PDB Short entry for 1DIC HEADER SERINE PROTEASE 08-JUL-98 1DIC TITLE STRUCTURE OF 3,4-DICHLOROISOCOUMARIN-INHIBITED FACTOR D COMPND MOL_ID: 1; COMPND 2 MOLECULE: FACTOR D; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.46; COMPND 5 OTHER_DETAILS: 3,4-DICHLOROISOCOUMARIN GROUP LINKED TO SERINE 195 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: ISOLATED FROM A PATIENT WITH FANCONI SYNDROME KEYWDS SERINE PROTEASE, COMPLEMENT, FACTOR D, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.B.COLE,J.M.KILPATRICK,N.CHU,Y.S.BABU REVDAT 3 09-AUG-23 1DIC 1 REMARK LINK REVDAT 2 24-FEB-09 1DIC 1 VERSN REVDAT 1 22-JUL-99 1DIC 0 JRNL AUTH L.B.COLE,J.M.KILPATRICK,N.CHU,Y.S.BABU JRNL TITL STRUCTURE OF 3,4-DICHLOROISOCOUMARIN-INHIBITED FACTOR D. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 711 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 9757085 JRNL DOI 10.1107/S0907444997010457 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 17696 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) : 0.182 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 585 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 30 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.064 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 115 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.300 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) : 1.500 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.6 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SIEMENS X1000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18850 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 8.650 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.08230 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1DSU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.78500 REMARK 290 SMTRY3 2 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O O A 245 O O A 246 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 41 -52.06 -122.15 REMARK 500 HIS A 71 -52.33 -123.52 REMARK 500 HIS A 171 -116.62 -123.70 REMARK 500 HIS A 172 75.48 -106.20 REMARK 500 ASP A 173 90.74 -46.02 REMARK 500 ARG A 187 -10.37 71.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DIC A 244 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: S1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: 3,4-DICHLOROISOCOUMARIN MOIETY LINKED TO O ATOM REMARK 800 OF SER 195. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIC A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O A 245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O A 246 DBREF 1DIC A 16 243 UNP P00746 CFAD_HUMAN 26 253 SEQRES 1 A 228 ILE LEU GLY GLY ARG GLU ALA GLU ALA HIS ALA ARG PRO SEQRES 2 A 228 TYR MET ALA SER VAL GLN LEU ASN GLY ALA HIS LEU CYS SEQRES 3 A 228 GLY GLY VAL LEU VAL ALA GLU GLN TRP VAL LEU SER ALA SEQRES 4 A 228 ALA HIS CYS LEU GLU ASP ALA ALA ASP GLY LYS VAL GLN SEQRES 5 A 228 VAL LEU LEU GLY ALA HIS SER LEU SER GLN PRO GLU PRO SEQRES 6 A 228 SER LYS ARG LEU TYR ASP VAL LEU ARG ALA VAL PRO HIS SEQRES 7 A 228 PRO ASP SER GLN PRO ASP THR ILE ASP HIS ASP LEU LEU SEQRES 8 A 228 LEU LEU GLN LEU SER GLU LYS ALA THR LEU GLY PRO ALA SEQRES 9 A 228 VAL ARG PRO LEU PRO TRP GLN ARG VAL ASP ARG ASP VAL SEQRES 10 A 228 ALA PRO GLY THR LEU CYS ASP VAL ALA GLY TRP GLY ILE SEQRES 11 A 228 VAL ASN HIS ALA GLY ARG ARG PRO ASP SER LEU GLN HIS SEQRES 12 A 228 VAL LEU LEU PRO VAL LEU ASP ARG ALA THR CYS ASN ARG SEQRES 13 A 228 ARG THR HIS HIS ASP GLY ALA ILE THR GLU ARG LEU MET SEQRES 14 A 228 CYS ALA GLU SER ASN ARG ARG ASP SER CYS LYS GLY ASP SEQRES 15 A 228 SER GLY GLY PRO LEU VAL CYS GLY GLY VAL LEU GLU GLY SEQRES 16 A 228 VAL VAL THR SER GLY SER ARG VAL CYS GLY ASN ARG LYS SEQRES 17 A 228 LYS PRO GLY ILE TYR THR ARG VAL ALA SER TYR ALA ALA SEQRES 18 A 228 TRP ILE ASP SER VAL LEU ALA HET DIC A 244 10 HET O A 245 1 HET O A 246 1 HETNAM DIC 3,4-DICHLOROISOCOUMARIN HETNAM O OXYGEN ATOM FORMUL 2 DIC C9 H4 CL2 O2 FORMUL 3 O 2(O) FORMUL 5 HOH *115(H2 O) HELIX 1 1 ALA A 56 ALA A 61A 1 7 HELIX 2 2 ARG A 165 ASN A 169 1 5 HELIX 3 3 ALA A 232 VAL A 241 5 10 SHEET 1 A 7 ARG A 81 ASP A 84 0 SHEET 2 A 7 VAL A 64 LEU A 68 -1 N LEU A 68 O ARG A 81 SHEET 3 A 7 MET A 30 LEU A 35 -1 N GLN A 34 O GLN A 65 SHEET 4 A 7 ALA A 39 ALA A 48 -1 N GLY A 44 O ALA A 31 SHEET 5 A 7 TRP A 51 SER A 54 -1 N LEU A 53 O VAL A 45 SHEET 6 A 7 LEU A 104 LEU A 108 -1 N LEU A 106 O VAL A 52 SHEET 7 A 7 VAL A 85 PRO A 90 -1 N VAL A 89 O LEU A 105 SHEET 1 B 2 LEU A 135 GLY A 140 0 SHEET 2 B 2 GLN A 156 PRO A 161 -1 N LEU A 160 O CYS A 136 SHEET 1 C 4 LEU A 180 ALA A 183 0 SHEET 2 C 4 GLY A 226 ARG A 230 -1 N TYR A 228 O MET A 181 SHEET 3 C 4 VAL A 208 VAL A 213 -1 N VAL A 212 O THR A 229 SHEET 4 C 4 PRO A 198 CYS A 201 -1 N CYS A 201 O VAL A 208 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.04 SSBOND 2 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 3 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 4 CYS A 191 CYS A 220 1555 1555 2.03 LINK OG SER A 195 C7 DIC A 244 1555 1555 1.29 LINK C9 DIC A 244 O O A 245 1555 1555 1.25 LINK C9 DIC A 244 O O A 246 1555 1555 1.25 SITE 1 S1 1 DIC A 244 SITE 1 AC1 8 LYS A 192 SER A 195 THR A 214 SER A 215 SITE 2 AC1 8 GLY A 216 ARG A 218 O A 245 O A 246 SITE 1 AC2 5 LYS A 192 GLY A 193 SER A 195 DIC A 244 SITE 2 AC2 5 O A 246 SITE 1 AC3 2 DIC A 244 O A 245 CRYST1 56.300 51.570 39.840 90.00 106.05 90.00 P 1 21 1 2 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 0.017762 0.000000 0.005110 0.00000 SCALE2 0.000000 0.019391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026118 0.00000