HEADER SIGNALING PROTEIN 11-MAY-03 1UEC TITLE CRYSTAL STRUCTURE OF AUTOINHIBITED FORM OF TANDEM SH3 DOMAIN OF TITLE 2 P47PHOX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL CYTOSOL FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AUTOINHIBITED TANDEM SH3 DOMAIN, REDIDUES 151-340; COMPND 5 SYNONYM: P47PHOX; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX HTB KEYWDS NADPH OXIDASE, P47PHOX, PHAGOCYTE, SH3 DOMAIN, AUTOINHIBITION, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.YUZAWA,N.N.SUZUKI,Y.FUJIOKA,K.OGURA,H.SUMIMOTO,F.INAGAKI REVDAT 5 27-DEC-23 1UEC 1 SEQADV REVDAT 4 13-JUL-11 1UEC 1 VERSN REVDAT 3 24-FEB-09 1UEC 1 VERSN REVDAT 2 01-FEB-05 1UEC 1 JRNL REVDAT 1 27-MAY-03 1UEC 0 JRNL AUTH S.YUZAWA,N.N.SUZUKI,Y.FUJIOKA,K.OGURA,H.SUMIMOTO,F.INAGAKI JRNL TITL A MOLECULAR MECHANISM FOR AUTOINHIBITION OF THE TANDEM SH3 JRNL TITL 2 DOMAINS OF P47PHOX, THE REGULATORY SUBUNIT OF THE PHAGOCYTE JRNL TITL 3 NADPH OXIDASE JRNL REF GENES CELLS V. 9 443 2004 JRNL REFN ISSN 1356-9597 JRNL PMID 15147273 JRNL DOI 10.1111/J.1356-9597.2004.00733.X REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1681677.680 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 20491 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) : 0.213 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2024 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2809 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 319 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1394 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.33000 REMARK 3 B22 (A**2) : 4.33000 REMARK 3 B33 (A**2) : -8.66000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 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) : 1.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.390 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.320 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.420 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 47.94 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 : 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000005727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 300.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 6000, 0.1M SODUIM CITRATE, REMARK 280 50MM SODIUM FLUORIDE, PH 5.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 22.46200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.10850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.10850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.23100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.10850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.10850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.69300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.10850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.10850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.23100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.10850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.10850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.69300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.46200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -44.92400 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 GLY A 148 REMARK 465 ALA A 149 REMARK 465 MET A 150 REMARK 465 ASP A 151 REMARK 465 ILE A 152 REMARK 465 THR A 153 REMARK 465 GLY A 154 REMARK 465 PRO A 155 REMARK 465 ILE A 156 REMARK 465 THR A 170 REMARK 465 SER A 171 REMARK 465 GLY A 172 REMARK 465 ARG A 337 REMARK 465 GLN A 338 REMARK 465 ALA A 339 REMARK 465 ARG A 340 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 ILE A 157 CG1 CG2 CD1 REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 GLU A 174 CG CD OE1 OE2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 ASP A 269 CG OD1 OD2 REMARK 470 ASP A 270 CG OD1 OD2 REMARK 470 ARG A 314 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 335 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 336 CG CD NE CZ NH1 NH2 DBREF 1UEC A 151 340 UNP P14598 NCF1_HUMAN 151 340 SEQADV 1UEC GLY A 148 UNP P14598 CLONING ARTIFACT SEQADV 1UEC ALA A 149 UNP P14598 CLONING ARTIFACT SEQADV 1UEC MET A 150 UNP P14598 CLONING ARTIFACT SEQRES 1 A 193 GLY ALA MET ASP ILE THR GLY PRO ILE ILE LEU GLN THR SEQRES 2 A 193 TYR ARG ALA ILE ALA ASP TYR GLU LYS THR SER GLY SER SEQRES 3 A 193 GLU MET ALA LEU SER THR GLY ASP VAL VAL GLU VAL VAL SEQRES 4 A 193 GLU LYS SER GLU SER GLY TRP TRP PHE CYS GLN MET LYS SEQRES 5 A 193 ALA LYS ARG GLY TRP ILE PRO ALA SER PHE LEU GLU PRO SEQRES 6 A 193 LEU ASP SER PRO ASP GLU THR GLU ASP PRO GLU PRO ASN SEQRES 7 A 193 TYR ALA GLY GLU PRO TYR VAL ALA ILE LYS ALA TYR THR SEQRES 8 A 193 ALA VAL GLU GLY ASP GLU VAL SER LEU LEU GLU GLY GLU SEQRES 9 A 193 ALA VAL GLU VAL ILE HIS LYS LEU LEU ASP GLY TRP TRP SEQRES 10 A 193 VAL ILE ARG LYS ASP ASP VAL THR GLY TYR PHE PRO SER SEQRES 11 A 193 MET TYR LEU GLN LYS SER GLY GLN ASP VAL SER GLN ALA SEQRES 12 A 193 GLN ARG GLN ILE LYS ARG GLY ALA PRO PRO ARG ARG SER SEQRES 13 A 193 SER ILE ARG ASN ALA HIS SER ILE HIS GLN ARG SER ARG SEQRES 14 A 193 LYS ARG LEU SER GLN ASP ALA TYR ARG ARG ASN SER VAL SEQRES 15 A 193 ARG PHE LEU GLN GLN ARG ARG ARG GLN ALA ARG FORMUL 2 HOH *154(H2 O) HELIX 1 1 PRO A 206 LEU A 210 5 5 HELIX 2 2 ASP A 286 GLN A 293 1 8 HELIX 3 3 ARG A 301 ILE A 305 5 5 HELIX 4 4 SER A 320 LEU A 332 1 13 SHEET 1 A 3 GLN A 159 ARG A 162 0 SHEET 2 A 3 VAL A 182 GLU A 187 -1 O VAL A 183 N TYR A 161 SHEET 3 A 3 PHE A 195 MET A 198 -1 O GLN A 197 N GLU A 184 SHEET 1 B 5 VAL A 271 PRO A 276 0 SHEET 2 B 5 TRP A 263 LYS A 268 -1 N ILE A 266 O GLY A 273 SHEET 3 B 5 ALA A 252 HIS A 257 -1 N GLU A 254 O ARG A 267 SHEET 4 B 5 GLU A 229 ALA A 233 -1 N TYR A 231 O VAL A 253 SHEET 5 B 5 LEU A 280 LYS A 282 -1 O GLN A 281 N VAL A 232 CRYST1 100.217 100.217 44.924 90.00 90.00 90.00 P 41 21 2 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 0.009978 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009978 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022260 0.00000