GLU PRO GLN ALA SEQRES 13 A 232 TYR ASN ASP ALA ILE THR PRO ARG MET LEU CYS ALA GLY SEQRES 14 A 232 SER LEU GLU GLY LYS THR ASP ALA CYS GLN GLY ASP SER SEQRES 15 A 232 GLY GLY PRO LEU VAL SER SER ASP ALA ARG ASP ILE TRP SEQRES 16 A 232 TYR LEU ALA GLY ILE VAL SER TRP GLY ASP GLU CYS ALA SEQRES 17 A 232 LYS PRO ASN LYS PRO GLY VAL TYR THR ARG VAL THR ALA SEQRES 18 A 232 LEU ARG ASP TRP ILE THR SER LYS THR GLY ILE HET BEN A 245 9 HETNAM BEN BENZAMIDINE FORMUL 2 BEN C7 H8 N2 FORMUL 3 HOH *126(H2 O) HELIX 1 1 ALA A 55 THR A 61 5 6 HELIX 2 2 ASN A 64A ALA A 64C 5 3 HELIX 3 3 ASP A 164 ASN A 169 1 6 HELIX 4 4 LEU A 234 GLY A 243 1 10 SHEET 1 A 8 THR A 20 GLU A 21 0 SHEET 2 A 8 ARG A 156 ILE A 163 -1 O GLN A 157 N THR A 20 SHEET 3 A 8 MET A 180 GLY A 184 -1 O CYS A 182 N ILE A 163 SHEET 4 A 8 GLY A 226 ARG A 230 -1 O TYR A 228 N LEU A 181 SHEET 5 A 8 TRP A 207 TRP A 215 -1 N TRP A 215 O VAL A 227 SHEET 6 A 8 PRO A 198 SER A 202 -1 N SER A 201 O TYR A 208 SHEET 7 A 8 VAL A 135 GLY A 140 -1 N PHE A 137 O VAL A 200 SHEET 8 A 8 ARG A 156 ILE A 163 -1 O VAL A 160 N MET A 136 SHEET 1 B 7 GLN A 30 TRP A 36 0 SHEET 2 B 7 SER A 39 ASN A 48 -1 O CYS A 42 N LEU A 33 SHEET 3 B 7 TRP A 51 SER A 54 -1 O VAL A 53 N THR A 45 SHEET 4 B 7 SER A 104 LEU A 108 -1 O SER A 104 N SER A 54 SHEET 5 B 7 MET A 80 VAL A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 B 7 TRP A 64E PHE A 68 -1 N ALA A 66 O ARG A 82 SHEET 7 B 7 GLN A 30 TRP A 36 -1 N GLN A 34 O THR A 65 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 3 CYS A 191 CYS A 219 1555 1555 2.03 CISPEP 1 HIS A 96 PRO A 97 0 0.25 SITE 1 AC1 8 ASP A 189 ALA A 190 GLN A 192 SER A 195 SITE 2 AC1 8 TRP A 215 GLU A 218 GLY A 226 HOH A 254 CRYST1 47.900 70.200 80.200 90.00 90.00 90.00 P 2 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 0.020877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012469 0.00000